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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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Fernando DD, Reynolds SL, Zakrzewski M, Mofiz E, Papenfuss AT, Holt D, Fischer K. Phylogenetic relationships, stage-specific expression and localisation of a unique family of inactive cysteine proteases in Sarcoptes scabiei. Parasit Vectors 2018; 11:301. [PMID: 29769145 PMCID: PMC5956821 DOI: 10.1186/s13071-018-2862-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 12/15/2017] [Accepted: 04/23/2018] [Indexed: 11/17/2022] Open
Abstract
Background Scabies is worldwide one of the most common, yet neglected, parasitic skin infections, affecting a wide range of mammals including humans. Limited treatment options and evidence of emerging mite resistance against the currently used drugs drive our research to explore new therapeutic candidates. Previously, we discovered a multicopy family of genes encoding cysteine proteases with their catalytic sites inactivated by mutation (SMIPP-Cs). This protein family is unique in parasitic scabies mites and is absent in related non-burrowing mites. We postulated that the SMIPP-Cs have evolved as an adaptation to the parasitic lifestyle of the scabies mite. To formulate testable hypotheses for their functions and to propose possible strategies for translational research we investigated whether the SMIPP-Cs are common to all scabies mite varieties and where within the mite body as well as when throughout the parasitic life-cycle they are expressed. Results SMIPP-C sequences from human, pig and dog mites were analysed bioinformatically and the phylogenetic relationships between the SMIPP-C multi-copy gene families of human, pig and dog mites were established. Results suggest that amplification of the SMIPP-C genes occurred in a common ancestor and individual genes evolved independently in the different mite varieties. Recombinant human mite SMIPP-C proteins were produced and used for murine polyclonal antibody production. Immunohistology on skin sections from human patients localised the SMIPP-Cs in the mite gut and in mite faeces within in the epidermal skin burrows. SMIPP-C transcription into mRNA in different life stages was assessed in human and pig mites by reverse transcription followed by droplet digital PCR (ddPCR). High transcription levels of SMIPP-C genes were detected in the adult female life stage in comparison to all other life stages. Conclusions The fact that the SMIPP-Cs are unique to three Sarcoptes varieties, present in all burrowing life stages and highly expressed in the digestive system of the infective adult female life stage may highlight an essential role in parasitism. As they are excreted from the gut in scybala they presumably are able to interact or interfere with host proteins present in the epidermis. Electronic supplementary material The online version of this article (10.1186/s13071-018-2862-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deepani D Fernando
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.,School of Veterinary Sciences, University of Queensland, Gatton, QLD, 4343, Australia.,Department of Veterinary Pathobiology, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Simone L Reynolds
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Martha Zakrzewski
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Ehtesham Mofiz
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Melbourne, 3000, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Deborah Holt
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
| | - Katja Fischer
- QIMR Berghofer Medical Research Institute, Infectious Diseases Program, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.
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Mofiz E, Holt DC, Seemann T, Currie BJ, Fischer K, Papenfuss AT. Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suis. Gigascience 2016; 5:23. [PMID: 27250856 PMCID: PMC4890329 DOI: 10.1186/s13742-016-0129-2] [Citation(s) in RCA: 19] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/11/2016] [Indexed: 12/03/2022] Open
Abstract
Background The scabies mite, Sarcoptes scabiei, is a parasitic arachnid and cause of the infectious skin disease scabies in humans and mange in other animal species. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where secondary group A streptococcal and Staphylococcus aureus infections of scabies sores are thought to drive the high rate of rheumatic heart disease and chronic kidney disease. Results We sequenced the genome of two samples of Sarcoptes scabiei var. hominis obtained from unrelated patients with crusted scabies located in different parts of northern Australia using the Illumina HiSeq. We also sequenced samples of Sarcoptes scabiei var. suis from a pig model. Because of the small size of the scabies mite, these data are derived from pools of thousands of mites and are metagenomic, including host and microbiome DNA. We performed cleaning and de novo assembly and present Sarcoptes scabiei var. hominis and var. suis draft reference genomes. We have constructed a preliminary annotation of this reference comprising 13,226 putative coding sequences based on sequence similarity to known proteins. Conclusions We have developed extensive genomic resources for the scabies mite, including reference genomes and a preliminary annotation. Electronic supplementary material The online version of this article (doi:10.1186/s13742-016-0129-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ehtesham Mofiz
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Deborah C Holt
- Menzies School of Health Research, Charles Darwin University, Casuarina, NT, 0811, Australia
| | - Torsten Seemann
- Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Bart J Currie
- Menzies School of Health Research, Charles Darwin University, Casuarina, NT, 0811, Australia
| | - Katja Fischer
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Anthony T Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
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Mofiz E, Seemann T, Bahlo M, Holt D, Currie BJ, Fischer K, Papenfuss AT. Mitochondrial Genome Sequence of the Scabies Mite Provides Insight into the Genetic Diversity of Individual Scabies Infections. PLoS Negl Trop Dis 2016; 10:e0004384. [PMID: 26872064 PMCID: PMC4752359 DOI: 10.1371/journal.pntd.0004384] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 09/06/2015] [Accepted: 12/20/2015] [Indexed: 11/19/2022] Open
Abstract
The scabies mite, Sarcoptes scabiei, is an obligate parasite of the skin that infects humans and other animal species, causing scabies, a contagious disease characterized by extreme itching. Scabies infections are a major health problem, particularly in remote Indigenous communities in Australia, where co-infection of epidermal scabies lesions by Group A Streptococci or Staphylococcus aureus is thought to be responsible for the high rate of rheumatic heart disease and chronic kidney disease. We collected and separately sequenced mite DNA from several pools of thousands of whole mites from a porcine model of scabies (S. scabiei var. suis) and two human patients (S. scabiei var. hominis) living in different regions of northern Australia. Our sequencing samples the mite and its metagenome, including the mite gut flora and the wound micro-environment. Here, we describe the mitochondrial genome of the scabies mite. We developed a new de novo assembly pipeline based on a bait-and-reassemble strategy, which produced a 14 kilobase mitochondrial genome sequence assembly. We also annotated 35 genes and have compared these to other Acari mites. We identified single nucleotide polymorphisms (SNPs) and used these to infer the presence of six haplogroups in our samples, Remarkably, these fall into two closely-related clades with one clade including both human and pig varieties. This supports earlier findings that only limited genetic differences may separate some human and animal varieties, and raises the possibility of cross-host infections. Finally, we used these mitochondrial haplotypes to show that the genetic diversity of individual infections is typically small with 1–3 distinct haplotypes per infestation. The scabies mite is a skin parasite that infects humans and other animal species, causing scabies, a contagious disease characterized by extreme itching. Scabies infections are a major health problem in developing countries and in indigenous Australian populations, where scabies is associated with pyoderma (skin sores) and linked to rheumatic fever and rheumatic heart disease. Little is known about the genetics of the scabies mite. We have assembled the mitochondrial genome of scabies mites obtained from human patients in Australia and from a pig model. While investigating the genetic diversity of each infestation, we found that mitochrondial genomes clustered into two broad clades and showed limited genetic diversity within each infestation. Remarkably, one closely related clade included both human and pig mites, suggesting that mite transmission from pig to human may be possible. This could have major implications in the management of porcine mange and human scabies.
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Affiliation(s)
- Ehtesham Mofiz
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Victorian Life Sciences Computation Initiative, University of Melbourne, Melbourne, Victoria, Australia
| | - Melanie Bahlo
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Mathematics and Statistics, University of Melbourne, Victoria, Australia
| | - Deborah Holt
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
| | - Bart J. Currie
- Menzies School of Health Research, Charles Darwin University, Casuarina, Northern Territory, Australia
| | - Katja Fischer
- QIMR Berghofer Medical Research, Herston, Queensland, Australia
| | - Anthony T. Papenfuss
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, East Melbourne, Australia
- * E-mail:
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Wong ESW, Morgenstern D, Mofiz E, Gombert S, Morris KM, Temple-Smith P, Renfree MB, Whittington CM, King GF, Warren WC, Papenfuss AT, Belov K. Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles. Mol Cell Proteomics 2012; 11:1354-64. [PMID: 22899769 DOI: 10.1074/mcp.m112.017491] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The platypus is a venomous monotreme. Male platypuses possess a spur on their hind legs that is connected to glands in the pelvic region. They produce venom only during the breeding season, presumably to fight off conspecifics. We have taken advantage of this unique seasonal production of venom to compare the transcriptomes of in- and out-of-season venom glands, in conjunction with proteomic analysis, to identify previously undiscovered venom genes. Comparison of the venom glands revealed distinct gene expression profiles that are consistent with changes in venom gland morphology and venom volumes in and out of the breeding season. Venom proteins were identified through shot-gun sequenced venom proteomes of three animals using RNA-seq-derived transcripts for peptide-spectral matching. 5,157 genes were expressed in the venom glands, 1,821 genes were up-regulated in the in-season gland, and 10 proteins were identified in the venom. New classes of platypus-venom proteins identified included antimicrobials, amide oxidase, serpin protease inhibitor, proteins associated with the mammalian stress response pathway, cytokines, and other immune molecules. Five putative toxins have only been identified in platypus venom: growth differentiation factor 15, nucleobindin-2, CD55, a CXC-chemokine, and corticotropin-releasing factor-binding protein. These novel venom proteins have potential biomedical and therapeutic applications and provide insights into venom evolution.
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Affiliation(s)
- Emily S W Wong
- Faculty of Veterinary Science, The University of Sydney, Camperdown, NSW 2006, Australia.
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