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)

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 Maitland, Ms Kirsty and Laing, Dr Roz and Cotton, Professor James and Britton, Professor Collette
• 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 > School of Biodiversity, One Health & Veterinary 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

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
190824		The BUG consortium Building Upon the Genome: using H. contortus genomic resources to develop novel interventions to control endemic GI parasites	Eileen Devaney	Biotechnology and Biological Sciences Research Council (BBSRC)	BB/M003949/1	Institute of Biodiversity, Animal Health and Comparative Medicine