Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm
Copyright policy )Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm
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.
- Département Sciences sociales, agriculture et alimentation, espace et environnement France
- University of Edinburgh United Kingdom
- Université François-Rabelais Tours France
- University of Calgary Canada
- Centre Val de Loire France
Male, Evolutionary biology, [SDV.GEN] Life Sciences [q-bio]/Genetics, Gene, 630, Computational biology, transcriptomics, Ecological Interactions of Parasites in Ecosystems, Haemonchus contortus, environment/Symbiosis, Intestinal Diseases, Parasitic, Small Animals, Nematode, Immunology and Microbiology, Genome, Ecology, Life Sciences, 600, Genomics, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, Veterinary, Bacterial artificial chromosome, Physical Sciences, Female, Haemonchus, environment, Anthelmintic Resistance in Veterinary Parasites, population genomics, Anthelmintic Resistance, Chromosome, Models, Biological, Article, Chromosomes, Global Impact of Helminth Infections and Control Strategies, [SDV.EE]Life Sciences [q-bio]/Ecology, Health Sciences, PacBio long-read sequencing, Genetics, Animals, Humans, Caenorhabditis elegans, Biology, Sequence assembly, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genome, Helminth, Life Cycle Stages, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, FOS: Biological sciences, chromosomal genome assembly, Iso- Seq cDNA sequencing, genetic variation, Environmental Science, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, Parasitology, Gene expression, Haemonchiasis, Transcriptome
Male, Evolutionary biology, [SDV.GEN] Life Sciences [q-bio]/Genetics, Gene, 630, Computational biology, transcriptomics, Ecological Interactions of Parasites in Ecosystems, Haemonchus contortus, environment/Symbiosis, Intestinal Diseases, Parasitic, Small Animals, Nematode, Immunology and Microbiology, Genome, Ecology, Life Sciences, 600, Genomics, [SDV.EE] Life Sciences [q-bio]/Ecology, environment, Veterinary, Bacterial artificial chromosome, Physical Sciences, Female, Haemonchus, environment, Anthelmintic Resistance in Veterinary Parasites, population genomics, Anthelmintic Resistance, Chromosome, Models, Biological, Article, Chromosomes, Global Impact of Helminth Infections and Control Strategies, [SDV.EE]Life Sciences [q-bio]/Ecology, Health Sciences, PacBio long-read sequencing, Genetics, Animals, Humans, Caenorhabditis elegans, Biology, Sequence assembly, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genome, Helminth, Life Cycle Stages, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, FOS: Biological sciences, chromosomal genome assembly, Iso- Seq cDNA sequencing, genetic variation, Environmental Science, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, Parasitology, Gene expression, Haemonchiasis, Transcriptome
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