Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm

Doyle, S. R. et al. (2020) Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm. Communications Biology, 3, 656. (doi: 10.1038/s42003-020-01377-3) (PMID:33168940) (PMCID:PMC7652881)

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Abstract

Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants and has become a key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Here, we report using PacBio long-read and OpGen and 10X Genomics long-molecule methods to generate a highly contiguous 283.4 Mbp chromosome-scale genome assembly including a resolved sex chromosome for the MHco3(ISE).N1 isolate. We show a remarkable pattern of conservation of chromosome content with Caenorhabditis elegans, but almost no conservation of gene order. Short and long-read transcriptome sequencing allowed us to define coordinated transcriptional regulation throughout the parasite’s life cycle and refine our understanding of cis- and trans-splicing. Finally, we provide a comprehensive picture of chromosome-wide genetic diversity both within a single isolate and globally. These data provide a high-quality comparison for understanding the evolution and genomics of Caenorhabditis and other nematodes and extend the experimental tractability of this model parasitic nematode in understanding helminth biology, drug discovery and vaccine development, as well as important adaptive traits such as drug resistance.

Item Type:Articles
Additional Information:Work described here was supported by Wellcome’s core funding of the Wellcome Sanger Institute (grant WT206194), a Wellcome Trust Project Grant to JSG (grant 067811), and the Biotechnology and Biological Sciences Research Council (BBSRC) grants (BB/M003949/1, BB/P024610/1 and BB/K020048/1). JDN was supported by a Graduate Mobility Award from McGill University.
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Devaney, Professor Eileen and Britton, Dr Collette and Laing, Dr Roz and Maitland, Ms Kirsty
Authors: Doyle, S. R., Tracey, A., Laing, R., Holroyd, N., Bartley, D., Bazant, W., Beasley, H., Beech, R., Britton, C., Brooks, K., Chaudhry, U., Maitland, K., Martinelli, A., Noonan, J. D., Paulini, M., Quail, M. A., Redman, E., Rodgers, F. H., Sallé, G., Shabbir, M. Z., Sankaranarayanan, G., Wit, J., Howe, K. L., Sargison, N., Devaney, E., Berriman, M., Gilleard, J. S., and Cotton, J. A.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
Journal Name:Communications Biology
Publisher:Nature Research
ISSN:2399-3642
ISSN (Online):2399-3642
Copyright Holders:Copyright © 2020 The Authors
First Published:First published in Communications Biology 3:656
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
190824The BUG consortium Building Upon the Genome: using H. contortus genomic resources to develop novel interventions to control endemic GI parasitesEileen DevaneyBiotechnology and Biological Sciences Research Council (BBSRC)BB/M003949/1Institute of Biodiversity, Animal Health and Comparative Medicine