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Korhonen PK, Wang T, Young ND, Byrne JJ, Campos TL, Chang BC, Taki AC, Gasser RB. Analysis of Haemonchus embryos at single cell resolution identifies two eukaryotic elongation factors as intervention target candidates. Comput Struct Biotechnol J 2024; 23:1026-1035. [PMID: 38435301 PMCID: PMC10907403 DOI: 10.1016/j.csbj.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 03/05/2024] Open
Abstract
Advances in single cell technologies are allowing investigations of a wide range of biological processes and pathways in animals, such as the multicellular model organism Caenorhabditis elegans - a free-living nematode. However, there has been limited application of such technology to related parasitic nematodes which cause major diseases of humans and animals worldwide. With no vaccines against the vast majority of parasitic nematodes and treatment failures due to drug resistance or inefficacy, new intervention targets are urgently needed, preferably informed by a deep understanding of these nematodes' cellular and molecular biology - which is presently lacking for most worms. Here, we created the first single cell atlas for an early developmental stage of Haemonchus contortus - a highly pathogenic, C. elegans-related parasitic nematode. We obtained and curated RNA sequence (snRNA-seq) data from single nuclei from embryonating eggs of H. contortus (150,000 droplets), and selected high-quality transcriptomic data for > 14,000 single nuclei for analysis, and identified 19 distinct clusters of cells. Guided by comparative analyses with C. elegans, we were able to reproducibly assign seven cell clusters to body wall muscle, hypodermis, neuronal, intestinal or seam cells, and identified eight genes that were transcribed in all cell clusters/types, three of which were inferred to be essential in H. contortus. Two of these genes (i.e. Hc-eef-1A and Hc-eef1G), coding for eukaryotic elongation factors (called Hc-eEF1A and Hc-eEF1G), were also demonstrated to be transcribed and expressed in all key developmental stages of H. contortus. Together with these findings, sequence- and structure-based comparative analyses indicated the potential of Hc-eEF1A and/or Hc-eEF1G as intervention targets within the protein biosynthesis machinery of H. contortus. Future work will focus on single cell studies of all key developmental stages and tissues of H. contortus, and on evaluating the suitability of the two elongation factor proteins as drug targets in H. contortus and related nematodes, with a view to finding new nematocidal drug candidates.
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Affiliation(s)
- Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tulio L. Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bill C.H. Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
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Shanley HT, Taki AC, Nguyen N, Wang T, Byrne JJ, Ang CS, Leeming MG, Nie S, Williamson N, Zheng Y, Young ND, Korhonen PK, Hofmann A, Chang BCH, Wells TNC, Häberli C, Keiser J, Jabbar A, Sleebs BE, Gasser RB. Structure-activity relationship and target investigation of 2-aryl quinolines with nematocidal activity. Int J Parasitol Drugs Drug Resist 2024; 24:100522. [PMID: 38295619 PMCID: PMC10845918 DOI: 10.1016/j.ijpddr.2024.100522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/02/2024]
Abstract
Within the context of our anthelmintic discovery program, we recently identified and evaluated a quinoline derivative, called ABX464 or obefazimod, as a nematocidal candidate; synthesised a series of analogues which were assessed for activity against the free-living nematode Caenorhabditis elegans; and predicted compound-target relationships by thermal proteome profiling (TPP) and in silico docking. Here, we logically extended this work and critically evaluated the anthelmintic activity of ABX464 analogues on Haemonchus contortus (barber's pole worm) - a highly pathogenic nematode of ruminant livestock. First, we tested a series of 44 analogues on H. contortus (larvae and adults) to investigate the nematocidal pharmacophore of ABX464, and identified one compound with greater potency than the parent compound and showed moderate activity against a select number of other parasitic nematodes (including Ancylostoma, Heligmosomoides and Strongyloides species). Using TPP and in silico modelling studies, we predicted protein HCON_00074590 (a predicted aldo-keto reductase) as a target candidate for ABX464 in H. contortus. Future work aims to optimise this compound as a nematocidal candidate and investigate its pharmacokinetic properties. Overall, this study presents a first step toward the development of a new nematocide.
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Affiliation(s)
- Harrison T Shanley
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia; Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Aya C Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Nghi Nguyen
- Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Joseph J Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ching-Seng Ang
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Michael G Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yuanting Zheng
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia; National Reference Centre for Authentic Food, Max Rubner-Institut, 95326, Kulmbach, Germany
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Tim N C Wells
- Medicines for Malaria Venture (MMV), 1215, Geneva, Switzerland
| | - Cécile Häberli
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4123, Allschwil, Switzerland; University of Basel, 4001, Basel, Switzerland
| | - Jennifer Keiser
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4123, Allschwil, Switzerland; University of Basel, 4001, Basel, Switzerland
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Brad E Sleebs
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia; Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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Shanley HT, Taki AC, Nguyen N, Wang T, Byrne JJ, Ang CS, Leeming MG, Nie S, Williamson N, Zheng Y, Young ND, Korhonen PK, Hofmann A, Wells TNC, Jabbar A, Sleebs BE, Gasser RB. Structure activity relationship and target prediction for ABX464 analogues in Caenorhabditis elegans. Bioorg Med Chem 2024; 98:117540. [PMID: 38134663 DOI: 10.1016/j.bmc.2023.117540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/20/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023]
Abstract
Global challenges with treatment failures and/or widespread resistance in parasitic worms against commercially available anthelmintics lend impetus to the development of new anthelmintics with novel mechanism(s) of action. The free-living nematode Caenorhabditis elegans is an important model organism used for drug discovery, including the screening and structure-activity investigation of new compounds, and target deconvolution. Previously, we conducted a whole-organism phenotypic screen of the 'Pandemic Response Box' (from Medicines for Malaria Venture, MMV) and identified a hit compound, called ABX464, with activity against C. elegans and a related, parasitic nematode, Haemonchus contortus. Here, we tested a series of 44 synthesized analogues to explore the pharmacophore of activity on C. elegans and revealed five compounds whose potency was similar or greater than that of ABX464, but which were not toxic to human hepatoma (HepG2) cells. Subsequently, we employed thermal proteome profiling (TPP), protein structure prediction and an in silico-docking algorithm to predict ABX464-target candidates. Taken together, the findings from this study contribute significantly to the early-stage drug discovery of a new nematocide based on ABX464. Future work is aimed at validating the ABX464-protein interactions identified here, and at assessing ABX464 and associated analogues against a panel of parasitic nematodes, towards developing a new anthelmintic with a mechanism of action that is distinct from any of the compounds currently-available commercially.
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Affiliation(s)
- Harrison T Shanley
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia; Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Aya C Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nghi Nguyen
- Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph J Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ching-Seng Ang
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael G Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yuanting Zheng
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia; National Reference Centre for Authentic Food, Max Rubner-Institut, 95326 Kulmbach, Germany
| | - Tim N C Wells
- Medicines for Malaria Venture (MMV), 1215 Geneva, Switzerland
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Brad E Sleebs
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia; Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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4
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Ma J, Song J, Young ND, Chang BCH, Korhonen PK, Campos TL, Liu H, Gasser RB. 'Bingo'-a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data. Brief Bioinform 2023; 25:bbad472. [PMID: 38152979 PMCID: PMC10753293 DOI: 10.1093/bib/bbad472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/22/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023] Open
Abstract
The identification and characterization of essential genes are central to our understanding of the core biological functions in eukaryotic organisms, and has important implications for the treatment of diseases caused by, for example, cancers and pathogens. Given the major constraints in testing the functions of genes of many organisms in the laboratory, due to the absence of in vitro cultures and/or gene perturbation assays for most metazoan species, there has been a need to develop in silico tools for the accurate prediction or inference of essential genes to underpin systems biological investigations. Major advances in machine learning approaches provide unprecedented opportunities to overcome these limitations and accelerate the discovery of essential genes on a genome-wide scale. Here, we developed and evaluated a large language model- and graph neural network (LLM-GNN)-based approach, called 'Bingo', to predict essential protein-coding genes in the metazoan model organisms Caenorhabditis elegans and Drosophila melanogaster as well as in Mus musculus and Homo sapiens (a HepG2 cell line) by integrating LLM and GNNs with adversarial training. Bingo predicts essential genes under two 'zero-shot' scenarios with transfer learning, showing promise to compensate for a lack of high-quality genomic and proteomic data for non-model organisms. In addition, the attention mechanisms and GNNExplainer were employed to manifest the functional sites and structural domain with most contribution to essentiality. In conclusion, Bingo provides the prospect of being able to accurately infer the essential genes of little- or under-studied organisms of interest, and provides a biological explanation for gene essentiality.
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Affiliation(s)
- Jiani Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Jiangning Song
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
- Bioinformatics Core Facility, Instituto Aggeu Magalhaes, Fundaçao Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Hui Liu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
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5
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Wang T, Koukoulis TF, Vella LJ, Su H, Purnianto A, Nie S, Ang CS, Ma G, Korhonen PK, Taki AC, Williamson NA, Reid GE, Gasser RB. The Proteome and Lipidome of Extracellular Vesicles from Haemonchus contortus to Underpin Explorations of Host-Parasite Cross-Talk. Int J Mol Sci 2023; 24:10955. [PMID: 37446130 DOI: 10.3390/ijms241310955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Many parasitic worms have a major adverse impact on human and animal populations worldwide due to the chronicity of their infections. There is a growing body of evidence indicating that extracellular vesicles (EVs) are intimately involved in modulating (suppressing) inflammatory/immune host responses and parasitism. As one of the most pathogenic nematodes of livestock animals, Haemonchus contortus is an ideal model system for EV exploration. Here, employing a multi-step enrichment process (in vitro culture, followed by ultracentrifugation, size exclusion and filtration), we enriched EVs from H. contortus and undertook the first comprehensive (qualitative and quantitative) multi-omic investigation of EV proteins and lipids using advanced liquid chromatography-mass spectrometry and informatics methods. We identified and quantified 561 proteins and 446 lipids in EVs and compared these molecules with those of adult worms. We identified unique molecules in EVs, such as proteins linked to lipid transportation and lipid species (i.e., sphingolipids) associated with signalling, indicating the involvement of these molecules in parasite-host cross-talk. This work provides a solid starting point to explore the functional roles of EV-specific proteins and lipids in modulating parasite-host cross-talk, and the prospect of finding ways of disrupting or interrupting this relationship to suppress or eliminate parasite infection.
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Affiliation(s)
- Tao Wang
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tiana F Koukoulis
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Laura J Vella
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Huaqi Su
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Adityas Purnianto
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Shuai Nie
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Guangxu Ma
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pasi K Korhonen
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Aya C Taki
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Gavin E Reid
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Robin B Gasser
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
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Kinkar L, Korhonen PK, Saarma U, Wang T, Zhu XQ, Harliwong I, Yang B, Fink JL, Wang D, Chang BCH, Chelomina GN, Koehler AV, Young ND, Gasser RB. Genome-wide exploration reveals distinctive northern and southern variants of Clonorchis sinensis in the Far East. Mol Ecol Resour 2023; 23:833-843. [PMID: 36727564 DOI: 10.1111/1755-0998.13760] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/06/2023] [Accepted: 01/30/2023] [Indexed: 02/03/2023]
Abstract
Clonorchis sinensis is a carcinogenic liver fluke that causes clonorchiasis-a neglected tropical disease (NTD) affecting ~35 million people worldwide. No vaccine is available, and chemotherapy relies on one anthelmintic, praziquantel. This parasite has a complex life history and is known to infect a range of species of intermediate (freshwater snails and fish) and definitive (piscivorous) hosts. Despite this biological complexity and the impact of this biocarcinogenic pathogen, there has been no previous study of molecular variation in this parasite on a genome-wide scale. Here, we conducted the first extensive nuclear genomic exploration of C. sinensis individuals (n = 152) representing five distinct populations from mainland China, and one from Far East Russia, and revealed marked genetic variation within this species between "northern" and "southern" geographical regions. The discovery of this variation indicates the existence of biologically distinct variants within C. sinensis, which may have distinct epidemiology, pathogenicity and/or chemotherapic responsiveness. The detection of high heterozygosity within C. sinensis specimens suggests that this parasite has developed mechanisms to readily adapt to changing environments and/or host species during its life history/evolution. From an applied perspective, the identification of invariable genes could assist in finding new intervention targets in this parasite, given the major clinical relevance of clonorchiasis. From a technical perspective, the genomic-informatic workflow established herein will be readily applicable to a wide range of other parasites that cause NTDs.
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Affiliation(s)
- Liina Kinkar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Xing-Quan Zhu
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, China
| | | | | | - J Lynn Fink
- BGI Australia, Herston, Queensland, Australia.,The University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Daxi Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia.,BGI-Shenzhen, Shenzhen, China
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia.,Yourgene Health, Taipei, Taiwan
| | - Galina N Chelomina
- Department of Parasitology, Federal Scientific Center of the East Asia Terrestrial Biodiversity FEB RAS, Vladivostok, Russia
| | - Anson V Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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7
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Thia JA, Korhonen PK, Young ND, Gasser RB, Umina PA, Yang Q, Edwards O, Walsh T, Hoffmann AA. The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range. J Evol Biol 2023; 36:381-398. [PMID: 36573922 PMCID: PMC10107102 DOI: 10.1111/jeb.14144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/13/2022] [Accepted: 11/03/2022] [Indexed: 12/28/2022]
Abstract
Genomic data provide valuable insights into pest management issues such as resistance evolution, historical patterns of pest invasions and ongoing population dynamics. We assembled the first reference genome for the redlegged earth mite, Halotydeus destructor (Tucker, 1925), to investigate adaptation to pesticide pressures and demography in its invasive Australian range using whole-genome pool-seq data from regionally distributed populations. Our reference genome comprises 132 autosomal contigs, with a total length of 48.90 Mb. We observed a large complex of ace genes, which has presumably evolved from a long history of organophosphate selection in H. destructor and may contribute towards organophosphate resistance through copy number variation, target-site mutations and structural variants. In the putative ancestral H. destructor ace gene, we identified three target-site mutations (G119S, A201S and F331Y) segregating in organophosphate-resistant populations. Additionally, we identified two new para sodium channel gene mutations (L925I and F1020Y) that may contribute to pyrethroid resistance. Regional structuring observed in population genomic analyses indicates that gene flow in H. destructor does not homogenize populations across large geographic distances. However, our demographic analyses were equivocal on the magnitude of gene flow; the short invasion history of H. destructor makes it difficult to distinguish scenarios of complete isolation vs. ongoing migration. Nonetheless, we identified clear signatures of reduced genetic diversity and smaller inferred effective population sizes in eastern vs. western populations, which is consistent with the stepping-stone invasion pathway of this pest in Australia. These new insights will inform development of diagnostic genetic markers of resistance, further investigation into the multifaceted organophosphate resistance mechanism and predictive modelling of resistance evolution and spread.
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Affiliation(s)
- Joshua A Thia
- Bio21 Institute, School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Qiong Yang
- Bio21 Institute, School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Owain Edwards
- Land and Water, CSIRO, Floreat, Western Australia, Australia
| | - Tom Walsh
- CSIRO, Black Mountain Laboratories, Canberra, Australian Capital Territory, Australia.,Applied BioSciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ary A Hoffmann
- Bio21 Institute, School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
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8
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Wang T, Gasser RB, Korhonen PK, Young ND, Ang CS, Williamson NA, Ma G, Samarawickrama GR, Fernando DD, Fischer K. Proteomic analysis of Sarcoptes scabiei reveals that proteins differentially expressed between eggs and female adult stages are involved predominantly in genetic information processing, metabolism and/or host-parasite interactions. PLoS Negl Trop Dis 2022; 16:e0010946. [PMID: 36472966 PMCID: PMC9725168 DOI: 10.1371/journal.pntd.0010946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Presently, there is a dearth of proteomic data for parasitic mites and their relationship with the host animals. Here, using a high throughput LC-MS/MS-based approach, we undertook the first comprehensive, large-scale proteomic investigation of egg and adult female stages of the scabies mite, Sarcoptes scabiei-one of the most important parasitic mites of humans and other animals worldwide. In total, 1,761 S. scabiei proteins were identified and quantified with high confidence. Bioinformatic analyses revealed differentially expressed proteins to be involved predominantly in biological pathways or processes including genetic information processing, energy (oxidative phosphorylation), nucleotide, amino acid, carbohydrate and/or lipid metabolism, and some adaptive processes. Selected, constitutively and highly expressed proteins, such as peptidases, scabies mite inactivated protease paralogues (SMIPPs) and muscle proteins (myosin and troponin), are proposed to be involved in key biological processes within S. scabiei, host-parasite interactions and/or the pathogenesis of scabies. These proteomic data will enable future molecular, biochemical and physiological investigations of early developmental stages of S. scabiei and the discovery of novel interventions, targeting the egg stage, given its non-susceptibility to acaricides currently approved for the treatment of scabies in humans.
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Affiliation(s)
- Tao Wang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
- * E-mail:
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Australia
| | - Nicholas A. Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Australia
| | - Guangxu Ma
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Australia
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China
| | - Gangi R. Samarawickrama
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- School of Veterinary Science, University of Queensland, Gatton, Australia
| | - Deepani D. Fernando
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Katja Fischer
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, Australia
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9
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Taki AC, Wang T, Nguyen NN, Ang CS, Leeming MG, Nie S, Byrne JJ, Young ND, Zheng Y, Ma G, Korhonen PK, Koehler AV, Williamson NA, Hofmann A, Chang BCH, Häberli C, Keiser J, Jabbar A, Sleebs BE, Gasser RB. Thermal proteome profiling reveals Haemonchus orphan protein HCO_011565 as a target of the nematocidal small molecule UMW-868. Front Pharmacol 2022; 13:1014804. [PMID: 36313370 PMCID: PMC9616048 DOI: 10.3389/fphar.2022.1014804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Parasitic roundworms (nematodes) cause destructive diseases, and immense suffering in humans and other animals around the world. The control of these parasites relies heavily on anthelmintic therapy, but treatment failures and resistance to these drugs are widespread. As efforts to develop vaccines against parasitic nematodes have been largely unsuccessful, there is an increased focus on discovering new anthelmintic entities to combat drug resistant worms. Here, we employed thermal proteome profiling (TPP) to explore hit pharmacology and to support optimisation of a hit compound (UMW-868), identified in a high-throughput whole-worm, phenotypic screen. Using advanced structural prediction and docking tools, we inferred an entirely novel, parasite-specific target (HCO_011565) of this anthelmintic small molecule in the highly pathogenic, blood-feeding barber’s pole worm, and in other socioeconomically important parasitic nematodes. The “hit-to-target” workflow constructed here provides a unique prospect of accelerating the simultaneous discovery of novel anthelmintics and associated parasite-specific targets.
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Affiliation(s)
- Aya C. Taki
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Nghi N. Nguyen
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ching-Seng Ang
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Michael G. Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Yuanting Zheng
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Guangxu Ma
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Anson V. Koehler
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Nicholas A. Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Bill C. H. Chang
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Cécile Häberli
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Jennifer Keiser
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Brad E. Sleebs
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- *Correspondence: Brad E. Sleebs, ; Robin B. Gasser,
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
- *Correspondence: Brad E. Sleebs, ; Robin B. Gasser,
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10
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Young ND, Kinkar L, Stroehlein AJ, Korhonen PK, Stothard JR, Rollinson D, Gasser RB. Mitochondrial genome of Bulinus truncatus (Gastropoda: Lymnaeoidea): Implications for snail systematics and schistosome epidemiology. Curr Res Parasitol Vector Borne Dis 2022; 1:100017. [PMID: 35284876 PMCID: PMC8906109 DOI: 10.1016/j.crpvbd.2021.100017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/29/2022]
Abstract
Many freshwater snails of the genus Bulinus act as intermediate hosts in the life-cycles of schistosomes in Africa and adjacent regions. Currently, 37 species of Bulinus representing four groups are recognised. The mitochondrial cytochrome c oxidase subunit 1 (cox1) gene has shown utility for identifying and differentiating Bulinus species and groups, but taxonomic relationships based on genetic data are not entirely consistent with those inferred using morphological and biological features. To underpin future systematic studies of members of the genus, we characterised here the mitochondrial genome of Bulinus truncatus (from a defined laboratory strain) using a combined second- and third-generation sequencing and informatics approach, enabling taxonomic comparisons with other planorbid snails for which mitochondrial (mt) genomes were available. Analyses showed consistency in gene order and length among mitochondrial genomes of representative planorbid snails, with the lowest and highest nucleotide diversities being in the cytochrome c oxidase and nicotinamide dehydrogenase subunit genes, respectively. This first mt genome for a representative of the genus Bulinus should provide a useful resource for future investigations of the systematics, population genetics, epidemiology and/or ecology of Bulinus and related snails. The sequencing and informatic workflow employed here should find broad applicability to a range of other snail intermediate hosts of parasitic trematodes.
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Affiliation(s)
- Neil D Young
- Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Liina Kinkar
- Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Andreas J Stroehlein
- Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K Korhonen
- Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - J Russell Stothard
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - David Rollinson
- Department of Life Sciences, Natural History Museum, London, UK.,London Centre for Neglected Tropical Disease Research, London, UK
| | - Robin B Gasser
- Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
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11
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Young ND, Stroehlein AJ, Wang T, Korhonen PK, Mentink-Kane M, Stothard JR, Rollinson D, Gasser RB. Nuclear genome of Bulinus truncatus, an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium. Nat Commun 2022; 13:977. [PMID: 35190553 PMCID: PMC8861042 DOI: 10.1038/s41467-022-28634-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 02/02/2022] [Indexed: 02/07/2023] Open
Abstract
Some snails act as intermediate hosts (vectors) for parasitic flatworms (flukes) that cause neglected tropical diseases, such as schistosomiases. Schistosoma haematobium is a blood fluke that causes urogenital schistosomiasis and induces bladder cancer and increased risk of HIV infection. Understanding the molecular biology of the snail and its relationship with the parasite could guide development of an intervention approach that interrupts transmission. Here, we define the genome for a key intermediate host of S. haematobium—called Bulinus truncatus—and explore protein groups inferred to play an integral role in the snail’s biology and its relationship with the schistosome parasite. Bu. truncatus shared many orthologous protein groups with Biomphalaria glabrata—the key snail vector for S. mansoni which causes hepatointestinal schistosomiasis in people. Conspicuous were expansions in signalling and membrane trafficking proteins, peptidases and their inhibitors as well as gene families linked to immune response regulation, such as a large repertoire of lectin-like molecules. This work provides a sound basis for further studies of snail-parasite interactions in the search for targets to block schistosomiasis transmission. The snail Bulinus truncatus is an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium. Here the authors report the genome of Bu. truncatus, explore protein groups inferred to play a role in its interaction with the schistosome parasite, and identify expansions in gene families linked to immune response regulation.
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12
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Korhonen PK, Shaban B, Faux NG, Kinkar L, Chang BCH, Wang D, Yang B, Young ND, Gasser RB. 'Escalibur' - a practical pipeline for the de novo-analysis of nucleotide variation in non-model eukaryotes. Mol Ecol Resour 2022; 22:2120-2126. [PMID: 35182034 PMCID: PMC9314989 DOI: 10.1111/1755-0998.13600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/03/2022] [Accepted: 02/14/2022] [Indexed: 11/10/2022]
Abstract
The revolution in genomics has enabled large‐scale population genetic investigations of a wide range of organisms, but there has been a relatively limited focus on improving analytical pipelines. To efficiently analyse large data sets, highly integrated and automated software pipelines, which are easy to use, efficient, reliable, reproducible and run in multiple computational environments, are required. A number of software workflows have been developed to handle and process such data sets for population genetic analyses, but effective, specialized pipelines for genetic and statistical analyses of nonmodel organisms are lacking. For most species, resources for variomes (sets of genetic variations found in populations of species) are not available, and/or genome assemblies are often incomplete and fragmented, complicating the selection of the most suitable reference genome when multiple assemblies are available. Additionally, the biological samples used often contain extraneous DNA from sources other than the species under investigation (e.g., microbial contamination), which needs to be removed prior to genetic analyses. For these reasons, we established a new pipeline, called Escalibur, which includes: functionalities, such as data trimming and mapping; selection of a suitable reference genome; removal of contaminating read data; recalibration of base calls; and variant‐calling. Escalibur uses a proven gatk variant caller and workflow description language (WDL), and is, therefore, a highly efficient and scalable pipeline for the genome‐wide identification of nucleotide variation in eukaryotes. This pipeline is available at https://gitlab.unimelb.edu.au/bioscience/escalibur (version 0.3‐beta) and is essentially applicable to any prokaryote or eukaryote.
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Affiliation(s)
- Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, 3010, Victoria, Australia
| | - Babak Shaban
- Melbourne Data Analytics Platform (MDAP), The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Noel G Faux
- Melbourne Data Analytics Platform (MDAP), The University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Liina Kinkar
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, 3010, Victoria, Australia
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, 3010, Victoria, Australia
| | - Daxi Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, 3010, Victoria, Australia.,BGI-Shenzhen, Shenzhen, China
| | - Bicheng Yang
- BGI Australia, Oceania, BGI Group, CBCRB Building, Herston Road, Herston, Queensland, 4006, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, 3010, Victoria, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, 3010, Victoria, Australia
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13
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Stroehlein AJ, Korhonen PK, Lee VV, Ralph SA, Mentink-Kane M, You H, McManus DP, Tchuenté LAT, Stothard JR, Kaur P, Dudchenko O, Aiden EL, Yang B, Yang H, Emery AM, Webster BL, Brindley PJ, Rollinson D, Chang BCH, Gasser RB, Young ND. Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation. PLoS Pathog 2022; 18:e1010288. [PMID: 35167626 PMCID: PMC8846543 DOI: 10.1371/journal.ppat.1010288] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/19/2022] [Indexed: 01/08/2023] Open
Abstract
Urogenital schistosomiasis is caused by the blood fluke Schistosoma haematobium and is one of the most neglected tropical diseases worldwide, afflicting > 100 million people. It is characterised by granulomata, fibrosis and calcification in urogenital tissues, and can lead to increased susceptibility to HIV/AIDS and squamous cell carcinoma of the bladder. To complement available treatment programs and break the transmission of disease, sound knowledge and understanding of the biology and ecology of S. haematobium is required. Hybridisation/introgression events and molecular variation among members of the S. haematobium-group might effect important biological and/or disease traits as well as the morbidity of disease and the effectiveness of control programs including mass drug administration. Here we report the first chromosome-contiguous genome for a well-defined laboratory line of this blood fluke. An exploration of this genome using transcriptomic data for all key developmental stages allowed us to refine gene models (including non-coding elements) and annotations, discover ‘new’ genes and transcription profiles for these stages, likely linked to development and/or pathogenesis. Molecular variation within S. haematobium among some geographical locations in Africa revealed unique genomic ‘signatures’ that matched species other than S. haematobium, indicating the occurrence of introgression events. The present reference genome (designated Shae.V3) and the findings from this study solidly underpin future functional genomic and molecular investigations of S. haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved and sustained control of urogenital schistosomiasis. More than 100 million people are infected with the carcinogenic blood fluke Schistosoma haematobium, the aetiological agent of urogenital schistosomiasis—a neglected tropical disease (NTD). In spite of its major significance, little is known about this fluke, its interactions with the human and snail intermediate hosts and the pathogenesis of the urogenital form of schistosomiasis at the molecular and biochemical levels. To enable research in these areas, we report the first chromosome-level genome and markedly enhanced gene models for S. haematobium. Comparative genomic analyses also reveal evidence of past introgression events between or among closely related schistosome species. This present reference genome for S. haematobium and the findings from this study should underpin future functional genomic and molecular investigations of S. haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved control of urogenital schistosomiasis.
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Affiliation(s)
- Andreas J. Stroehlein
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - V. Vern Lee
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Stuart A. Ralph
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Margaret Mentink-Kane
- NIH-NIAID Schistosomiasis Resource Center, Biomedical Research Institute, Rockville, Maryland, United States of America
| | - Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Donald P. McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Louis-Albert Tchuem Tchuenté
- Faculty of Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - J. Russell Stothard
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
| | - Erez Lieberman Aiden
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, Western Australia, Australia
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Center for Theoretical Biological Physics, Rice University, Houston, Texas, United States of America
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong, China
- Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Bicheng Yang
- BGI Australia, Oceania, BGI Group, CBCRB Building, Herston, Queensland, Australia
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Aidan M. Emery
- Parasites and Vectors Division, The Natural History Museum, London, United Kingdom
- London Centre for Neglected Tropical Disease Research (LCNTDR), London, United Kingdom
| | - Bonnie L. Webster
- Parasites and Vectors Division, The Natural History Museum, London, United Kingdom
- London Centre for Neglected Tropical Disease Research (LCNTDR), London, United Kingdom
| | - Paul J. Brindley
- School of Medicine & Health Sciences, Department of Microbiology, Immunology & Tropical Medicine, George Washington University, Washington DC, United States of America
| | - David Rollinson
- Parasites and Vectors Division, The Natural History Museum, London, United Kingdom
- London Centre for Neglected Tropical Disease Research (LCNTDR), London, United Kingdom
| | - Bill C. H. Chang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (RBG); (NDY)
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (RBG); (NDY)
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14
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Fernando DD, Korhonen PK, Gasser RB, Fischer K. An RNA Interference Tool to Silence Genes in Sarcoptes scabiei Eggs. Int J Mol Sci 2022; 23:ijms23020873. [PMID: 35055058 PMCID: PMC8777771 DOI: 10.3390/ijms23020873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/05/2022] [Accepted: 01/11/2022] [Indexed: 12/10/2022] Open
Abstract
In a quest for new interventions against scabies-a highly significant skin disease of mammals, caused by a parasitic mite Sarcoptes scabiei-we are focusing on finding new intervention targets. RNA interference (RNAi) could be an efficient functional genomics approach to identify such targets. The RNAi pathway is present in S. scabiei and operational in the female adult mite, but other developmental stages have not been assessed. Identifying potential intervention targets in the egg stage is particularly important because current treatments do not kill this latter stage. Here, we established an RNAi tool to silence single-copy genes in S. scabiei eggs. Using sodium hypochlorite pre-treatment, we succeeded in rendering the eggshell permeable to dsRNA without affecting larval hatching. We optimised the treatment of eggs with gene-specific dsRNAs to three single-copy target genes (designated Ss-Cof, Ss-Ddp, and Ss-Nan) which significantly and repeatedly suppressed transcription by ~66.6%, 74.3%, and 84.1%, respectively. Although no phenotypic alterations were detected in dsRNA-treated eggs for Ss-Cof and Ss-Nan, the silencing of Ss-Ddp resulted in a 38% reduction of larval hatching. This RNAi method is expected to provide a useful tool for larger-scale functional genomic investigations for the identification of essential genes as potential drug targets.
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Affiliation(s)
- Deepani D. Fernando
- Infectious Diseases Program, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia;
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3052, Australia; (P.K.K.); (R.B.G.)
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3052, Australia; (P.K.K.); (R.B.G.)
| | - Katja Fischer
- Infectious Diseases Program, Cell and Molecular Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia;
- Correspondence:
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15
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Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Harnessing model organism genomics to underpin the machine learning-based prediction of essential genes in eukaryotes - Biotechnological implications. Biotechnol Adv 2021; 54:107822. [PMID: 34461202 DOI: 10.1016/j.biotechadv.2021.107822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the 'elegant worm' (Caenorhabditis elegans; Nematoda) and the 'vinegar fly' (Drosophila melanogaster; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeconomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available 'omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could 'open the door' to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML-engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthropods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resistance in parasite populations.
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Taki AC, Byrne JJ, Wang T, Sleebs BE, Nguyen N, Hall RS, Korhonen PK, Chang BC, Jackson P, Jabbar A, Gasser RB. High-Throughput Phenotypic Assay to Screen for Anthelmintic Activity on Haemonchus contortus. Pharmaceuticals (Basel) 2021; 14:ph14070616. [PMID: 34206910 PMCID: PMC8308562 DOI: 10.3390/ph14070616] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
Parasitic worms cause very significant diseases in animals and humans worldwide, and their control is critical to enhance health, well-being and productivity. Due to widespread drug resistance in many parasitic worms of animals globally, there is a major, continuing demand for the discovery and development of anthelmintic drugs for use to control these worms. Here, we established a practical, cost-effective and semi-automated high throughput screening (HTS) assay, which relies on the measurement of motility of larvae of the barber’s pole worm (Haemonchus contortus) using infrared light-interference. Using this assay, we screened 80,500 small molecules and achieved a hit rate of 0.05%. We identified three small molecules that reproducibly inhibited larval motility and/or development (IC50 values of ~4 to 41 µM). Future work will critically assess the potential of selected hits as candidates for subsequent optimisation or repurposing against parasitic nematodes. This HTS assay has a major advantage over most previous assays in that it achieves a ≥ 10-times higher throughput (i.e., 10,000 compounds per week), and is thus suited to the screening of libraries of tens of thousands to hundreds of thousands of compounds for subsequent hit-to-lead optimisation or effective repurposing and development. The current assay should be adaptable to many socioeconomically important parasitic nematodes, including those that cause neglected tropical diseases (NTDs). This aspect is of relevance, given the goals of the World Health Organization (WHO) Roadmap for NTDs 2021–2030, to develop more effective drugs and drug combinations to improve patient outcomes and circumvent the ineffectiveness of some current anthelmintic drugs and possible drug resistance.
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Affiliation(s)
- Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (T.W.); (B.E.S.); (R.S.H.); (P.K.K.); (B.C.H.C.); (A.J.)
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (T.W.); (B.E.S.); (R.S.H.); (P.K.K.); (B.C.H.C.); (A.J.)
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (T.W.); (B.E.S.); (R.S.H.); (P.K.K.); (B.C.H.C.); (A.J.)
| | - Brad E. Sleebs
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (T.W.); (B.E.S.); (R.S.H.); (P.K.K.); (B.C.H.C.); (A.J.)
- Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
- Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nghi Nguyen
- Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
- Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ross S. Hall
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (T.W.); (B.E.S.); (R.S.H.); (P.K.K.); (B.C.H.C.); (A.J.)
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (T.W.); (B.E.S.); (R.S.H.); (P.K.K.); (B.C.H.C.); (A.J.)
| | - Bill C.H. Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (T.W.); (B.E.S.); (R.S.H.); (P.K.K.); (B.C.H.C.); (A.J.)
| | - Paul Jackson
- Johnson & Johnson, Global Public Health, Janssen Research and Development, San Diego, CA 92121, USA;
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (T.W.); (B.E.S.); (R.S.H.); (P.K.K.); (B.C.H.C.); (A.J.)
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (A.C.T.); (J.J.B.); (T.W.); (B.E.S.); (R.S.H.); (P.K.K.); (B.C.H.C.); (A.J.)
- Correspondence:
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Campos TL, Korhonen PK, Young ND. Cross-Predicting Essential Genes between Two Model Eukaryotic Species Using Machine Learning. Int J Mol Sci 2021; 22:5056. [PMID: 34064595 PMCID: PMC8150380 DOI: 10.3390/ijms22105056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/07/2021] [Accepted: 05/08/2021] [Indexed: 12/24/2022] Open
Abstract
Experimental studies of Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular and cellular processes in metazoans at large. Since the publication of their genomes, functional genomic investigations have identified genes that are essential or non-essential for survival in each species. Recently, a range of features linked to gene essentiality have been inferred using a machine learning (ML)-based approach, allowing essentiality predictions within a species. Nevertheless, predictions between species are still elusive. Here, we undertake a comprehensive study using ML to discover and validate features of essential genes common to both C. elegans and D. melanogaster. We demonstrate that the cross-species prediction of gene essentiality is possible using a subset of features linked to nucleotide/protein sequences, protein orthology and subcellular localisation, single-cell RNA-seq, and histone methylation markers. Complementary analyses showed that essential genes are enriched for transcription and translation functions and are preferentially located away from heterochromatin regions of C. elegans and D. melanogaster chromosomes. The present work should enable the cross-prediction of essential genes between model and non-model metazoans.
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Affiliation(s)
- Tulio L. Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (T.L.C.); (P.K.K.)
- Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife 50740-465, PE, Brazil
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (T.L.C.); (P.K.K.)
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia; (T.L.C.); (P.K.K.)
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18
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Young ND, Stroehlein AJ, Kinkar L, Wang T, Sohn WM, Chang BCH, Kaur P, Weisz D, Dudchenko O, Aiden EL, Korhonen PK, Gasser RB. High-quality reference genome for Clonorchis sinensis. Genomics 2021; 113:1605-1615. [PMID: 33677057 DOI: 10.1016/j.ygeno.2021.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/18/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022]
Abstract
The Chinese liver fluke, Clonorchis sinensis, causes the disease clonorchiasis, affecting ~35 million people in regions of China, Vietnam, Korea and the Russian Far East. Chronic clonorchiasis causes cholangitis and can induce a malignant cancer, called cholangiocarcinoma, in the biliary system. Control in endemic regions is challenging, and often relies largely on chemotherapy with one anthelmintic, called praziquantel. Routine treatment carries a significant risk of inducing resistance to this anthelmintic in the fluke, such that the discovery of new interventions is considered important. It is hoped that the use of molecular technologies will assist this endeavour by enabling the identification of drug or vaccine targets involved in crucial biological processes and/or pathways in the parasite. Although draft genomes of C. sinensis have been published, their assemblies are fragmented. In the present study, we tackle this genome fragmentation issue by utilising, in an integrated way, advanced (second- and third-generation) DNA sequencing and informatic approaches to build a high-quality reference genome for C. sinensis, with chromosome-level contiguity and curated gene models. This substantially-enhanced genome provides a resource that could accelerate fundamental and applied molecular investigations of C. sinensis, clonorchiasis and/or cholangiocarcinoma, and assist in the discovery of new interventions against what is a highly significant, but neglected disease-complex.
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Affiliation(s)
- Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Liina Kinkar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Woon-Mok Sohn
- Department of Parasitology and Institute of Health Sciences, School of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, Faculty of Science, University of Western Australia, Perth, Western Australia 6009, Australia
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA
| | - Erez Lieberman Aiden
- UWA School of Agriculture and Environment, Faculty of Science, University of Western Australia, Perth, Western Australia 6009, Australia; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
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19
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Liu GH, Korhonen PK, Young ND, Lu J, Wang T, Fu YT, Koehler AV, Hofmann A, Chang BCH, Wang S, Li N, Lin CY, Zhang H, Xiangli L, Lin L, Liu WM, Li N, Li HW, Gasser RB, Zhu XQ. Dipylidium caninum draft genome - a new resource for comparative genomic and genetic explorations of flatworms. Genomics 2021; 113:1272-1280. [PMID: 33677058 DOI: 10.1016/j.ygeno.2021.02.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 02/15/2021] [Accepted: 02/28/2021] [Indexed: 12/30/2022]
Abstract
Here, we present a draft genome of the tapeworm Dipylidium caninum (family Dipylidiidae) and compare it with other cestode genomes. This draft genome of D. caninum is 110 Mb in size, has a repeat content of ~13.4% and is predicted to encode ~10,000 protein-coding genes. We inferred excretory/secretory molecules (representing the secretome), other key groups of proteins (including peptidases, kinases, phosphatases, GTPases, receptors, transporters and ion-channels) and predicted potential intervention targets for future evaluation. Using 144 shared single-copy orthologous sequences, we investigated the genetic relationships of cestodes for which nuclear genomes are available. This study provides first insights into the molecular biology of D. caninum and a new resource for comparative genomic and genetic explorations of this and other flatworms.
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Affiliation(s)
- Guo-Hua Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville 3010, Australia
| | - Jiang Lu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518124, China
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville 3010, Australia
| | - Yi-Tian Fu
- College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, China
| | - Anson V Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville 3010, Australia; Griffith Institute for Drug Discovery, Griffith University, Dathan 4111, Australia
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville 3010, Australia
| | - Shuai Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Nan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518124, China
| | - Chu-Yu Lin
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518124, China
| | - Hui Zhang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518124, China
| | - Lingzi Xiangli
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518124, China
| | - Lin Lin
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518124, China
| | - Wei-Min Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518124, China
| | - Nan Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518124, China
| | - Hua-Wei Li
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China; Shenzhen Zhong Nong Jing Yue Biotech Company Limited, Shenzhen 518124, China
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville 3010, Australia.
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; College of Veterinary Medicine, Shanxi Agricultural University, Taigu 030801, China.
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20
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Chng L, Holt DC, Field M, Francis JR, Tilakaratne D, Dekkers MH, Robinson G, Mounsey K, Pavlos R, Bowen AC, Fischer K, Papenfuss AT, Gasser RB, Korhonen PK, Currie BJ, McCarthy JS, Pasay C. Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome. PLoS Negl Trop Dis 2021; 15:e0009149. [PMID: 33626043 PMCID: PMC7939366 DOI: 10.1371/journal.pntd.0009149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/08/2021] [Accepted: 01/15/2021] [Indexed: 01/23/2023] Open
Abstract
Background The suboptimal sensitivity and specificity of available diagnostic methods for scabies hampers clinical management, trials of new therapies and epidemiologic studies. Additionally, parasitologic diagnosis by microscopic examination of skin scrapings requires sample collection with a sharp scalpel blade, causing discomfort to patients and difficulty in children. Polymerase chain reaction (PCR)-based diagnostic assays, combined with non-invasive sampling methods, represent an attractive approach. In this study, we aimed to develop a real-time probe-based PCR test for scabies, test a non-invasive sampling method and evaluate its diagnostic performance in two clinical settings. Methodology/Principal findings High copy-number repetitive DNA elements were identified in draft Sarcoptes scabiei genome sequences and used as assay targets for diagnostic PCR. Two suitable repetitive DNA sequences, a 375 base pair microsatellite (SSR5) and a 606 base pair long tandem repeat (SSR6), were identified. Diagnostic sensitivity and specificity were tested using relevant positive and negative control materials and compared to a published assay targeting the mitochondrial cox1 gene. Both assays were positive at a 1:100 dilution of DNA from a single mite; no amplification was observed in DNA from samples from 19 patients with other skin conditions nor from house dust, sheep or dog mites, head and body lice or from six common skin bacterial and fungal species. Moderate sensitivity of the assays was achieved in a pilot study, detecting 5/7 (71.4% [95% CI: 29.0% - 96.3%]) of clinically diagnosed untreated scabies patients). Greater sensitivity was observed in samples collected by FLOQ swabs compared to skin scrapings. Conclusions/Significance This newly developed qPCR assay, combined with the use of an alternative non-invasive swab sampling technique offers the possibility of enhanced diagnosis of scabies. Further studies will be required to better define the diagnostic performance of these tests. As scabies control efforts continue to grow, scarcity of diagnostic options hinders success of elimination efforts in endemic areas. Efficiency in large-scale monitoring is further obstructed by invasive sample collection techniques, which are often uncomfortable for patients, and lack sensitivity. We have developed two PCR-based diagnostic assays targeting repetitive DNA elements. These were identified using new data on the S. scabiei genome. Targeting these elements by PCR improved the detection of scabies DNA. Enhanced sensitivity was demonstrated when tested against routine microscopy and a published PCR-based diagnostic assay. When combined with a non-invasive, effective FLOQ swab sampling method, the developed qPCR-based assays may provide a useful complementary tool for diagnosis of scabies, and its application will likely improve scabies control in target populations.
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Affiliation(s)
- Lena Chng
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Deborah C. Holt
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- College of Health and Human Sciences, Charles Darwin University, Darwin, Australia
| | - Matt Field
- Centre for Tropical Bioinformatics and Molecular Biology and Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
- Genome Informatics, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Joshua R. Francis
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Royal Darwin Hospital, Tiwi, Australia
| | - Dev Tilakaratne
- Royal Darwin Hospital, Tiwi, Australia
- Darwin Dermatology, Tiwi, Australia
| | - Milou H. Dekkers
- Queensland Animal Science Precinct, University of Queensland, Gatton, Australia
| | - Greg Robinson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kate Mounsey
- University of Sunshine Coast, Sippy Downs, Australia
| | - Rebecca Pavlos
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Asha C. Bowen
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Australia
- Department of Infectious Diseases, Perth Children’s Hospital, Perth, Australia
| | - Katja Fischer
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary Sciences, The University of Melbourne, Parkville, Australia
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary Sciences, The University of Melbourne, Parkville, Australia
| | - Bart J. Currie
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Royal Darwin Hospital, Tiwi, Australia
| | | | - Cielo Pasay
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
- * E-mail:
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21
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Gurumayum S, Jiang P, Hao X, Campos TL, Young ND, Korhonen PK, Gasser RB, Bork P, Zhao XM, He LJ, Chen WH. OGEE v3: Online GEne Essentiality database with increased coverage of organisms and human cell lines. Nucleic Acids Res 2021; 49:D998-D1003. [PMID: 33084874 PMCID: PMC7779042 DOI: 10.1093/nar/gkaa884] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022] Open
Abstract
OGEE is an Online GEne Essentiality database. Gene essentiality is not a static and binary property, rather a context-dependent and evolvable property in all forms of life. In OGEE we collect not only experimentally tested essential and non-essential genes, but also associated gene properties that contributes to gene essentiality. We tagged conditionally essential genes that show variable essentiality statuses across datasets to highlight complex interplays between gene functions and environmental/experimental perturbations. OGEE v3 contains gene essentiality datasets for 91 species; almost doubled from 48 species in previous version. To accommodate recent advances on human cancer essential genes (as known as tumor dependency genes) that could serve as targets for cancer treatment and/or drug development, we expanded the collection of human essential genes from 16 cell lines in previous to 581. These human cancer cell lines were tested with high-throughput experiments such as CRISPR-Cas9 and RNAi; in total, 150 of which were tested by both techniques. We also included factors known to contribute to gene essentiality for these cell lines, such as genomic mutation, methylation and gene expression, along with extensive graphical visualizations for ease of understanding of these factors. OGEE v3 can be accessible freely at https://v3.ogee.info.
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Affiliation(s)
- Sanathoi Gurumayum
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Puzi Jiang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Xiaowen Hao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
| | - Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
- Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peer Bork
- European molecular biology laboratory (EMBL), Meyerhof Strasse 1, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany
- Max-Delbrück-Centre for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, 200433 Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, China
| | - Li-jie He
- Department of Medical Oncology, People's Hospital of Liaoning Province, 110016 Shenyang, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), 430074 Wuhan, Hubei, China
- College of Life Science, Henan Normal University, 453007 Xinxiang, Henan, China
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22
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Stroehlein AJ, Korhonen PK, Rollinson D, Stothard JR, Hall RS, Gasser RB, Young ND. Bulinus truncatus transcriptome – a resource to enable molecular studies of snail and schistosome biology. Current Research in Parasitology & Vector-Borne Diseases 2021; 1:100015. [PMID: 35284899 PMCID: PMC8906107 DOI: 10.1016/j.crpvbd.2021.100015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 11/05/2022]
Abstract
Despite advances in high-throughput sequencing and bioinformatics, molecular investigations of snail intermediate hosts that transmit parasitic trematodes are scant. Here, we report the first transcriptome for Bulinus truncatus – a key intermediate host of Schistosoma haematobium – a blood fluke that causes urogenital schistosomiasis in humans. We assembled this transcriptome from short- and long-read RNA-sequence data. From this transcriptome, we predicted 12,998 proteins, 58% of which had orthologs in Biomphalaria glabrata – an intermediate host of Schistosoma mansoni – a blood fluke that causes hepato-intestinal schistosomiasis. We predicted that select protein groups are involved in signal transduction, cell growth and death, the immune system, environmental adaptation and/or the excretory/secretory system, suggesting roles in immune responses, pathogen defence and/or parasite-host interactions. The transcriptome of Bu. truncatus provides a useful resource to underpin future molecular investigations of this and related snail species, and its interactions with pathogens including S. haematobium. The present resource should enable comparative investigations of other molluscan hosts of socioeconomically important parasites in the future. First transcriptome to represent Bulinus truncatus – a snail intermediate host of Schistosoma haematobium. Select protein groups of Bu. truncatus are inferred to associate with innate immune responses against pathogens. Transcriptome provides a resource for future studies of parasite-host interactions and snail-host resistance to pathogens.
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Korhonen PK, Gasser RB, Ma G, Wang T, Stroehlein AJ, Young ND, Ang CS, Fernando DD, Lu HC, Taylor S, Reynolds SL, Mofiz E, Najaraj SH, Gowda H, Madugundu A, Renuse S, Holt D, Pandey A, Papenfuss AT, Fischer K. High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite. PLoS Negl Trop Dis 2020; 14:e0008720. [PMID: 33001992 PMCID: PMC7591027 DOI: 10.1371/journal.pntd.0008720] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 10/27/2020] [Accepted: 08/17/2020] [Indexed: 12/16/2022] Open
Abstract
The parasitic mite Sarcoptes scabiei is an economically highly significant parasite of the skin of humans and animals worldwide. In humans, this mite causes a neglected tropical disease (NTD), called scabies. This disease results in major morbidity, disability, stigma and poverty globally and is often associated with secondary bacterial infections. Currently, anti-scabies treatments are not sufficiently effective, resistance to them is emerging and no vaccine is available. Here, we report the first high-quality genome and transcriptomic data for S. scabiei. The genome is 56.6 Mb in size, has a a repeat content of 10.6% and codes for 9,174 proteins. We explored key molecules involved in development, reproduction, host-parasite interactions, immunity and disease. The enhanced 'omic data sets for S. scabiei represent comprehensive and critical resources for genetic, functional genomic, metabolomic, phylogenetic, ecological and/or epidemiological investigations, and will underpin the design and development of new treatments, vaccines and/or diagnostic tests.
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Affiliation(s)
- Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Guangxu Ma
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Tao Wang
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Andreas J. Stroehlein
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, Victoria, Australia
| | - Deepani D. Fernando
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Hieng C. Lu
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sara Taylor
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Simone L. Reynolds
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ehtesham Mofiz
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Shivashankar H. Najaraj
- Faculty of Health, School—Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Harsha Gowda
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Anil Madugundu
- Institute of Bioinformatics, Bangalore, India
- Center for Individualized Medicine and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, India
| | | | - Deborah Holt
- Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- College of Health and Human Sciences, Charles Darwin University, Darwin, Australia
| | - Akhilesh Pandey
- Center for Individualized Medicine and Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States of America
| | - Anthony T. Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Katja Fischer
- Cell and Molecular Biology Department, Infectious Diseases Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
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Kinkar L, Young ND, Sohn WM, Stroehlein AJ, Korhonen PK, Gasser RB. First record of a tandem-repeat region within the mitochondrial genome of Clonorchis sinensis using a long-read sequencing approach. PLoS Negl Trop Dis 2020; 14:e0008552. [PMID: 32845881 PMCID: PMC7449408 DOI: 10.1371/journal.pntd.0008552] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
Background Mitochondrial genomes provide useful genetic markers for systematic and population genetic studies of parasitic helminths. Although many such genome sequences have been published and deposited in public databases, there is evidence that some of them are incomplete relating to an inability of conventional techniques to reliably sequence non-coding (repetitive) regions. In the present study, we characterise the complete mitochondrial genome—including the long, non-coding region—of the carcinogenic Chinese liver fluke, Clonorchis sinensis, using long-read sequencing. Methods The mitochondrial genome was sequenced from total high molecular-weight genomic DNA isolated from a pool of 100 adult worms of C. sinensis using the MinION sequencing platform (Oxford Nanopore Technologies), and assembled and annotated using an informatic approach. Results From > 93,500 long-reads, we assembled a 18,304 bp-mitochondrial genome for C. sinensis. Within this genome we identified a novel non-coding region of 4,549 bp containing six tandem-repetitive units of 719–809 bp each. Given that genomic DNA from pooled worms was used for sequencing, some variability in length/sequence in this tandem-repetitive region was detectable, reflecting population variation. Conclusions For C. sinensis, we report the complete mitochondrial genome, which includes a long (> 4.5 kb) tandem-repetitive region. The discovery of this non-coding region using a nanopore-sequencing/informatic approach now paves the way to investigating the nature and extent of length/sequence variation in this region within and among individual worms, both within and among C. sinensis populations, and to exploring whether this region has a functional role in the regulation of replication and transcription, akin to the mitochondrial control region in mammals. Although applied to C. sinensis, the technological approach established here should be broadly applicable to characterise complex tandem-repetitive or homo-polymeric regions in the mitochondrial genomes of a wide range of taxa. In the present study, we characterised the complete mitochondrial genome of Clonorchis sinensis—a carcinogenic liver fluke. To do this, we sequenced from total genomic DNA from multiple adult worms using a new method (Oxford Nanopore technology) to obtain data for long stretches of DNA, and then assembled these data to construct a mitochondrial genome of 18,304 bp, containing a > 4.5 kb-long tandem-repetitive region—not previously detected in this species. The results demonstrate that this method is effective at sequencing long and complex non-coding elements—not achievable using conventional techniques. The discovery of this long tandem-repetitive region in C. sinensis provides an opportunity to now explore its origin(s) and length/sequence diversity in populations of this species, and also to characterise its function(s). The technological approach employed here should have broad applicability to characterise previously-elusive non-coding mitochondrial genomic regions in a wide range of taxa.
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Affiliation(s)
- Liina Kinkar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (NDY); (RBG)
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Andreas J. Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (NDY); (RBG)
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Kinkar L, Korhonen PK, Wang D, Zhu XQ, Chelomina GN, Wang T, Hall RS, Koehler AV, Harliwong I, Yang B, Fink JL, Young ND, Gasser RB. Marked mitochondrial genetic variation in individuals and populations of the carcinogenic liver fluke Clonorchis sinensis. PLoS Negl Trop Dis 2020; 14:e0008480. [PMID: 32813714 PMCID: PMC7437864 DOI: 10.1371/journal.pntd.0008480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/12/2020] [Indexed: 01/24/2023] Open
Abstract
Clonorchiasis is a neglected tropical disease caused by the Chinese liver fluke, Clonorchis sinensis, and is often associated with a malignant form of bile duct cancer (cholangiocarcinoma). Although some aspects of the epidemiology of clonorchiasis are understood, little is known about the genetics of C. sinensis populations. Here, we conducted a comprehensive genetic exploration of C. sinensis from endemic geographic regions using complete mitochondrial protein gene sets. Genomic DNA samples from C. sinensis individuals (n = 183) collected from cats and dogs in China (provinces of Guangdong, Guangxi, Hunan, Heilongjiang and Jilin) as well as from rats infected with metacercariae from cyprinid fish from the Russian Far East (Primorsky Krai region) were deep sequenced using the BGISEQ-500 platform. Informatic analyses of mitochondrial protein gene data sets revealed marked genetic variation within C. sinensis; significant variation was identified within and among individual worms from distinct geographical locations. No clear affiliation with a particular location or host species was evident, suggesting a high rate of dispersal of the parasite across endemic regions. The present work provides a foundation for future biological, epidemiological and ecological studies using mitochondrial protein gene data sets, which could aid in elucidating associations between particular C. sinensis genotypes/haplotypes and the pathogenesis or severity of clonorchiasis and its complications (including cholangiocarcinoma) in humans. Clonorchiasis is an important neglected tropical disease caused by the Chinese liver fluke, Clonorchis sinensis, which can induce malignant bile duct cancer (cholangiocarcinoma). Little precise information is available on the biology, epidemiology and population genetics of C. sinensis. For this reason, we explored here the genetic composition of C. sinensis populations in distinct endemic areas in China and Russia. Using a deep sequencing-informatic approach, we revealed marked mitochondrial genetic variation within and between individuals and populations of C. sinensis, with no particular affiliation with geographic or host origin. These molecular findings and the methodology established should underpin future genetic studies of C. sinensis causing human clonorchiasis and associated complications (cancer) as well as transmission patterns in endemic regions.
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Affiliation(s)
- Liina Kinkar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Daxi Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- BGI International, Shenzhen, China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Galina N. Chelomina
- Department of Parasitology, Federal Scientific Center of the East Asia Terrestrial Biodiversity FEB RAS, Vladivostok, Russia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ross S. Hall
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Anson V. Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | | | | | | | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (NDY); (RBG)
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (NDY); (RBG)
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Ma G, Gasser RB, Wang T, Korhonen PK, Young ND. Toward integrative 'omics of the barber's pole worm and related parasitic nematodes. Infect Genet Evol 2020; 85:104500. [PMID: 32795511 DOI: 10.1016/j.meegid.2020.104500] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/15/2022]
Abstract
Advances in nucleic acid sequencing, mass spectrometry and computational biology have facilitated the identification, annotation and analysis of genes, transcripts, proteins and metabolites in model nematodes (Caenorhabditis elegans and Pristionchus pacificus) and socioeconomically important parasitic nematodes (Clades I, III, IV and V). Significant progress has been made in genomics and transcriptomics as well as in the proteomics and lipidomics of Haemonchus contortus (the barber's pole worm) - one of the most pathogenic representatives of the order Strongylida. Here, we review salient aspects of genomics, transcriptomics, proteomics, lipidomics, glycomics and functional genomics, and discuss the rise of integrative 'omics of this economically important parasite. Although our knowledge of the molecular biology, genetics and biochemistry of H. contortus and related species has progressed significantly, much remains to be explored, particularly in areas such as drug resistance, unique/unknown genes, host-parasite interactions, parasitism and the pathogenesis of disease, by integrating the use of multiple 'omics methods. This approach should lead to a better understanding of H. contortus and its relatives at a 'systems biology' level, and should assist in developing new interventions against these parasites.
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Affiliation(s)
- Guangxu Ma
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, China; Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
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Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Combined use of feature engineering and machine-learning to predict essential genes in Drosophila melanogaster. NAR Genom Bioinform 2020; 2:lqaa051. [PMID: 33575603 PMCID: PMC7671374 DOI: 10.1093/nargab/lqaa051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/05/2020] [Accepted: 07/04/2020] [Indexed: 12/17/2022] Open
Abstract
Characterizing genes that are critical for the survival of an organism (i.e. essential) is important to gain a deep understanding of the fundamental cellular and molecular mechanisms that sustain life. Functional genomic investigations of the vinegar fly, Drosophila melanogaster, have unravelled the functions of numerous genes of this model species, but results from phenomic experiments can sometimes be ambiguous. Moreover, the features underlying gene essentiality are poorly understood, posing challenges for computational prediction. Here, we harnessed comprehensive genomic-phenomic datasets publicly available for D. melanogaster and a machine-learning-based workflow to predict essential genes of this fly. We discovered strong predictors of such genes, paving the way for computational predictions of essentiality in less-studied arthropod pests and vectors of infectious diseases.
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
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Campos TL, Korhonen PK, Sternberg PW, Gasser RB, Young ND. Predicting gene essentiality in Caenorhabditis elegans by feature engineering and machine-learning. Comput Struct Biotechnol J 2020; 18:1093-1102. [PMID: 32489524 PMCID: PMC7251299 DOI: 10.1016/j.csbj.2020.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023] Open
Abstract
Defining genes that are essential for life has major implications for understanding critical biological processes and mechanisms. Although essential genes have been identified and characterised experimentally using functional genomic tools, it is challenging to predict with confidence such genes from molecular and phenomic data sets using computational methods. Using extensive data sets available for the model organism Caenorhabditis elegans, we constructed here a machine-learning (ML)-based workflow for the prediction of essential genes on a genome-wide scale. We identified strong predictors for such genes and showed that trained ML models consistently achieve highly-accurate classifications. Complementary analyses revealed an association between essential genes and chromosomal location. Our findings reveal that essential genes in C. elegans tend to be located in or near the centre of autosomal chromosomes; are positively correlated with low single nucleotide polymorphim (SNP) densities and epigenetic markers in promoter regions; are involved in protein and nucleotide processing; are transcribed in most cells; are enriched in reproductive tissues or are targets for small RNAs bound to the argonaut CSR-1. Based on these results, we hypothesise an interplay between epigenetic markers and small RNA pathways in the germline, with transcription-based memory; this hypothesis warrants testing. From a technical perspective, further work is needed to evaluate whether the present ML-based approach will be applicable to other metazoans (including Drosophila melanogaster) for which comprehensive data sets (i.e. genomic, transcriptomic, proteomic, variomic, epigenetic and phenomic) are available.
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Key Words
- CDS, coding sequence
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- Caenorhabditis elegans
- ES, Essentiality Score
- EST, expressed sequence tag
- Essential genes
- Essentiality predictions
- GBM, Gradient Boosting Method
- GFF, general feature format
- GLM, Generalised Linear Model
- GO, gene ontology
- ML, machine-learning
- Machine-learning
- NN, Artificial Neural Network
- PPI, protein-protein interaction
- PR-AUC, Area Under the Precision-Recall Curve
- RF, Random Forest
- RNAi, RNA interference
- ROC-AUC, Area Under the Receiver Operating Characteristic Curve
- SNP, single nucleotide polymorphism
- SPLS, Sparse Partial Least Squares
- SVM, Support-Vector Machine
- TEA, Tissue Enrichment Analysis tool (WormBase)
- TSS, transcription start site
- VCF, variant call file
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.,Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
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Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, Anstead CA, Ayoub NA, Batterham P, Bellair M, Binford GJ, Chao H, Chen YH, Childers C, Dinh H, Doddapaneni HV, Duan JJ, Dugan S, Esposito LA, Friedrich M, Garb J, Gasser RB, Goodisman MAD, Gundersen-Rindal DE, Han Y, Handler AM, Hatakeyama M, Hering L, Hunter WB, Ioannidis P, Jayaseelan JC, Kalra D, Khila A, Korhonen PK, Lee CE, Lee SL, Li Y, Lindsey ARI, Mayer G, McGregor AP, McKenna DD, Misof B, Munidasa M, Munoz-Torres M, Muzny DM, Niehuis O, Osuji-Lacy N, Palli SR, Panfilio KA, Pechmann M, Perry T, Peters RS, Poynton HC, Prpic NM, Qu J, Rotenberg D, Schal C, Schoville SD, Scully ED, Skinner E, Sloan DB, Stouthamer R, Strand MR, Szucsich NU, Wijeratne A, Young ND, Zattara EE, Benoit JB, Zdobnov EM, Pfrender ME, Hackett KJ, Werren JH, Worley KC, Gibbs RA, Chipman AD, Waterhouse RM, Bornberg-Bauer E, Hahn MW, Richards S. Gene content evolution in the arthropods. Genome Biol 2020; 21:15. [PMID: 31969194 PMCID: PMC6977273 DOI: 10.1186/s13059-019-1925-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/26/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. RESULTS Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. CONCLUSIONS These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.
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Affiliation(s)
- Gregg W. C. Thomas
- 0000 0001 0790 959Xgrid.411377.7Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN USA
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münsterss, 48149 Münster, Germany ,0000 0001 2287 2617grid.9026.dInstitute for Bioinformatics and Chemoinformatics, University of Hamburg, Hamburg, Germany ,Westphalian University of Applied Sciences, 45665 Recklinghausen, Germany
| | - Daniel S. T. Hughes
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,0000000419368729grid.21729.3fPresent Address: Institute for Genomic Medicine, Columbia University, New York, NY 10032 USA
| | - Shwetha C. Murali
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,0000000122986657grid.34477.33Present Address: Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195 USA
| | - Monica Poelchau
- 0000 0001 2113 2895grid.483014.aNational Agricultural Library, USDA, Beltsville, MD 20705 USA
| | - Karl Glastad
- 0000 0001 2097 4943grid.213917.fSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA ,0000 0004 1936 8972grid.25879.31Present Address: Penn Epigenetics Institute, Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
| | - Clare A. Anstead
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Nadia A. Ayoub
- grid.268042.aDepartment of Biology, Washington and Lee University, 204 West Washington Street, Lexington, VA 24450 USA
| | - Phillip Batterham
- 0000 0001 2179 088Xgrid.1008.9School of BioSciences Science Faculty, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Michelle Bellair
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,Present Address: CooperGenomics, Houston, TX USA
| | - Greta J. Binford
- 0000 0004 1936 9043grid.259053.8Department of Biology, Lewis & Clark College, Portland, OR 97219 USA
| | - Hsu Chao
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Yolanda H. Chen
- 0000 0004 1936 7689grid.59062.38Department of Plant and Soil Sciences, University of Vermont, Burlington, USA
| | - Christopher Childers
- 0000 0001 2113 2895grid.483014.aNational Agricultural Library, USDA, Beltsville, MD 20705 USA
| | - Huyen Dinh
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Harsha Vardhan Doddapaneni
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Jian J. Duan
- 0000 0004 0404 0958grid.463419.dBeneficial Insects Introduction Research Unit, United States Department of Agriculture, Agricultural Research Service, Newark, DE USA
| | - Shannon Dugan
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Lauren A. Esposito
- 0000 0004 0461 6769grid.242287.9Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118 USA
| | - Markus Friedrich
- 0000 0001 1456 7807grid.254444.7Department of Biological Sciences, Wayne State University, Detroit, MI 48202 USA
| | - Jessica Garb
- 0000 0000 9620 1122grid.225262.3Department of Biological Sciences, University of Massachusetts Lowell, 198 Riverside Street, Lowell, MA 01854 USA
| | - Robin B. Gasser
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Michael A. D. Goodisman
- 0000 0001 2097 4943grid.213917.fSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332 USA
| | - Dawn E. Gundersen-Rindal
- 0000 0004 0404 0958grid.463419.dUSDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, MD USA
| | - Yi Han
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Alfred M. Handler
- 0000 0004 0404 0958grid.463419.dUSDA-ARS, Center for Medical, Agricultural, and Veterinary Entomology, 1700 S.W. 23rd Drive, Gainesville, FL 32608 USA
| | - Masatsugu Hatakeyama
- 0000 0001 0699 0373grid.410590.9Division of Insect Sciences, National Institute of Agrobiological Sciences, Owashi, Tsukuba, 305-8634 Japan
| | - Lars Hering
- 0000 0001 1089 1036grid.5155.4Department of Zoology, Institute of Biology, University of Kassel, 34132 Kassel, Germany
| | - Wayne B. Hunter
- 0000 0004 0404 0958grid.463419.dUSDA ARS, U. S. Horticultural Research Laboratory, Ft. Pierce, FL 34945 USA
| | - Panagiotis Ioannidis
- 0000 0001 2322 4988grid.8591.5Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211 Geneva, Switzerland ,0000 0004 0635 685Xgrid.4834.bPresent Address: Foundation for Research and Technology Hellas, Institute of Molecular Biology and Biotechnology, Vassilika Vouton, 70013 Heraklion, Greece
| | - Joy C. Jayaseelan
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Divya Kalra
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Abderrahman Khila
- 0000 0001 2150 7757grid.7849.2Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, 69364 Lyon, France
| | - Pasi K. Korhonen
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Carol Eunmi Lee
- 0000 0001 0701 8607grid.28803.31Department of Integrative Biology, University of Wisconsin, Madison, WI 53706 USA
| | - Sandra L. Lee
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Yiyuan Li
- 0000 0001 2168 0066grid.131063.6Department of Biological Sciences, University of Notre Dame, 109B Galvin Life Sciences, Notre Dame, IN 46556 USA
| | - Amelia R. I. Lindsey
- 0000 0001 2222 1582grid.266097.cDepartment of Entomology, University of California Riverside, Riverside, CA USA ,0000 0001 0790 959Xgrid.411377.7Present Address: Department of Biology, Indiana University, Bloomington, IN USA
| | - Georg Mayer
- 0000 0001 1089 1036grid.5155.4Department of Zoology, Institute of Biology, University of Kassel, 34132 Kassel, Germany
| | - Alistair P. McGregor
- 0000 0001 0726 8331grid.7628.bDepartment of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP UK
| | - Duane D. McKenna
- 0000 0000 9560 654Xgrid.56061.34Department of Biological Sciences, University of Memphis, 3700 Walker Ave, Memphis, TN 38152 USA
| | - Bernhard Misof
- 0000 0001 2216 5875grid.452935.cCenter for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Mala Munidasa
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Monica Munoz-Torres
- 0000 0001 2231 4551grid.184769.5Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, USA ,0000 0004 4665 2899grid.497331.bPresent Address: Phoenix Bioinformatics, 39221 Paseo Padre Parkway, Ste. J., Fremont, CA 94538 USA
| | - Donna M. Muzny
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Oliver Niehuis
- grid.5963.9Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University of Freiburg, 79104 Freiburg (Brsg.), Germany
| | - Nkechinyere Osuji-Lacy
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Subba R. Palli
- 0000 0004 1936 8438grid.266539.dDepartment of Entomology, University of Kentucky, Lexington, KY 40546 USA
| | - Kristen A. Panfilio
- 0000 0000 8809 1613grid.7372.1School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL UK
| | - Matthias Pechmann
- 0000 0000 8580 3777grid.6190.eCologne Biocenter, Zoological Institute, Department of Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | - Trent Perry
- 0000 0001 2179 088Xgrid.1008.9School of BioSciences Science Faculty, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Ralph S. Peters
- 0000 0001 2216 5875grid.452935.cCentre of Taxonomy and Evolutionary Research, Arthropoda Department, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Helen C. Poynton
- 0000 0004 0386 3207grid.266685.9School for the Environment, University of Massachusetts Boston, Boston, MA 02125 USA
| | - Nikola-Michael Prpic
- 0000 0001 2364 4210grid.7450.6Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Abteilung für Entwicklungsbiologie, Georg-August-Universität Göttingen, Göttingen, Germany ,0000 0001 2364 4210grid.7450.6Göttingen Center for Molecular Biosciences (GZMB), Georg-August-Universität Göttingen, Göttingen, Germany
| | - Jiaxin Qu
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Dorith Rotenberg
- 0000 0001 2173 6074grid.40803.3fDepartment of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606 USA
| | - Coby Schal
- 0000 0001 2173 6074grid.40803.3fDepartment of Entomology and W.M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695 USA
| | - Sean D. Schoville
- 0000 0001 2167 3675grid.14003.36Department of Entomology, University of Wisconsin-Madison, Madison, USA
| | - Erin D. Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS Center for Grain and Animal Health Research, Manhattan, KS 66502 USA
| | - Evette Skinner
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Daniel B. Sloan
- 0000 0004 1936 8083grid.47894.36Department of Biology, Colorado State University, Ft. Collins, CO USA
| | - Richard Stouthamer
- 0000 0001 2222 1582grid.266097.cDepartment of Entomology, University of California Riverside, Riverside, CA USA
| | - Michael R. Strand
- 0000 0004 1936 738Xgrid.213876.9Department of Entomology, University of Georgia, Athens, GA USA
| | - Nikolaus U. Szucsich
- 0000 0001 2169 5989grid.252381.fPresent Address: Arkansas Biosciences Institute, Arkansas State University, Jonesboro, AR USA
| | - Asela Wijeratne
- 0000 0000 9560 654Xgrid.56061.34Department of Biological Sciences, University of Memphis, 3700 Walker Ave, Memphis, TN 38152 USA ,0000 0001 2112 4115grid.425585.bNatural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Neil D. Young
- 0000 0001 2179 088Xgrid.1008.9Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Eduardo E. Zattara
- 0000 0001 2112 473Xgrid.412234.2INIBIOMA, Univ. Nacional del Comahue – CONICET, Bariloche, Argentina
| | - Joshua B. Benoit
- 0000 0001 2179 9593grid.24827.3bDepartment of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221 USA
| | - Evgeny M. Zdobnov
- 0000 0001 2322 4988grid.8591.5Department of Genetic Medicine and Development and Swiss Institute of Bioinformatics, University of Geneva, 1211 Geneva, Switzerland
| | - Michael E. Pfrender
- 0000 0001 2168 0066grid.131063.6Department of Biological Sciences, University of Notre Dame, 109B Galvin Life Sciences, Notre Dame, IN 46556 USA
| | - Kevin J. Hackett
- 0000 0004 0404 0958grid.463419.dCrop Production and Protection, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705 USA
| | - John H. Werren
- 0000 0004 1936 9174grid.16416.34Department of Biology, University of Rochester, Rochester, NY 14627 USA
| | - Kim C. Worley
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Richard A. Gibbs
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Ariel D. Chipman
- 0000 0004 1937 0538grid.9619.7Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 91904 Jerusalem, Israel
| | - Robert M. Waterhouse
- 0000 0001 2165 4204grid.9851.5Department of Ecology & Evolution and Swiss Institute of Bioinformatics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münsterss, 48149 Münster, Germany ,0000 0001 2287 2617grid.9026.dInstitute for Bioinformatics and Chemoinformatics, University of Hamburg, Hamburg, Germany ,0000 0001 1014 8330grid.419495.4Department Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Matthew W. Hahn
- 0000 0001 0790 959Xgrid.411377.7Department of Biology and Department of Computer Science, Indiana University, Bloomington, IN USA
| | - Stephen Richards
- 0000 0001 2160 926Xgrid.39382.33Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,0000 0004 1936 9684grid.27860.3bPresent Address: UC Davis Genome Center, University of California, Davis, CA 95616 USA
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30
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Wang T, Ma G, Ang CS, Korhonen PK, Stroehlein AJ, Young ND, Hofmann A, Chang BCH, Williamson NA, Gasser RB. The developmental phosphoproteome of Haemonchus contortus. J Proteomics 2019; 213:103615. [PMID: 31846766 DOI: 10.1016/j.jprot.2019.103615] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/22/2019] [Accepted: 12/13/2019] [Indexed: 12/22/2022]
Abstract
Protein phosphorylation plays essential roles in many cellular processes. Despite recent progress in the genomics, transcriptomics and proteomics of socioeconomically important parasitic nematodes, there is scant phosphoproteomic data to underpin molecular biological discovery. Here, using the phosphopeptide enrichment-based LC-MS/MS and data-independent acquisition (DIA) quantitation, we characterised the first developmental phosphoproteome of the parasitic nematode Haemonchus contortus - one of the most pathogenic parasites of ruminant livestock. Totally, 1804 phosphorylated proteins with 4406 phosphorylation sites ('phosphosites') from different developmental stages/sexes were identified. Bioinformatic analyses of quantified 'phosphosites' exhibited distinctive stage- and sex-specific patterns during development, and identified a subset of phosphoproteins proposed to play crucial roles in processes such as spindle positioning, signal transduction and kinase activity. A sequence-based comparison of the phosphoproteome of H. contortus with those of two free-living nematode species (Caenorhabditis elegans and Pristionchus pacificus) suggested a limited number of common protein phosphorylation events among these species. Our findings infer active roles for protein phosphorylation in the adaptation of a parasitic nematode to a constantly changing external environment. The phosphoproteomic data set for H. contortus provides a basis to better understand phosphorylation and associated biological processes (e.g., regulation of signal transduction), and might enable the discovery of novel anthelmintic targets. SIGNIFICANCE: Here, we report the first phosphoproteome for a socioeconomically parasitic nematode (Haemonchus contortus). This phosphoproteome exhibits distinctive patterns during development, suggesting active roles of post-translational modification in the parasite's adaptation to changing environments within and outside of the host animal. This work sheds a light on the developmental phosphorylation in a parasitic nematode, and could enable the discovery of novel interventions against major pathogens.
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Affiliation(s)
- Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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31
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Stroehlein AJ, Korhonen PK, Chong TM, Lim YL, Chan KG, Webster B, Rollinson D, Brindley PJ, Gasser RB, Young ND. High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing. Gigascience 2019; 8:giz108. [PMID: 31494670 PMCID: PMC6736295 DOI: 10.1093/gigascience/giz108] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/25/2019] [Accepted: 08/10/2019] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting >100 million people worldwide. Chronic infection with this parasitic trematode can lead to urogenital conditions including female genital schistosomiasis and bladder cancer. At the molecular level, little is known about this blood fluke and the pathogenesis of the disease that it causes. To support molecular studies of this carcinogenic worm, we reported a draft genome for S. haematobium in 2012. Although a useful resource, its utility has been somewhat limited by its fragmentation. FINDINGS Here, we systematically enhanced the draft genome of S. haematobium using a single-molecule and long-range DNA-sequencing approach. We achieved a major improvement in the accuracy and contiguity of the genome assembly, making it superior or comparable to assemblies for other schistosome species. We transferred curated gene models to this assembly and, using enhanced gene annotation pipelines, inferred a gene set with as many or more complete gene models as those of other well-studied schistosomes. Using conserved, single-copy orthologs, we assessed the phylogenetic position of S. haematobium in relation to other parasitic flatworms for which draft genomes were available. CONCLUSIONS We report a substantially enhanced genomic resource that represents a solid foundation for molecular research on S. haematobium and is poised to better underpin population and functional genomic investigations and to accelerate the search for new disease interventions.
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Affiliation(s)
- Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
| | - Teik Min Chong
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Yan Lue Lim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Bonnie Webster
- Parasites and Vectors Division, The Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
| | - David Rollinson
- Parasites and Vectors Division, The Natural History Museum, Cromwell Rd, South Kensington, London SW7 5BD, UK
| | - Paul J Brindley
- School of Medicine & Health Sciences, Department of Microbiology, Immunology & Tropical Medicine, George Washington University, 2300 Eye Street, NW, Suite 502, Washington, DC 20037, USA
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia
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Ma G, Wang T, Korhonen PK, Young ND, Nie S, Ang CS, Williamson NA, Reid GE, Gasser RB. Dafachronic acid promotes larval development in Haemonchus contortus by modulating dauer signalling and lipid metabolism. PLoS Pathog 2019; 15:e1007960. [PMID: 31335899 PMCID: PMC6677322 DOI: 10.1371/journal.ppat.1007960] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/02/2019] [Accepted: 07/04/2019] [Indexed: 02/07/2023] Open
Abstract
Here, we discovered an endogenous dafachronic acid (DA) in the socioeconomically important parasitic nematode Haemonchus contortus. We demonstrate that DA promotes larval exsheathment and development in this nematode via a relatively conserved nuclear hormone receptor (DAF-12). This stimulatory effect is dose- and time-dependent, and relates to a modulation of dauer-like signalling, and glycerolipid and glycerophospholipid metabolism, likely via a negative feedback loop. Specific chemical inhibition of DAF-9 (cytochrome P450) was shown to significantly reduce the amount of endogenous DA in H. contortus; compromise both larval exsheathment and development in vitro; and modulate lipid metabolism. Taken together, this evidence shows that DA plays a key functional role in the developmental transition from the free-living to the parasitic stage of H. contortus by modulating the dauer-like signalling pathway and lipid metabolism. Understanding the intricacies of the DA-DAF-12 system and associated networks in H. contortus and related parasitic nematodes could pave the way to new, nematode-specific treatments. In the present study, using an integrative multi-omics approach, we show that dafachronic acid (DA) plays a critical functional role in the developmental transition in larvae of the parasitic nematode Haemonchus contortus (barber’s pole worm) by modulating the dauer-like signalling pathway and lipid metabolism. The DA-DAF-12 signalling module in H. contortus provides a paradigm to explore its developmental and reproductive biology at the molecular level, to study physiochemical cross-talk between the parasite and its hosts, and to discover novel anthelmintic targets.
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Affiliation(s)
- Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Shuai Nie
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas A. Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria, Australia
| | - Gavin E. Reid
- School of Chemistry, The University of Melbourne, Parkville, Victoria, Australia
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, Australia
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail:
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33
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Lelwala RV, Korhonen PK, Young ND, Scott JB, Ades PK, Gasser RB, Taylor PWJ. Comparative genome analysis indicates high evolutionary potential of pathogenicity genes in Colletotrichum tanaceti. PLoS One 2019; 14:e0212248. [PMID: 31150449 PMCID: PMC6544218 DOI: 10.1371/journal.pone.0212248] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/02/2019] [Indexed: 01/30/2023] Open
Abstract
Colletotrichum tanaceti is an emerging foliar fungal pathogen of commercially grown pyrethrum (Tanacetum cinerariifolium). Despite being reported consistently from field surveys in Australia, the molecular basis of pathogenicity of C. tanaceti on pyrethrum is unknown. Herein, the genome of C. tanaceti (isolate BRIP57314) was assembled de novo and annotated using transcriptomic evidence. The inferred putative pathogenicity gene suite of C. tanaceti comprised a large array of genes encoding secreted effectors, proteases, CAZymes and secondary metabolites. Comparative analysis of its putative pathogenicity gene profiles with those of closely related species suggested that C. tanaceti likely has additional hosts to pyrethrum. The genome of C. tanaceti had a high repeat content and repetitive elements were located significantly closer to genes inferred to influence pathogenicity than other genes. These repeats are likely to have accelerated mutational and transposition rates in the genome, resulting in a rapid evolution of certain CAZyme families in this species. The C. tanaceti genome showed strong signals of Repeat Induced Point (RIP) mutation which likely caused its bipartite nature consisting of distinct gene-sparse, repeat and A-T rich regions. Pathogenicity genes within these RIP affected regions were likely to have a higher evolutionary rate than the rest of the genome. This "two-speed" genome phenomenon in certain Colletotrichum spp. was hypothesized to have caused the clustering of species based on the pathogenicity genes, to deviate from taxonomic relationships. The large repertoire of pathogenicity factors that potentially evolve rapidly due to the plasticity of the genome, indicated that C. tanaceti has a high evolutionary potential. Therefore, C. tanaceti poses a high-risk to the pyrethrum industry. Knowledge of the evolution and diversity of the putative pathogenicity genes will facilitate future research in disease management of C. tanaceti and other Colletotrichum spp.
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Affiliation(s)
- Ruvini V. Lelwala
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Jason B. Scott
- Tasmanian Institute of Agriculture, University of Tasmania, Burnie, Tasmania, Australia
| | - Peter K. Ades
- Faculty of Science, The University of Melbourne, Parkville, Victoria, Australia
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Paul W. J. Taylor
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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34
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Kinkar L, Korhonen PK, Cai H, Gauci CG, Lightowlers MW, Saarma U, Jenkins DJ, Li J, Li J, Young ND, Gasser RB. Long-read sequencing reveals a 4.4 kb tandem repeat region in the mitogenome of Echinococcus granulosus (sensu stricto) genotype G1. Parasit Vectors 2019; 12:238. [PMID: 31097022 PMCID: PMC6521400 DOI: 10.1186/s13071-019-3492-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/06/2019] [Indexed: 01/08/2023] Open
Abstract
Background Echinococcus tapeworms cause a severe helminthic zoonosis called echinococcosis. The genus comprises various species and genotypes, of which E. granulosus (sensu stricto) represents a significant global public health and socioeconomic burden. Mitochondrial (mt) genomes have provided useful genetic markers to explore the nature and extent of genetic diversity within Echinococcus and have underpinned phylogenetic and population structure analyses of this genus. Our recent work indicated a sequence gap (> 1 kb) in the mt genomes of E. granulosus genotype G1, which could not be determined by PCR-based Sanger sequencing. The aim of the present study was to define the complete mt genome, irrespective of structural complexities, using a long-read sequencing method. Methods We extracted high molecular weight genomic DNA from protoscoleces from a single cyst of E. granulosus genotype G1 from a sheep from Australia using a conventional method and sequenced it using PacBio Sequel (long-read) technology, complemented by BGISEQ-500 short-read sequencing. Sequence data obtained were assembled using a recently-developed workflow. Results We assembled a complete mt genome sequence of 17,675 bp, which is > 4 kb larger than the complete mt genomes known for E. granulosus genotype G1. This assembly includes a previously-elusive tandem repeat region, which is 4417 bp long and consists of ten near-identical 441–445 bp repeat units, each harbouring a 184 bp non-coding region and adjacent regions. We also identified a short non-coding region of 183 bp, which includes an inverted repeat. Conclusions We report what we consider to be the first complete mt genome of E. granulosus genotype G1 and characterise all repeat regions in this genome. The numbers, sizes, sequences and functions of tandem repeat regions remain to be studied in different isolates of genotype G1 and in other genotypes and species. The discovery of such ‘new’ repeat elements in the mt genome of genotype G1 by PacBio sequencing raises a question about the completeness of some published genomes of taeniid cestodes assembled from conventional or short-read sequence datasets. This study shows that long-read sequencing readily overcomes the challenges of assembling repeat elements to achieve improved genomes.
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Affiliation(s)
- Liina Kinkar
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Pasi K Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Huimin Cai
- BGI Research, Shenzhen, Guangdong, China
| | - Charles G Gauci
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Marshall W Lightowlers
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - David J Jenkins
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga, Wagga, NSW, Australia
| | | | - Junhua Li
- BGI Research, Shenzhen, Guangdong, China
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Robin B Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.
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Wang T, Ma G, Ang CS, Korhonen PK, Koehler AV, Young ND, Nie S, Williamson NA, Gasser RB. High throughput LC-MS/MS-based proteomic analysis of excretory-secretory products from short-term in vitro culture of Haemonchus contortus. J Proteomics 2019; 204:103375. [PMID: 31071474 DOI: 10.1016/j.jprot.2019.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/08/2019] [Accepted: 05/02/2019] [Indexed: 12/27/2022]
Abstract
Parasitic nematodes of humans, animals and plants have a major, adverse impact on global health and agricultural production worldwide. To cope with their surrounding environment in and the immune attack from the host, excretory-secretory (ES) proteins are released by nematodes to orchestrate or regulate parasite-host interactions. In the present study, we characterised the ES products from short-term (12 h) in vitro culture of different developmental stages/sexes of Haemonchus contortus (one of the most important parasitic nematodes of livestock animals worldwide) using a high throughput tandem mass-spectrometry, underpinned by the most recent genomic dataset. In total, 878 unique proteins from key developmental stages/sexes (third-stage and fourth-stage larvae, and female and male adults) were identified and quantified with high confidence. Bioinformatic analyses showed noteworthy ES protein alterations during the transition from the free-living to the parasitic phase, especially for proteins which are likely involved in nutrient digestion and acquisition as well as parasite-host interactions, such as proteolytic cascade-related peptidases, glycoside hydrolases, C-type lectins and sperm-coating protein/Tpx/antigen 5/pathogenesis related-1/Sc7 (= SCP/TAPS) proteins. Our findings provide an avenue to better explore interactive processes between the host and this highly significant parasitic nematode, to underpin the search for novel drug and vaccine targets. SIGNIFICANCE: The present study represents a comprehensive proteomic analysis of the secretome of key developmental stages/sexes of H. contortus maintained in short-term in vitro culture. High throughput LC-MS/MS analysis of ES products allowed the identification of a large repertoire of proteins (secretome) and the establishment of a new proteomic database for H. contortus. The secretome of H. contortus undergoes substantial changes during the nematode's transition from free-living to parasitic stages, suggesting a constant adaptation to different environments outside of and within the host animal. Understanding the host-parasite relationship at the molecular level could assist significantly in the development of intervention strategies (i.e. novel drugs and vaccines) against H. contortus and related nematodes.
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Affiliation(s)
- Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Anson V Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Shuai Nie
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Abstract
BACKGROUND Signalling pathways have been extensively investigated in the free-living nematode Caenorhabditis elegans, but very little is known about these pathways in parasitic nematodes. Here, we constructed a model for the dauer-associated signalling pathways in an economically highly significant parasitic worm, Haemonchus contortus. METHODS Guided by data and information available for C. elegans, we used extensive genomic and transcriptomic datasets to infer gene homologues in the dauer-associated pathways, explore developmental transcriptomic, proteomic and phosphoproteomic profiles in H. contortus and study selected molecular structures. RESULTS The canonical cyclic guanosine monophosphate (cGMP), transforming growth factor-β (TGF-β), insulin-like growth factor 1 (IGF-1) and steroid hormone signalling pathways of H. contortus were inferred to represent a total of 61 gene homologues. Compared with C. elegans, H. contortus has a reduced set of genes encoding insulin-like peptides, implying evolutionary and biological divergences between the parasitic and free-living nematodes. Similar transcription profiles were found for all gene homologues between the infective stage of H. contortus and dauer stage of C. elegans. High transcriptional levels for genes encoding G protein-coupled receptors (GPCRs), TGF-β, insulin-like ligands (e.g. ins-1, ins-17 and ins-18) and transcriptional factors (e.g. daf-16) in the infective L3 stage of H. contortus were suggestive of critical functional roles in this stage. Conspicuous protein expression patterns and extensive phosphorylation of some components of these pathways suggested marked post-translational modifications also in the L3 stage. The high structural similarity in the DAF-12 ligand binding domain among nematodes indicated functional conservation in steroid (i.e. dafachronic acid) signalling linked to worm development. CONCLUSIONS Taken together, this pathway model provides a basis to explore hypotheses regarding biological processes and regulatory mechanisms (via particular microRNAs, phosphorylation events and/or lipids) associated with the development of H. contortus and related nematodes as well as parasite-host cross talk, which could aid the discovery of new therapeutic targets.
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Affiliation(s)
- Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Andreas J. Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC 3010 Australia
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Korhonen PK, Hall RS, Young ND, Gasser RB. Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data. Gigascience 2019; 8:giz014. [PMID: 30821816 PMCID: PMC6451199 DOI: 10.1093/gigascience/giz014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/03/2018] [Accepted: 01/25/2019] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Here, we created an automated pipeline for the de novoassembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (∼100 Mb), Drosophila melanogaster (∼138 Mb), and Plasmodium falciparum (∼23 Mb) directly from publicly accessible nucleotide sequence datasets and assessed the quality of the assemblies against curated reference genomes. FINDINGS We showed a dependency of the accuracy of assembly on sequencing technology and GC content and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses. CONCLUSIONS This CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse datasets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes.
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Affiliation(s)
- Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ross S Hall
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
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Wang T, Ma G, Ang CS, Korhonen PK, Xu R, Nie S, Koehler AV, Simpson RJ, Greening DW, Reid GE, Williamson NA, Gasser RB. Somatic proteome of Haemonchus contortus. Int J Parasitol 2019; 49:311-320. [PMID: 30771357 DOI: 10.1016/j.ijpara.2018.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 12/12/2018] [Accepted: 12/17/2018] [Indexed: 01/09/2023]
Abstract
Currently, there is a dearth of proteomic data to underpin fundamental investigations of parasites and parasitism at the molecular level. Here, using a high throughput LC-MS/MS-based approach, we undertook the first reported comprehensive, large-scale proteomic investigation of the barber's pole worm (Haemonchus contortus) - one of the most important parasitic nematodes of livestock animals worldwide. In total, 2487 unique H. contortus proteins representing different developmental stages/sexes (i.e. eggs, L3s and L4s, female (Af) and male (Am) adults) were identified and quantified with high confidence. Bioinformatic analyses of this proteome revealed substantial alterations in protein profiles during the life cycle, particularly in the transition from the free-living to the parasitic phase, and key groups of proteins involved specifically in feeding, digestion, metabolism, development, parasite-host interactions (including immunomodulation), structural remodelling of the body wall and adaptive processes during parasitism. This proteomic data set will facilitate future molecular, biochemical and physiological investigations of H. contortus and related nematodes, and the discovery of novel intervention targets against haemonchosis.
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Affiliation(s)
- Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rong Xu
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria 3086, Australia
| | - Shuai Nie
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Anson V Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Richard J Simpson
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria 3086, Australia
| | - David W Greening
- Department of Biochemistry, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Bundoora, Victoria 3086, Australia
| | - Gavin E Reid
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010 Australia; Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia; Bio21 Molecular Science and Biotechnology Institute. The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Oey H, Zakrzewski M, Gravermann K, Young ND, Korhonen PK, Gobert GN, Nawaratna S, Hasan S, Martínez DM, You H, Lavin M, Jones MK, Ragan MA, Stoye J, Oleaga A, Emery AM, Webster BL, Rollinson D, Gasser RB, McManus DP, Krause L. Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium. PLoS Pathog 2019; 15:e1007513. [PMID: 30673782 PMCID: PMC6361461 DOI: 10.1371/journal.ppat.1007513] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 02/04/2019] [Accepted: 12/07/2018] [Indexed: 11/18/2022] Open
Abstract
Mesenteric infection by the parasitic blood fluke Schistosoma bovis is a common veterinary problem in Africa and the Middle East and occasionally in the Mediterranean Region. The species also has the ability to form interspecific hybrids with the human parasite S. haematobium with natural hybridisation observed in West Africa, presenting possible zoonotic transmission. Additionally, this exchange of alleles between species may dramatically influence disease dynamics and parasite evolution. We have generated a 374 Mb assembly of the S. bovis genome using Illumina and PacBio-based technologies. Despite infecting different hosts and organs, the genome sequences of S. bovis and S. haematobium appeared strikingly similar with 97% sequence identity. The two species share 98% of protein-coding genes, with an average sequence identity of 97.3% at the amino acid level. Genome comparison identified large continuous parts of the genome (up to several 100 kb) showing almost 100% sequence identity between S. bovis and S. haematobium. It is unlikely that this is a result of genome conservation and provides further evidence of natural interspecific hybridization between S. bovis and S. haematobium. Our results suggest that foreign DNA obtained by interspecific hybridization was maintained in the population through multiple meiosis cycles and that hybrids were sexually reproductive, producing viable offspring. The S. bovis genome assembly forms a highly valuable resource for studying schistosome evolution and exploring genetic regions that are associated with species-specific phenotypic traits. In this article we detail the assembly and functional annotation of the Schistosoma bovis genome. S. bovis is a parasitic flatworm that primarily infects bovines, with important economic consequences in affected countries. However, it is also a close relative of the human carcinogenic parasite Schistosoma haematobium which is a serious health issue in many endemic countries in Sub-Saharan Africa. The close relationship and overlapping geographical distribution of S. bovis and S. haematobium allows these to hybridise in the wild increasing their genetic diversity and presenting the risk of zoonotic transmission, i.e. the transmission from animals to humans. The hybridization between human and ruminant schistosomes is of particular interest as interspecific hybridization may have dramatic impacts on transmission rates, disease dynamics, control interventions and parasite evolution. By whole-genome sequencing and comparative genomics we present evidence that fertile hybrids are indeed present in the wild, presenting the potential risk of transmission from animal reservoirs to humans.
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Affiliation(s)
- Harald Oey
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Martha Zakrzewski
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kerstin Gravermann
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Neil D. Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Geoffrey N. Gobert
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biological Sciences, Queen’s University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Sujeevi Nawaratna
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Shihab Hasan
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - David M. Martínez
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Hong You
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Martin Lavin
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia
| | - Malcolm K. Jones
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Veterinary Science, University of Queensland, Gatton, QLD, Australia
| | - Mark A. Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Jens Stoye
- Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Ana Oleaga
- Institute of Natural Resources and Agrobiology (IRNASA, CSIC), Cordel de Merinas, Salamanca, Spain
| | - Aidan M. Emery
- Natural History Museum, Life Sciences Department, Parasites and Vectors Division, Cromwell Road, London, United Kingdom
| | - Bonnie L. Webster
- Natural History Museum, Life Sciences Department, Parasites and Vectors Division, Cromwell Road, London, United Kingdom
| | - David Rollinson
- Natural History Museum, Life Sciences Department, Parasites and Vectors Division, Cromwell Road, London, United Kingdom
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Donald P. McManus
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Lutz Krause
- The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
- Genetics & Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- * E-mail:
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Ma G, Wang T, Korhonen PK, Nie S, Reid GE, Stroehlein AJ, Koehler AV, Chang BCH, Hofmann A, Young ND, Gasser RB. Comparative bioinformatic analysis suggests that specific dauer-like signalling pathway components regulate Toxocara canis development and migration in the mammalian host. Parasit Vectors 2019; 12:32. [PMID: 30642380 PMCID: PMC6332619 DOI: 10.1186/s13071-018-3265-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 12/12/2018] [Indexed: 01/28/2023] Open
Abstract
Background Toxocara canis is quite closely related to Ascaris suum but its biology is more complex, involving a phase of arrested development (diapause or hypobiosis) in tissues as well as transplacental and transmammary transmission routes. In the present study, we explored and compared dauer-like signalling pathways of T. canis and A. suum to infer which components in these pathways might associate with, or regulate, this added complexity in T. canis. Methods Guided by information for Caenorhabditis elegans, we bioinformatically inferred and compared components of dauer-like signalling pathways in T. canis and A. suum using genomic and transcriptomic data sets. In these two ascaridoids, we also explored endogenous dafachronic acids (DAs), which are known to be critical in regulating larval developmental processes in C. elegans and other nematodes, by liquid chromatography-mass spectrometry (LC-MS). Results Orthologues of C. elegans dauer signalling genes were identified in T. canis (n = 55) and A. suum (n = 51), inferring the presence of a dauer-like signalling pathway in both species. Comparisons showed clear differences between C. elegans and these ascaridoids as well as between T. canis and A. suum, particularly in the transforming growth factor-β (TGF-β) and insulin-like signalling pathways. Specifically, in both A. suum and T. canis, there was a paucity of genes encoding SMAD transcription factor-related protein (daf-3, daf-5, daf-8 and daf-14) and insulin/insulin-like peptide (daf-28, ins-4, ins-6 and ins-7) homologues, suggesting an evolution and adaptation of the signalling pathway in these parasites. In T. canis, there were more orthologues coding for homologues of antagonist insulin-like peptides (Tc-ins-1 and Tc-ins-18), an insulin receptor substrate (Tc-ist-1) and a serine/threonine kinase (Tc-akt-1) than in A. suum, suggesting potentiated functional roles for these molecules in regulating larval diapause and reactivation. A relatively conserved machinery was proposed for DA synthesis in the two ascaridoids, and endogenous Δ4- and Δ7-DAs were detected in them by LC-MS analysis. Differential transcription analysis between T. canis and A. suum suggests that ins-17 and ins-18 homologues are specifically involved in regulating development and migration in T. canis larvae in host tissues. Conclusion The findings of this study provide a basis for functional explorations of insulin-like peptides, signalling hormones (i.e. DAs) and related nuclear receptors, proposed to link to development and/or parasite-host interactions in T. canis. Elucidating the functional roles of these molecules might contribute to the discovery of novel anthelmintic targets in ascaridoids. Electronic supplementary material The online version of this article (10.1186/s13071-018-3265-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Shuai Nie
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Gavin E Reid
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Anson V Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Andreas Hofmann
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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Wang T, Nie S, Ma G, Korhonen PK, Koehler AV, Ang CS, Reid GE, Williamson NA, Gasser RB. The developmental lipidome of Haemonchus contortus. Int J Parasitol 2018; 48:887-895. [DOI: 10.1016/j.ijpara.2018.06.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 11/25/2022]
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He L, Gasser RB, Korhonen PK, Di W, Li F, Zhang H, Li F, Zhou Y, Fang R, Zhao J, Hu M. A TGF-β type I receptor-like molecule with a key functional role in Haemonchus contortus development. Int J Parasitol 2018; 48:1023-1033. [PMID: 30266591 DOI: 10.1016/j.ijpara.2018.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/09/2018] [Accepted: 06/19/2018] [Indexed: 01/13/2023]
Abstract
Here we investigated the gene of a transforming growth factor (TGF)-β type I receptor-like molecule in Haemonchus contortus, a highly pathogenic and economically important parasitic nematode of small ruminants. Designated Hc-tgfbr1, this gene is transcribed in all developmental stages of H. contortus, and the encoded protein has glycine-serine rich and kinase domains characteristic of a TGF-β family type I receptor. Expression of a GFP reporter driven by the putative Hc-tgfbr1 promoter localised to two intestinal rings, the anterior-most intestinal ring (int ring I) and the posterior-most intestinal ring (int ring IX) in Caenorhabditis elegans in vivo. Heterologous genetic complementation using a plasmid construct containing Hc-tgfbr1 genomic DNA failed to rescue the function of Ce-daf-1 (a known TGF-β type I receptor gene) in a daf-1-deficient mutant strain of C. elegans. In addition, a TGF-β type I receptor inhibitor, galunisertib, and double-stranded RNA interference (RNAi) were employed to assess the function of Hc-tgfbr1 in the transition from exsheathed L3 (xL3) to the L4 of H. contortus in vitro, revealing that both galunisertib and Hc-tgfbr1-specific double-stranded RNA could retard L4 development. Taken together, these results provide evidence that Hc-tgfbr1 is involved in developmental processes in H. contortus in the transition from the free-living to the parasitic stage.
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Affiliation(s)
- Li He
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Robin B Gasser
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Wenda Di
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Fangfang Li
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Hongrun Zhang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Facai Li
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China; State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, Gansu, PR China
| | - Yanqin Zhou
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Rui Fang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Junlong Zhao
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Best practice data life cycle approaches for the life sciences. F1000Res 2018; 6:1618. [PMID: 30109017 DOI: 10.12688/f1000research.12344.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/17/2017] [Indexed: 11/20/2022] Open
Abstract
Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a 'life cycle' view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on 'omics' datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.
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Affiliation(s)
- Philippa C Griffin
- EMBL Australia Bioinformatics Resource, The University of Melbourne, Parkville, VIC, 3010, Australia.,Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jyoti Khadake
- NIHR BioResource, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust Hills Road, Cambridge , CB2 0QQ, UK
| | - Kate S LeMay
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, 94720, USA
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - Andrew Pask
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Bernard Pope
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Keith Russell
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Torsten Seemann
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Treloar
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Sonika Tyagi
- Australian Genome Research Facility Ltd, Parkville, VIC, 3052, Australia.,Monash Bioinformatics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Jeffrey H Christiansen
- Queensland Cyber Infrastructure Foundation and the University of Queensland Research Computing Centre, St Lucia, QLD, 4072, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Simon Gladman
- EMBL Australia Bioinformatics Resource, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sandra B Hangartner
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Helen L Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, VIC, 3083, Australia
| | - William W H Ho
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Gabriel Keeble-Gagnère
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, VIC, 3083, Australia
| | - Pasi K Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter Neish
- The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Priscilla R Prestes
- Faculty of Science and Engineering, Federation University Australia, Mt Helen , VIC, 3350, Australia
| | - Mark F Richardson
- Bioinformatics Core Research Group & Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3220, Australia
| | - Nathan S Watson-Haigh
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Maria Victoria Schneider
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia.,The University of Melbourne, Parkville, VIC, 3010, Australia
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Stroehlein AJ, Young ND, Korhonen PK, Hall RS, Jex AR, Webster BL, Rollinson D, Brindley PJ, Gasser RB. The small RNA complement of adult Schistosoma haematobium. PLoS Negl Trop Dis 2018; 12:e0006535. [PMID: 29813122 PMCID: PMC5993326 DOI: 10.1371/journal.pntd.0006535] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/08/2018] [Accepted: 05/17/2018] [Indexed: 01/24/2023] Open
Abstract
Background Blood flukes of the genus Schistosoma cause schistosomiasis—a neglected tropical disease (NTD) that affects more than 200 million people worldwide. Studies of schistosome genomes have improved our understanding of the molecular biology of flatworms, but most of them have focused largely on protein-coding genes. Small non-coding RNAs (sncRNAs) have been explored in selected schistosome species and are suggested to play essential roles in the post-transcriptional regulation of genes, and in modulating flatworm-host interactions. However, genome-wide small RNA data are currently lacking for key schistosomes including Schistosoma haematobium—the causative agent of urogenital schistosomiasis of humans. Methodology MicroRNAs (miRNAs) and other sncRNAs of male and female adults of S. haematobium and small RNA transcription levels were explored by deep sequencing, genome mapping and detailed bioinformatic analyses. Principal findings In total, 89 transcribed miRNAs were identified in S. haematobium—a similar complement to those reported for the congeners S. mansoni and S. japonicum. Of these miRNAs, 34 were novel, with no homologs in other schistosomes. Most miRNAs (n = 64) exhibited sex-biased transcription, suggestive of roles in sexual differentiation, pairing of adult worms and reproductive processes. Of the sncRNAs that were not miRNAs, some related to the spliceosome (n = 21), biogenesis of other RNAs (n = 3) or ribozyme functions (n = 16), whereas most others (n = 3798) were novel (‘orphans’) with unknown functions. Conclusions This study provides the first genome-wide sncRNA resource for S. haematobium, extending earlier studies of schistosomes. The present work should facilitate the future curation and experimental validation of sncRNA functions in schistosomes to enhance our understanding of post-transcriptional gene regulation and of the roles that sncRNAs play in schistosome reproduction, development and parasite-host cross-talk. Human schistosomiasis is a chronic, neglected tropical disease (NTD) that is predominantly caused by the blood flukes Schistosoma haematobium, S. mansoni and S. japonicum. Infections by S. haematobium and/or S. mansoni are highly prevalent in Africa, affecting ~ 200 million people. The decoding of schistosome draft genomes has, to some extent, improved our understanding of the molecular biology of these parasites and now allows for non-protein-coding regions in these genomes to be characterised. Here, we explored small RNAs in adult S. haematobium by deep sequencing, reference genome mapping and detailed bioinformatic analyses. This study provides the first genome-wide miRNA and sncRNA resource for S. haematobium, extending earlier work on schistosomes and facilitating future curation efforts and functional investigations of schistosome sncRNAs. These efforts should enable a better understanding of post-transcriptional RNA modifications, gene regulation and novel aspects of parasite development, parasite-host cross-talk and disease at the molecular level.
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Affiliation(s)
- Andreas J. Stroehlein
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AJS); (RBG)
| | - Neil D. Young
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K. Korhonen
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ross S. Hall
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Aaron R. Jex
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Bonnie L. Webster
- Parasites and Vectors Division, The Natural History Museum, London, United Kingdom
| | - David Rollinson
- Parasites and Vectors Division, The Natural History Museum, London, United Kingdom
| | - Paul J. Brindley
- School of Medicine & Health Sciences, Department of Microbiology, Immunology & Tropical Medicine, The George Washington University, Washington, DC, United States of America
| | - Robin B. Gasser
- Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
- * E-mail: (AJS); (RBG)
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Ma G, Wang T, Korhonen PK, Ang CS, Williamson NA, Young ND, Stroehlein AJ, Hall RS, Koehler AV, Hofmann A, Gasser RB. Molecular alterations during larval development of Haemonchus contortus in vitro are under tight post-transcriptional control. Int J Parasitol 2018; 48:763-772. [PMID: 29792880 DOI: 10.1016/j.ijpara.2018.03.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/20/2018] [Accepted: 03/26/2018] [Indexed: 12/23/2022]
Abstract
In this study, we explored the molecular alterations in the developmental switch from the L3 to the exsheathed L3 (xL3) and to the L4 stage of Haemonchus contortus in vitro using an integrated transcriptomic, proteomic and bioinformatic approach. Totals of 9,754 mRNAs, 88 microRNAs (miRNAs) and 1,591 proteins were identified, and 6,686 miRNA-mRNA pairs inferred in all larval stages studied. Approximately 16% of transcripts in the combined transcriptome (representing all three larval stages) were expressed as proteins, and there were positive correlations (r = 0.39-0.44) between mRNA transcription and protein expression in the three distinct developmental stages of the parasite. Of the predicted targets, 1,019 (27.0%) mRNA transcripts were expressed as proteins, and there was a negative correlation (r = -0.60 to -0.50) in the differential mRNA transcription and protein expression between developmental stages upon pairwise comparison. The changes in transcription (mRNA and miRNA) and protein expression from the free-living to the parasitic life cycle phase of H. contortus related to enrichments in biological pathways associated with metabolism (e.g., carbohydrate and lipid degradation, and amino acid metabolism), environmental information processing (e.g., signal transduction, signalling molecules and interactions) and/or genetic information processing (e.g., transcription and translation). Specifically, fatty acid degradation, steroid hormone biosynthesis and the Rap1 signalling pathway were suppressed, whereas transcription, translation and protein processing in the endoplasmic reticulum were upregulated during the transition from the free-living L3 to the parasitic xL3 and L4 stages of the nematode in vitro. Dominant post-transcriptional regulation was inferred to elicit these changes, and particular miRNAs (e.g., hco-miR-34 and hco-miR-252) appear to play roles in stress responses and/or environmental adaptations during developmental transitions of H. contortus. Taken together, these integrated results provide a comprehensive insight into the developmental biology of this important parasite at the molecular level in vitro. The approach applied here to H. contortus can be readily applied to other parasitic nematodes.
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Affiliation(s)
- Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ching-Seng Ang
- The Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas A Williamson
- The Bio21 Institute of Molecular Science and Biotechnology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ross S Hall
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Anson V Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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46
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Koehler AV, Korhonen PK, Hall RS, Young ND, Wang T, Haydon SR, Gasser RB. Use of a bioinformatic-assisted primer design strategy to establish a new nested PCR-based method for Cryptosporidium. Parasit Vectors 2017; 10:509. [PMID: 29061171 PMCID: PMC5654123 DOI: 10.1186/s13071-017-2462-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 10/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The accurate tracking of Cryptosporidium in faecal, water and/or soil samples in water catchment areas is central to developing strategies to manage the potential risk of cryptosporidiosis transmission to humans. Various PCR assays are used for this purpose. Although some assays achieve specific amplification from Cryptosporidium DNA in animal faecal samples, some do not. Indeed, we have observed non-specificity of some oligonucleotide primers in the small subunit of nuclear ribosomal RNA gene (SSU), which has presented an obstacle to the identification and classification of Cryptosporidium species and genotypes (taxa) from faecal samples. RESULTS Using a novel bioinformatic approach, we explored all available Cryptosporidium genome sequences for new and diagnostically-informative, multi-copy regions to specifically design oligonucleotide primers in the large subunit of nuclear ribosomal RNA gene (LSU) as a basis for an effective nested PCR-based sequencing method for the identification and/or classification of Cryptosporidium taxa. CONCLUSION This newly established PCR, which has high analytical specificity and sensitivity, is now in routine use in our laboratory, together with other assays developed by various colleagues. Although the present bioinformatic workflow used here was for the specific design of primers in nuclear DNA of Cryptosporidium, this approach should be broadly applicable to many other microorganisms.
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Affiliation(s)
- Anson V Koehler
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ross S Hall
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia.
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47
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Griffin PC, Khadake J, LeMay KS, Lewis SE, Orchard S, Pask A, Pope B, Roessner U, Russell K, Seemann T, Treloar A, Tyagi S, Christiansen JH, Dayalan S, Gladman S, Hangartner SB, Hayden HL, Ho WWH, Keeble-Gagnère G, Korhonen PK, Neish P, Prestes PR, Richardson MF, Watson-Haigh NS, Wyres KL, Young ND, Schneider MV. Best practice data life cycle approaches for the life sciences. F1000Res 2017; 6:1618. [PMID: 30109017 PMCID: PMC6069748 DOI: 10.12688/f1000research.12344.2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/29/2018] [Indexed: 11/20/2022] Open
Abstract
Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a 'life cycle' view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on 'omics' datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.
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Affiliation(s)
- Philippa C Griffin
- EMBL Australia Bioinformatics Resource, The University of Melbourne, Parkville, VIC, 3010, Australia.,Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jyoti Khadake
- NIHR BioResource, University of Cambridge and Cambridge University Hospitals NHS Foundation Trust Hills Road, Cambridge , CB2 0QQ, UK
| | - Kate S LeMay
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Suzanna E Lewis
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, 94720, USA
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Cambridge, CB10 1SD, UK
| | - Andrew Pask
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Bernard Pope
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ute Roessner
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Keith Russell
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Torsten Seemann
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Andrew Treloar
- Australian National Data Service, Monash University, Malvern East , VIC, 3145, Australia
| | - Sonika Tyagi
- Australian Genome Research Facility Ltd, Parkville, VIC, 3052, Australia.,Monash Bioinformatics Platform, Monash University, Clayton, VIC, 3800, Australia
| | - Jeffrey H Christiansen
- Queensland Cyber Infrastructure Foundation and the University of Queensland Research Computing Centre, St Lucia, QLD, 4072, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Simon Gladman
- EMBL Australia Bioinformatics Resource, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sandra B Hangartner
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Helen L Hayden
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, VIC, 3083, Australia
| | - William W H Ho
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Gabriel Keeble-Gagnère
- School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Department of Economic Development, Jobs, Transport and Resources (DEDJTR), Bundoora, VIC, 3083, Australia
| | - Pasi K Korhonen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peter Neish
- The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Priscilla R Prestes
- Faculty of Science and Engineering, Federation University Australia, Mt Helen , VIC, 3350, Australia
| | - Mark F Richardson
- Bioinformatics Core Research Group & Centre for Integrative Ecology, Deakin University, Geelong, VIC, 3220, Australia
| | - Nathan S Watson-Haigh
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Neil D Young
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Maria Victoria Schneider
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, 3010, Australia.,The University of Melbourne, Parkville, VIC, 3010, Australia
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Preston S, Korhonen PK, Mouchiroud L, Cornaglia M, McGee SL, Young ND, Davis RA, Crawford S, Nowell C, Ansell BRE, Fisher GM, Andrews KT, Chang BCH, Gijs MAM, Sternberg PW, Auwerx J, Baell J, Hofmann A, Jabbar A, Gasser RB. Deguelin exerts potent nematocidal activity
via
the mitochondrial respiratory chain. FASEB J 2017; 31:4515-4532. [DOI: 10.1096/fj.201700288r] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/12/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Sarah Preston
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVictoriaAustralia
- Faculty of Science and TechnologyFederation UniversityBallaratVictoriaAustralia
| | - Pasi K. Korhonen
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVictoriaAustralia
| | - Laurent Mouchiroud
- Laboratory of Integrative and Systems PhysiologyÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Matteo Cornaglia
- Laboratory of MicrosystemsÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Sean L. McGee
- Metabolic Research UnitMetabolic Reprogramming LaboratorySchool of Medicine, Faculty of Health, Deakin UniversityWaurn PondsVictoriaAustralia
| | - Neil D. Young
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVictoriaAustralia
| | - Rohan A. Davis
- Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
| | - Simon Crawford
- School of Biosciences, University of MelbourneParkvilleVictoriaAustralia
| | - Cameron Nowell
- Drug Discovery BiologyMonash University Institute of Pharmaceutical SciencesMonash UniversityParkvilleVictoriaAustralia
| | - Brendan R. E. Ansell
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVictoriaAustralia
| | - Gillian M. Fisher
- Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
| | - Katherine T. Andrews
- Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
| | - Bill C. H. Chang
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVictoriaAustralia
- Yourgene BioscienceTaipeiTaiwan
| | - Martin A. M. Gijs
- Laboratory of MicrosystemsÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Paul W. Sternberg
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCaliforniaUSA
| | - Johan Auwerx
- Laboratory of Integrative and Systems PhysiologyÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Jonathan Baell
- Medicinal ChemistryMonash University Institute of Pharmaceutical SciencesMonash UniversityParkvilleVictoriaAustralia
| | - Andreas Hofmann
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVictoriaAustralia
- Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
| | - Abdul Jabbar
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVictoriaAustralia
| | - Robin B. Gasser
- Faculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVictoriaAustralia
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49
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Wang D, Young ND, Koehler AV, Tan P, Sohn WM, Korhonen PK, Gasser RB. Mitochondrial genomic comparison of Clonorchis sinensis from South Korea with other isolates of this species. Infection, Genetics and Evolution 2017; 51:160-166. [DOI: 10.1016/j.meegid.2017.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/06/2017] [Accepted: 02/21/2017] [Indexed: 12/26/2022]
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Stroehlein AJ, Young ND, Korhonen PK, Chang BCH, Nejsum P, Pozio E, La Rosa G, Sternberg PW, Gasser RB. Whipworm kinomes reflect a unique biology and adaptation to the host animal. Int J Parasitol 2017; 47:857-866. [PMID: 28606697 DOI: 10.1016/j.ijpara.2017.04.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/14/2017] [Accepted: 04/20/2017] [Indexed: 01/19/2023]
Abstract
Roundworms belong to a diverse phylum (Nematoda) which is comprised of many parasitic species including whipworms (genus Trichuris). These worms have adapted to a biological niche within the host and exhibit unique morphological characteristics compared with other nematodes. Although these adaptations are known, the underlying molecular mechanisms remain elusive. The availability of genomes and transcriptomes of some whipworms now enables detailed studies of their molecular biology. Here, we defined and curated the full complement of an important class of enzymes, the protein kinases (kinomes) of two species of Trichuris, using an advanced and integrated bioinformatic pipeline. We investigated the transcription of Trichuris suis kinase genes across developmental stages, sexes and tissues, and reveal that selectively transcribed genes can be linked to central roles in developmental and reproductive processes. We also classified and functionally annotated the curated kinomes by integrating evidence from structural modelling and pathway analyses, and compared them with other curated kinomes of phylogenetically diverse nematode species. Our findings suggest unique adaptations in signalling processes governing worm morphology and biology, and provide an important resource that should facilitate experimental investigations of kinases and the biology of signalling pathways in nematodes.
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Affiliation(s)
- Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia; Yourgene Bioscience, New Taipei City, Taiwan
| | - Peter Nejsum
- Department of Clinical Medicine, Department of Infectious Diseases, Aarhus University, Aarhus, Denmark
| | | | | | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria, Australia.
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