Extensive genomic and transcriptomic variation defines the chromosome-scale assembly ofHaemonchus contortus, a model gastrointestinal worm

Abstract

Background Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants, and has become the key nematode model for studying anthelmintic resistance and other parasite-specific traits among a wider group of parasites including major human pathogens. Two draft genome assemblies for H. contortus were reported in 2013, however, both were highly fragmented, incomplete, and differed from one another in important respects. While the introduction of long-read sequencing has significantly increased the rate of production and contiguity of de novo genome assemblies broadly, achieving high quality genome assemblies for small, genetically diverse, outcrossing eukaryotic organisms such as H. contortus remains a significant challenge. ResultsHere, 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. We show a remarkable pattern of almost complete conservation of chromosome content (synteny) with Caenorhabditis elegans , but almost no conservation of gene order. Long-read transcriptome sequence data has allowed us to define coordinated transcriptional regulation throughout the life cycle of the parasite, and refine our understanding of cisand trans -splicing relative to that observed in C. elegans .Finally, we use this assembly to give a comprehensive picture of chromosome-wide genetic diversity both within a single isolate and globally. ConclusionsThe H. contortus MHco3(ISE).N1 genome assembly presented here represents the most contiguous and resolved nematode assembly outside of the Caenorhabditis genus to date, together with one of the highest-quality set of predicted gene features. These data provide a high-quality comparison for understanding the evolution and genomics of Caenorhabditis and other nematodes, and extends the experimental tractability of this model parasitic nematode in understanding pathogen biology, drug discovery and vaccine development, and important adaptive traits such as drug resistance.

A Whole Genome Re-Sequencing Based GWA Analysis Reveals Candidate Genes Associated with Ivermectin Resistance in Haemonchus contortus

“…The effects of SNP and InDel were annotated using SnpEff-4.3T [50]. The annotated genome of H. contortus [51] was obtained from WormBase ParaSite [52]. Schematic of bioinformatics analysis of sequenced data is presented in Figure F1.2 (Supplementary file F1).…”

“…So, we were unable to say anything about their IVM candidature. The remaining 771 genes were analyzed (based on associated GO terms or based on their C. elegans orthologues) using WormBase ParaSite [52] and H. contortus resources [36,51]. Based on the functional annotations of outliers by interrogating at WormBase database [38], a total of 26 genes across the genome were finally selected as candidates of IVM resistance.…”

Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons

“…Long-read RNA sequencing can overcome many of the limitations inherent to short-read sequencing and can substantially improve gene predictions and annotations in genome assemblies (Fig 1). Only two long-read RNA sequencing datasets exist for parasitic nematodes, the zoonotic hookworm Ancylostoma ceylanicum and the barber's pole worm Haemonchus contortus [25,26]. Here, we report long-read RNA sequencing of the filarial parasites B. malayi and D. immitis.…”

Complementary Approaches to Understand Anthelmintic Resistance Using Free-Living and Parasitic Nematodes

“…However, studies of specific anthelmintic modes of action and resistance in helminths have been limited because parasite life cycles make isolation and maintenance extremely challenging in a controlled laboratory setting. H. contortus, a gastrointestinal nematode of small ruminants, has been a long-standing model because it is easier to establish and culture in host animals than most other parasites [77,78] and its high-quality reference genome has been updated recently to a chromosome-level assembly [79]. In addition, resistance to all major classes of anthelmintics is widespread across this species [80].…”