biostudies-literatureDoyle SRRCUK | Biotechnology and Biological Sciences Research CouncilWellcome TrustBiotechnology and Biological Sciences Research Council656https://www.ebi.ac.uk/biostudies/studies/S-EPMC7652881biostudies-literatureUnknown3(1)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 cycCommunications biologyGenomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm.PMC7652881WT206194BB/M003949/1BB/K020048/1BB/P024610/1067811Bazant WSargison NRodgers FHNoonan JDQuail MATracey AHolroyd NLaing RBeasley HSankaranarayanan GDoyle SRHowe KLBeech RSalle GBartley DCotton JAWit JBritton CDevaney EChaudhry UPaulini MGilleard JSRedman EBrooks KShabbir MZMartinelli ABerriman MMaitland KfalseGenomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm.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 cyc2020-01-01T00:00:00Z2020 Nov2026-05-02T23:43:12.546Z2020-11-19T16:13:36ZS-EPMC76528813316894010.1038/s42003-020-01377-3