The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus

Abstract

Background: The barber's pole worm, Haemonchus contortus, is one of the most economically important parasites of small ruminants worldwide. Although this parasite can be controlled using anthelmintic drugs, resistance against most drugs in common use has become a widespread problem. We provide a draft of the genome and the transcriptomes of all key developmental stages of H. contortus to support biological and biotechnological research areas of this and related parasites.

Results: The draft genome of H. contortus is 320 Mb in size and encodes 23,610 protein-coding genes. On a fundamental level, we elucidate transcriptional alterations taking place throughout the life cycle, characterize the parasite's gene silencing machinery, and explore molecules involved in development, reproduction, host-parasite interactions, immunity, and disease. The secretome of H. contortus is particularly rich in peptidases linked to blood-feeding activity and interactions with host tissues, and a diverse array of molecules is involved in complex immune responses. On an applied level, we predict drug targets and identify vaccine molecules.

Conclusions: The draft genome and developmental transcriptome of H. contortus provide a major resource to the scientific community for a wide range of genomic, genetic, proteomic, metabolomic, evolutionary, biological, ecological, and epidemiological investigations, and a solid foundation for biotechnological outcomes, including new anthelmintics, vaccines and diagnostic tests. This first draft genome of any strongylid nematode paves the way for a rapid acceleration in our understanding of a wide range of socioeconomically important parasites of one of the largest nematode orders.

Figure 1

Venn diagram showing the numbers of homologs between Haemonchus contortus and four other nematode species (Ascaris suum, Brugia malayi, Caenorhabditis elegans, and Trichinella spiralis) after pairwise comparison.

Figure 2

Transcriptional changes in the life cycle of Haemonchus contortus. In a 3-week life cycle of the parasite, eggs (E) are excreted in host feces; the first-stage larva (L1) develops inside the egg to hatch and molt through to the second-stage (L2) and third-stage (L3) larval stages within a week. The infective L3s are then ingested by the small ruminant host, where they exsheath and, after a short tissue phase, develop through the fourth-stage larval (L4) stage to dioecious adults; both of these stages feed on host blood from capillaries in the internal wall of the stomach. Disease in the host relates to this blood-feeding activity. In this figure, changes in transcription in the transition from stage to stage are summarized and interpreted in the context of the biology of the parasite. Information is given on key genes differentially transcribed between adult female (Af) and male (Am) H. contortus, and involved in reproductive and other biological processes; gene codes follow those of Caenorhabditis elegans orthologs.

Figure 3

Proposed RNA interference (RNAi) pathway of Haemonchus contortus. The genes predicted in H. contortus contain all of the previously identified core functional groups in nematode RNAi machinery [85], small RNA biosynthesis, double-stranded RNA (dsRNA) uptake and spreading, catalytic components, argonauts (AGO) of the RNA-induced silencing complex (RISC), RNAi inhibitors, and nuclear effectors. Genes present in H. contortus are represented by black codes, and those common to nematode RISC machinery are in gray. (A) Exogenous dsRNA and small interfering RNA (siRNA) enters cells via transporter SID-1. Internally produced secondary siRNA is spread to other cells via the transporter RSD-2. (B) Endogenous pre-microRNAs (pre-miRNAs) and siRNAs are produced in the nucleus, and exported to the cytosol via the nuclear export receptors XPO-1 and XPO-3. (C) Both the exogenous dsRNA and endogenous pre-miRNAs are cleaved by a dicer complex to produce siRNA and mature miRNA, respectively. (D) These RNAs are then bound to RISC, resulting in mRNA destruction or translational repression. (E) RNAi inhibitors can downregulate both siRNAs and miRNAs. (F) Secondary siRNAs produced by the catalytic components (MUT, SMF, and RRF) can contribute to downregulation of the target transcript. These siRNAs can also spread to other cells via (G) transporter RSD-2, and can be imported into the nucleus by (H) NRDE-3, in which they integrate to nuclear RISC to silence nascent RNA transcripts.