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Ahmed M, Roberts NG, Adediran F, Smythe AB, Kocot KM, Holovachov O. Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.769565] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Phylogenetic relationships within many lineages of the phylum Nematoda remain unresolved, despite numerous morphology-based and molecular analyses. We performed several phylogenomic analyses using 286 published genomes and transcriptomes and 19 new transcriptomes by focusing on Trichinellida, Spirurina, Rhabditina, and Tylenchina separately, and by analyzing a selection of species from the whole phylum Nematoda. The phylogeny of Trichinellida supported the division of Trichinella into encapsulated and non-encapsulated species and placed them as sister to Trichuris. The Spirurina subtree supported the clades formed by species from Ascaridomorpha and Spiruromorpha respectively, but did not support Dracunculoidea. The analysis of Tylenchina supported a clade that included all sampled species from Tylenchomorpha and placed it as sister to clades that included sampled species from Cephalobomorpha and Panagrolaimomorpha, supporting the hypothesis that postulates the single origin of the stomatostylet. The Rhabditina subtree placed a clade composed of all sampled species from Diplogastridae as sister to a lineage consisting of paraphyletic Rhabditidae, a single representative of Heterorhabditidae and a clade composed of sampled species belonging to Strongylida. It also strongly supported all suborders within Strongylida. In the phylum-wide analysis, a clade composed of all sampled species belonging to Enoplia were consistently placed as sister to Dorylaimia + Chromadoria. The topology of the Nematoda backbone was consistent with previous studies, including polyphyletic placement of sampled representatives of Monhysterida and Araeolaimida.
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Foster JM, Grote A, Mattick J, Tracey A, Tsai YC, Chung M, Cotton JA, Clark TA, Geber A, Holroyd N, Korlach J, Li Y, Libro S, Lustigman S, Michalski ML, Paulini M, Rogers MB, Teigen L, Twaddle A, Welch L, Berriman M, Dunning Hotopp JC, Ghedin E. Sex chromosome evolution in parasitic nematodes of humans. Nat Commun 2020; 11:1964. [PMID: 32327641 PMCID: PMC7181701 DOI: 10.1038/s41467-020-15654-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/20/2020] [Indexed: 11/09/2022] Open
Abstract
Sex determination mechanisms often differ even between related species yet the evolution of sex chromosomes remains poorly understood in all but a few model organisms. Some nematodes such as Caenorhabditis elegans have an XO sex determination system while others, such as the filarial parasite Brugia malayi, have an XY mechanism. We present a complete B. malayi genome assembly and define Nigon elements shared with C. elegans, which we then map to the genomes of other filarial species and more distantly related nematodes. We find a remarkable plasticity in sex chromosome evolution with several distinct cases of neo-X and neo-Y formation, X-added regions, and conversion of autosomes to sex chromosomes from which we propose a model of chromosome evolution across different nematode clades. The phylum Nematoda offers a new and innovative system for gaining a deeper understanding of sex chromosome evolution.
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Affiliation(s)
- Jeremy M Foster
- Division of Protein Expression & Modification, New England Biolabs, Ipswich, MA, 01938, USA
| | - Alexandra Grote
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - John Mattick
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Alan Tracey
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Matthew Chung
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - James A Cotton
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Adam Geber
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Yichao Li
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, 45701, USA
| | - Silvia Libro
- Division of Protein Expression & Modification, New England Biolabs, Ipswich, MA, 01938, USA
| | - Sara Lustigman
- Laboratory of Molecular Parasitology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY, 10065, USA
| | - Michelle L Michalski
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
| | - Michael Paulini
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Matthew B Rogers
- Department of Surgery, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, 15224, USA
| | - Laura Teigen
- Department of Biology and Microbiology, University of Wisconsin Oshkosh, Oshkosh, WI, 54901, USA
| | - Alan Twaddle
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Lonnie Welch
- School of Electrical Engineering and Computer Science, Ohio University, Athens, OH, 45701, USA
| | - Matthew Berriman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Julie C Dunning Hotopp
- Institute for Genome Science, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Elodie Ghedin
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA.
- Department of Epidemiology, School of Global Public Health, New York University, New York, NY, 10003, USA.
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Elashry AM, Habash SS, Vijayapalani P, Brocke-Ahmadinejad N, Blümel R, Seetharam A, Schoof H, Grundler FMW. Transcriptome and Parasitome Analysis of Beet Cyst Nematode Heterodera schachtii. Sci Rep 2020; 10:3315. [PMID: 32094373 PMCID: PMC7039985 DOI: 10.1038/s41598-020-60186-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 12/20/2019] [Indexed: 11/17/2022] Open
Abstract
Beet cyst nematodes depend on a set of secretory proteins (effectors) for the induction and maintenance of their syncytial feeding sites in plant roots. In order to understand the relationship between the beet cyst nematode H. schachtii and its host, identification of H. schachtii effectors is crucial and to this end, we sequenced a whole animal pre-infective J2-stage transcriptome in addition to pre- and post-infective J2 gland cell transcriptome using Next Generation Sequencing (NGS) and identified a subset of sequences representing putative effectors. Comparison between the transcriptome of H. schachtii and previously reported related cyst nematodes and root-knot nematodes revealed a subset of esophageal gland related sequences and putative effectors in common across the tested species. Structural and functional annotation of H. schachtii transcriptome led to the identification of nearly 200 putative effectors. Six putative effector expressions were quantified using qPCR and three of them were functionally analyzed using RNAi. Phenotyping of the RNAi nematodes indicated that all tested genes decrease the level of nematodes pathogenicity and/or the average female size, thereby regulating cyst nematode parasitism. These discoveries contribute to further understanding of the cyst nematode parasitism.
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Affiliation(s)
- Abdelnaser M Elashry
- INRES Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, 53115, Germany. .,Strube research GmbH & Co. KG, Hauptstrasse 1, 38387, Söllingen, Germany.
| | - Samer S Habash
- INRES Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, 53115, Germany
| | | | - Nahal Brocke-Ahmadinejad
- INRES Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115, Bonn, Germany.,Institute of Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Roman Blümel
- INRES Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, 53115, Germany.,Bayer Crop Science, Alfred-Nobel-Str. 50, 40789, Monheim, Germany
| | - Arun Seetharam
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.,Genome Informatics Facility, Office of Biotechnology, 448 Bessey Hall, Iowa State University, Ames, USA
| | - Heiko Schoof
- INRES Crop Bioinformatics, University of Bonn, Katzenburgweg 2, 53115, Bonn, Germany
| | - Florian M W Grundler
- INRES Molecular Phytomedicine, University of Bonn, Karlrobert-Kreiten-Str. 13, Bonn, 53115, Germany
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Smythe AB, Holovachov O, Kocot KM. Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny. BMC Evol Biol 2019; 19:121. [PMID: 31195978 PMCID: PMC6567515 DOI: 10.1186/s12862-019-1444-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/27/2019] [Indexed: 11/18/2022] Open
Abstract
Background Nematodes are among the most diverse and abundant metazoans on Earth, but research on them has been biased toward parasitic taxa and model organisms. Free-living nematodes, particularly from the clades Enoplia and Dorylaimia, have been underrepresented in genome-scale phylogenetic analyses to date, leading to poor resolution of deep relationships within the phylum. Results We supplemented publicly available data by sequencing transcriptomes of nine free-living nematodes and two important outgroups and conducted a phylum-wide phylogenomic analysis including a total of 108 nematodes. Analysis of a dataset generated using a conservative orthology inference strategy resulted in a matrix with a high proportion of missing data and moderate to weak support for branching within and placement of Enoplia. A less conservative orthology inference approach recovered more genes and resulted in higher support for the deepest splits within Nematoda, recovering Enoplia as the sister taxon to the rest of Nematoda. Relationships within major clades were similar to those found in previously published studies based on 18S rDNA. Conclusions Expanded transcriptome sequencing of free-living nematodes has contributed to better resolution among deep nematode lineages, though the dataset is still strongly biased toward parasites. Inclusion of more free-living nematodes in future phylogenomic analyses will allow a clearer understanding of many interesting aspects of nematode evolution, such as morphological and molecular adaptations to parasitism and whether nematodes originated in a marine or terrestrial environment. Electronic supplementary material The online version of this article (10.1186/s12862-019-1444-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ashleigh B Smythe
- Department of Biology, Virginia Military Institute, 301B Maury-Brooke Hall, Lexington, VA, 24450, USA
| | - Oleksandr Holovachov
- Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-104 05, Stockholm, Sweden
| | - Kevin M Kocot
- Department of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Campus Box 870344, Tuscaloosa, AL, 35487, USA.
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The Caenorhabditis elegans Female-Like State: Decoupling the Transcriptomic Effects of Aging and Sperm Status. G3-GENES GENOMES GENETICS 2017; 7:2969-2977. [PMID: 28751504 PMCID: PMC5592924 DOI: 10.1534/g3.117.300080] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding genome and gene function in a whole organism requires us to fully comprehend the life cycle and the physiology of the organism in question. Caenorhabditis elegans XX animals are hermaphrodites that exhaust their sperm after 3 d of egg-laying. Even though C. elegans can live for many days after cessation of egg-laying, the molecular physiology of this state has not been as intensely studied as other parts of the life cycle, despite documented changes in behavior and metabolism. To study the effects of sperm depletion and aging of C. elegans during the first 6 d of adulthood, we measured the transcriptomes of first-day adult hermaphrodites and sixth-day sperm-depleted adults, and, at the same time points, mutant fog-2(lf) worms that have a feminized germline phenotype. We found that we could separate the effects of biological aging from sperm depletion. For a large subset of genes, young adult fog-2(lf) animals had the same gene expression changes as sperm-depleted sixth-day wild-type hermaphrodites, and these genes did not change expression when fog-2(lf) females reached the sixth day of adulthood. Taken together, this indicates that changing sperm status causes a change in the internal state of the worm, which we call the female-like state. Our data provide a high-quality picture of the changes that happen in global gene expression throughout the period of early aging in the worm.
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Stoltzfus JD, Pilgrim AA, Herbert DR. Perusal of parasitic nematode 'omics in the post-genomic era. Mol Biochem Parasitol 2016; 215:11-22. [PMID: 27887974 DOI: 10.1016/j.molbiopara.2016.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/17/2016] [Accepted: 11/21/2016] [Indexed: 01/09/2023]
Abstract
The advent of high-throughput, next-generation sequencing methods combined with advances in computational biology and bioinformatics have greatly accelerated discovery within biomedical research. This "post-genomics" era has ushered in powerful approaches allowing one to quantify RNA transcript and protein abundance for every gene in the genome - often for multiple conditions. Herein, we chronicle how the post-genomics era has advanced our overall understanding of parasitic nematodes through transcriptomics and proteomics and highlight some of the important advances made in each major nematode clade. We primarily focus on organisms relevant to human health, given that nematode infections significantly impact disability-adjusted life years (DALY) scores within the developing world, but we also discuss organisms of veterinary importance as well as those used as laboratory models. As such, we envision that this review will serve as a comprehensive resource for those seeking a better understanding of basic parasitic nematode biology as well as those interested in targets for vaccination and pharmacological intervention.
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Affiliation(s)
- Jonathan D Stoltzfus
- Department of Biology, Millersville University, Millersville, PA, United States.
| | - Adeiye A Pilgrim
- Emory University School of Medicine MD/PhD Program, Atlanta, GA, United States
| | - De'Broski R Herbert
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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7
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Zheng M, Long H, Zhao Y, Li L, Xu D, Zhang H, Liu F, Deng G, Pan Z, Yu M. RNA-Seq Based Identification of Candidate Parasitism Genes of Cereal Cyst Nematode (Heterodera avenae) during Incompatible Infection to Aegilops variabilis. PLoS One 2015; 10:e0141095. [PMID: 26517841 PMCID: PMC4627824 DOI: 10.1371/journal.pone.0141095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 10/05/2015] [Indexed: 11/19/2022] Open
Abstract
One of the reasons for the progressive yield decline observed in cereals production is the rapid build-up of populations of the cereal cyst nematode (CCN, Heterodera avenae). These nematodes secrete so-call effectors into their host plant to suppress the plant defense responses, alter plant signaling pathways and then induce the formation of syncytium after infection. However, little is known about its molecular mechanism and parasitism during incompatible infection. To gain insight into its repertoire of parasitism genes, we investigated the transcriptome of the early parasitic second-stage (30 hours, 3 days and 9 days post infection) juveniles of the CCN as well as the CCN infected tissue of the host Aegilops variabilis by Illumina sequencing. Among all assembled unigenes, 681 putative genes of parasitic nematode were found, in which 56 putative effectors were identified, including novel pioneer genes and genes corresponding to previously reported effectors. All the 681 CCN unigenes were mapped to 229 GO terms and 200 KEGG pathways, including growth, development and several stimulus-related signaling pathways. Sixteen clusters were involved in the CCN unigene expression atlas at the early stages during infection process, and three of which were significantly gene-enriched. Besides, the protein-protein interaction network analysis revealed 35 node unigenes which may play an important role in the plant-CCN interaction. Moreover, in a comparison of differentially expressed genes between the pre-parasitic juveniles and the early parasitic juveniles, we found that hydrolase activity was up-regulated in pre J2s whereas binding activity was upregulated in infective J2s. RT-qPCR analysis on some selected genes showed detectable expression, indicating possible secretion of the proteins and putative role in infection. This study provided better insights into the incompatible interaction between H. avenae and the host plant Ae. varabilis. Moreover, RNAi targets with potential lethality were screened out and primarily validated, which provide candidates for engineering-based control of cereal cyst nematode in crops breeding.
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Affiliation(s)
- Minghui Zheng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yun Zhao
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Lin Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Delin Xu
- Zunyi Medical University, Zunyi, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Feng Liu
- Plant Protection College, Shandong Agriculture University, Tai’an, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhifen Pan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- * E-mail:
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Modelling the effects of mass drug administration on the molecular epidemiology of schistosomes. ADVANCES IN PARASITOLOGY 2015; 87:293-327. [PMID: 25765198 DOI: 10.1016/bs.apar.2014.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
As national governments scale up mass drug administration (MDA) programs aimed to combat neglected tropical diseases (NTDs), novel selection pressures on these parasites increase. To understand how parasite populations are affected by MDA and how to maximize the success of control programmes, it is imperative for epidemiological, molecular and mathematical modelling approaches to be combined. Modelling of parasite population genetic and genomic structure, particularly of the NTDs, has been limited through the availability of only a few molecular markers to date. The landscape of infectious disease research is being dramatically reshaped by next-generation sequencing technologies and our understanding of how repeated selective pressures are shaping parasite populations is radically altering. Genomics can provide high-resolution data on parasite population structure, and identify how loci may contribute to key phenotypes such as virulence and/or drug resistance. We discuss the incorporation of genetic and genomic data, focussing on the recently sequenced Schistosoma spp., into novel mathematical transmission models to inform our understanding of the impact of MDA and other control methods. We summarize what is known to date, the models that exist and how population genetics has given us an understanding of the effects of MDA on the parasites. We consider how genetic and genomic data have the potential to shape future research, highlighting key areas where data are lacking, and how future molecular epidemiology knowledge can aid understanding of transmission dynamics and the effects of MDA, ultimately informing public health policy makers of the best interventions for NTDs.
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Huang RE, Ren X, Qiu Y, Zhao Z. Description of Caenorhabditis sinica sp. n. (Nematoda: Rhabditidae), a nematode species used in comparative biology for C. elegans. PLoS One 2014; 9:e110957. [PMID: 25375770 PMCID: PMC4222906 DOI: 10.1371/journal.pone.0110957] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 07/20/2014] [Indexed: 02/06/2023] Open
Abstract
We re-isolated in China a relative of the nematode model Caenorhabditis elegans that was previously referred to informally as C. sp. 5. In spite of its importance for comparative biology, C. sp. 5 has remained morphologically uncharacterized. Therefore, we now provide detailed description of morphology and anatomy, assigning the name of Caenorhabditis sinica sp. n. to this nematode that is found frequently in China. C. sinica sp. n. belongs to the Elegans group in the genus Caenorhabditis, being phylogenetically close to C. briggsae although differing in reproductive mode. The gonochoristic C. sinica sp. n. displays two significantly larger distal parts of uteri filled with sperms in the female/hermaphroditic gonad than does the androdioecious C. briggsae. The new species can be differentiated morphologically from all known Caenorhabditis species within the Elegans group by presenting a uniquely shaped, three-pointed hook structure on the male precloacal lip. The lateral field of C. sinica sp. n. is marked by three ridges that are flanked by two additional incisures, sometimes appearing as five ridges in total. This study ends the prolonged period of the 'undescribed' anonymity for C. sinica sp. n. since its discovery and use in comparative biological research. Significant and crossing-direction dependent hybrid incompatibilities in F1 and F2 crossing progeny make C. sinica sp. n. an excellent model for studies of population and speciation genetics. The abundance of nematode species lacking detailed taxonomic characterization deserves renewed attention to address the species description gap for this important yet morphologically 'difficult' group of animals.
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Affiliation(s)
- Ren-E Huang
- School of Life Sciences, Tsinghua University, Beijing, China
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
| | - Xiaoliang Ren
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
| | - Yifei Qiu
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
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10
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Abstract
Nematodes are abundant and diverse, and include many parasitic species. Molecular phylogenetic analyses have shown that parasitism of plants and animals has arisen at least 15 times independently. Extant nematode species also display lifestyles that are proposed to be on the evolutionary trajectory to parasitism. Recent advances have permitted the determination of the genomes and transcriptomes of many nematode species. These new data can be used to further resolve the phylogeny of Nematoda, and identify possible genetic patterns associated with parasitism. Plant-parasitic nematode genomes show evidence of horizontal gene transfer from other members of the rhizosphere, and these genes play important roles in the parasite-host interface. Similar horizontal transfer is not evident in animal parasitic groups. Many nematodes have bacterial symbionts that can be essential for survival. Horizontal transfer from symbionts to the nematode is also common, but its biological importance is unclear. Over 100 nematode species are currently targeted for sequencing, and these data will yield important insights into the biology and evolutionary history of parasitism. It is important that these new technologies are also applied to free-living taxa, so that the pre-parasitic ground state can be inferred, and the novelties associated with parasitism isolated.
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11
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Sakthidevi M, Hoti SL, Kaliraj P. Functional analysis of a highly conserved abundant larval transcript-2 (alt-2) intron 2 repeat region of lymphatic filarial parasites. INFECTION GENETICS AND EVOLUTION 2014; 24:177-82. [PMID: 24681262 DOI: 10.1016/j.meegid.2014.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 03/12/2014] [Accepted: 03/17/2014] [Indexed: 11/17/2022]
Abstract
The filarial-specific protein abundant larval transcript-2 (ALT-2) is expressed exclusively in the infective larval stage (L3) and is a crucial protein for establishing immunopathogenesis in human hosts. The alt-2 gene has a conserved minisatellite repeat (29 or 27bp) in intron 2 (IR2) whose significance within lymphatic filarial species is unknown. Here, we report the role of IR2 in the regulation of alt-2 gene expression using an in vitro model. Using electrophoretic mobility shift assays, we identified the presence of a putative nuclear protein binding region within IR2. Subsequent transient expression experiments in eukaryotic cell lines demonstrated that the IR2 downregulated the expression of a downstream luciferase reporter gene, which was further validated with RT-PCR. We therefore identify IR2 as a suppressor element that regulates L3 stage-specific expression of alt-2.
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Affiliation(s)
- Moorthy Sakthidevi
- Centre for Biotechnology, Anna University, Chennai, Tamil Nadu 600 025, India
| | | | - Perumal Kaliraj
- Centre for Biotechnology, Anna University, Chennai, Tamil Nadu 600 025, India.
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12
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Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ, Thorpe P, Tsai IJ, Beasley H, Blok V, Cock PJA, den Akker SEV, Holroyd N, Hunt M, Mantelin S, Naghra H, Pain A, Palomares-Rius JE, Zarowiecki M, Berriman M, Jones JT, Urwin PE. The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biol 2014; 15:R43. [PMID: 24580726 PMCID: PMC4054857 DOI: 10.1186/gb-2014-15-3-r43] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 03/03/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security. RESULTS We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control. CONCLUSIONS The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens.
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Affiliation(s)
- James A Cotton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | | | - Laura M Jones
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Taisei Kikuchi
- Forestry and Forest Products Research Institute, Tsukuba, Japan
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Adam J Reid
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Peter Thorpe
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Isheng J Tsai
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Division of Parasitology, Department of Infectious Disease, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Helen Beasley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Vivian Blok
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter J A Cock
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Sebastian Eves-van den Akker
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Nancy Holroyd
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Martin Hunt
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | | | - Hardeep Naghra
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Present address: School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Arnab Pain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
- Present address: Computational Bioscience Research Center (CBRC), Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Juan E Palomares-Rius
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- Present address: Institute for Sustainable Agriculture (IAS), Spanish National Research Council (CSIC), Alameda del Obispo s/n Apdo 4084, 14080 Córdoba, Spain
| | - Magdalena Zarowiecki
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Matthew Berriman
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - John T Jones
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Peter E Urwin
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, UK
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13
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Lettoof DC, Greenlees MJ, Stockwell M, Shine R. Do invasive cane toads affect the parasite burdens of native Australian frogs? Int J Parasitol Parasites Wildl 2013; 2:155-64. [PMID: 24533330 PMCID: PMC3862496 DOI: 10.1016/j.ijppaw.2013.04.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/05/2013] [Accepted: 04/10/2013] [Indexed: 01/08/2023]
Abstract
One of the most devastating impacts of an invasive species is the introduction of novel parasites or diseases to native fauna. Invasive cane toads (Rhinella marina) in Australia contain several types of parasites, raising concern that the toads may increase rates of parasitism in local anuran species. We sampled cane toads and sympatric native frogs (Limnodynastes peronii, Litoria latopalmata, and Litoria nasuta) at the southern invasion front of cane toads in north-eastern New South Wales (NSW). We dissected and swabbed these anurans to score the presence and abundance of nematodes (Rhabdias lungworms, and gastric encysting nematodes), myxozoans, and chytrid fungus. To determine if cane toad invasion influences rates of parasitism in native frogs, we compared the prevalence and intensity of parasites in frogs from areas with toads, to frogs from areas without toads. Contrary to the situation on the (rapidly-expanding) tropical invasion front, cane toads on the slowly-expanding southern front were heavily infected with rhabditoid lungworms. Toads also contained gastric-encysting nematodes, and one toad was infected by chytrid fungus, but we did not find myxozoans in any toads. All parasite groups were recorded in native frogs, but were less common in areas invaded by toads than in nearby yet to be invaded areas. Contrary to our predictions, toad invasion was associated with a reduced parasite burden in native frogs. Thus, cane toads do not appear to transfer novel parasites to native frog populations, or act as a reservoir for native parasites to 'spill-back' into native frogs. Instead, cane toads may reduce frog-parasite numbers by taking up native parasites that are then killed by the toad's immune defences.
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Affiliation(s)
- Damian C. Lettoof
- School of Biological Sciences A08, University of Sydney, NSW 2006, Australia
| | | | - Michelle Stockwell
- School of Biological Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Richard Shine
- School of Biological Sciences A08, University of Sydney, NSW 2006, Australia
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14
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Kumar S, Jones M, Koutsovoulos G, Clarke M, Blaxter M. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Front Genet 2013; 4:237. [PMID: 24348509 PMCID: PMC3843372 DOI: 10.3389/fgene.2013.00237] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 10/23/2013] [Indexed: 12/16/2022] Open
Abstract
Generating the raw data for a de novo genome assembly project for a target eukaryotic species is relatively easy. This democratization of access to large-scale data has allowed many research teams to plan to assemble the genomes of non-model organisms. These new genome targets are very different from the traditional, inbred, laboratory-reared model organisms. They are often small, and cannot be isolated free of their environment – whether ingested food, the surrounding host organism of parasites, or commensal and symbiotic organisms attached to or within the individuals sampled. Preparation of pure DNA originating from a single species can be technically impossible, but assembly of mixed-organism DNA can be difficult, as most genome assemblers perform poorly when faced with multiple genomes in different stoichiometries. This class of problem is common in metagenomic datasets that deliberately try to capture all the genomes present in an environment, but replicon assembly is not often the goal of such programs. Here we present an approach to extracting, from mixed DNA sequence data, subsets that correspond to single species’ genomes and thus improving genome assembly. We use both numerical (proportion of GC bases and read coverage) and biological (best-matching sequence in annotated databases) indicators to aid partitioning of draft assembly contigs, and the reads that contribute to those contigs, into distinct bins that can then be subjected to rigorous, optimized assembly, through the use of taxon-annotated GC-coverage plots (TAGC plots). We also present Blobsplorer, a tool that aids exploration and selection of subsets from TAGC-annotated data. Partitioning the data in this way can rescue poorly assembled genomes, and reveal unexpected symbionts and commensals in eukaryotic genome projects. The TAGC plot pipeline script is available from https://github.com/blaxterlab/blobology, and the Blobsplorer tool from https://github.com/mojones/Blobsplorer.
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Affiliation(s)
- Sujai Kumar
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh Edinburgh, UK
| | - Martin Jones
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh Edinburgh, UK
| | - Georgios Koutsovoulos
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh Edinburgh, UK
| | - Michael Clarke
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh Edinburgh, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh Edinburgh, UK ; Edinburgh Genomics, University of Edinburgh Edinburgh, UK
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15
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Derycke S, Backeljau T, Moens T. Dispersal and gene flow in free-living marine nematodes. Front Zool 2013; 10:1. [PMID: 23356547 PMCID: PMC3567977 DOI: 10.1186/1742-9994-10-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 01/21/2013] [Indexed: 11/10/2022] Open
Abstract
Dispersal and gene flow determine connectivity among populations, and can be studied through population genetics and phylogeography. We here review the results of such a framework for free-living marine nematodes. Although field experiments have illustrated substantial dispersal in nematodes at ecological time scales, analysis of the genetic diversity illustrated the importance of priority effects, founder effects and genetic bottlenecks for population structuring between patches <1 km apart. In contrast, only little genetic structuring was observed within an estuary (<50 km), indicating that these small scale fluctuations in genetic differentiation are stabilized over deeper time scales through extensive gene flow. Interestingly, nematode species with contrasting life histories (extreme colonizers vs persisters) or with different habitat preferences (algae vs sediment) show similar, low genetic structuring. Finally, historical events have shaped the genetic pattern of marine nematodes and show that gene flow is restricted at large geographical scales. We also discuss the presence of substantial cryptic diversity in marine nematodes, and end with highlighting future important steps to further unravel nematode evolution and diversity.
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Affiliation(s)
- Sofie Derycke
- Department of Biology, Marine Biology section, Ghent University, Krijgslaan 281, S8, 9000, Ghent, Belgium.
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16
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BREHM K, CARLTON JM, HOFFMANN KF. Parasite genomics and post-genomic activities: 21st century resources for the parasite immunologist. Parasite Immunol 2012; 34:47-9. [DOI: 10.1111/j.1365-3024.2011.01346.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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