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

Stephen R. Doyle, Alan Tracey, Roz Laing, Nancy E. Holroyd, David Bartley, Wojtek Bazant, Helen Beasley, Robin N. Beech, Collette Britton , Karen Brooks, Umer Naveed Chaudhry, Kirsty Maitland, Axel Martinelli, Jennifer Noonan, Michael Paulini, Michael A Quail, Elizabeth Redman, Faye H. Rodgers, Guillaume Sallé, Muhammad Zubair ShabbirGeetha Sankaranarayanan , Janneke Wit, Kevin L Howe, Neil Sargison, Eileen Devaney, Matthew Berriman, John S Gilleard, James A. Cotton

Research output: Contribution to journalArticlepeer-review

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 ong-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.
Original languageEnglish
JournalCommunications biology
DOIs
Publication statusPublished - 9 Nov 2020

Keywords

  • Haemonchus contortus
  • chromosomal genome assembly
  • PacBio long-read sequencing
  • Iso- Seq cDNA sequencing
  • genetic variation
  • transcriptomics
  • population genomics

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