A Genome Resequencing-Based Genetic Map Reveals the Recombination Landscape of an Outbred Parasitic Nematode in the Presence of Polyploidy and Polyandry

Abstract

The parasitic nematode Haemonchus contortus is an economically and clinically important pathogen of small ruminants, and a model system for understanding the mechanisms and evolution of traits such as anthelmintic resistance. Anthelmintic resistance is widespread and is a major threat to the sustainability of livestock agriculture globally; however, little is known about the genome architecture and parameters such as recombination that will ultimately influence the rate at which resistance may evolve and spread. Here, we performed a genetic cross between two divergent strains of H. contortus, and subsequently used whole-genome resequencing of a female worm and her brood to identify the distribution of genome-wide variation that characterizes these strains. Using a novel bioinformatic approach to identify variants that segregate as expected in a pseudotestcross, we characterized linkage groups and estimated genetic distances between markers to generate a chromosome-scale F1 genetic map. We exploited this map to reveal the recombination landscape, the first for any helminth species, demonstrating extensive variation in recombination rate within and between chromosomes. Analyses of these data also revealed the extent of polyandry, whereby at least eight males were found to have contributed to the genetic variation of the progeny analyzed. Triploid offspring were also identified, which we hypothesize are the result of nondisjunction during female meiosis or polyspermy. These results expand our knowledge of the genetics of parasitic helminths and the unusual life-history of H. contortus, and enhance ongoing efforts to understand the genetic basis of resistance to the drugs used to control these worms and for related species that infect livestock and humans throughout the world. This study also demonstrates the feasibility of using whole-genome resequencing data to directly construct a genetic map in a single generation cross from a noninbred nonmodel organism with a complex lifecycle.

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

“…The autosomal estimates of nucleotide diversity were three to four times higher than those of X-chromosomal estimates. Low level of X-chromosomal estimates of nucleotide diversity in relation to autosomes were also reported in previous genome-wide studies [40,41].…”

“…This lack of consistency and discordance among the studies accompanied by extremely high level of genetic diversity of H. contortus has led to much discussion on the complexity of the genetic basis of IVM resistance [21,[33][34][35]. At the advent of high-throughput sequencing technology and enrichment of genomic resources of H. contortus [36][37][38][39], the genome-wide approaches (for characterizing drug resistance) are now feasible and are emerging for H. contortus [34,[40][41][42][43][44]. Under population genomics approach, genome-wide scans for potential SNPs and their allele frequencies across the IVM-susceptible and resistant populations of H. contortus can reveal the IVM-resistance-associated variants.…”

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

“…Particular repeat classes, including LINEs, LTRs and DNA elements, were enriched towards the middle of the chromosomes and the chromosome ends ( Figure 2 C , inner circle; Additional file 1: Figure S5 ). This distribution pattern is negatively correlated with observed recombination rate domains in both H. contortus [33] and C. elegans [34] , Distribution (x-axis) and length (y-axis) of mapped haplotype sequences to the chromosome, with sequence similarity between the mapped haplotype and chromosomes indicated by the grey-scale gradient (high similarity = dark, low = light); third: proportion of chromosome covered by a least one haplotype, measured in 1 Mbp windows; inner: density of annotated repeats, including LINEs (green), SINEs (red), DNA (blue), and LTRs (orange). Data is visualised using the R package circulize .…”

“…The difference in nucleotide diversity between the X chromosome and autosomes further emphasises the impact of putative sex biases on the evolution of the X chromosome. H. contortus is polyandrous [29,33] and highly fecund, so that reproductive fitness is likely overdispersed between males and females, potentially resulting in different effective population sizes for male and female parasites. These differences may be exacerbated if males and females are differentially affected by anthelmintic exposure as has been demonstrated for some compounds [57] .…”

“…The V3 assembly, used in the H. contortus genetic map [33] , consisted of five autosomal chromosomes, with the X chromosome in two major scaffolds. The X chromosome-associated scaffolds were identified by synteny to the C. elegans X chromosome using promer [74] , and by the expected ~0.75× coverage relative to the autosomes in pooled sequencing (due to a mixture of male and females present) and ~0.5×…”