Haemonchus contortus

Genome Assembly & Annotation

Assembly

The assembly presented here has been sequenced at the Parasite Genomics group at the Wellcome Sanger Institute. The previous reference genome (Laing et al. (2013)) was improved through additional sequencing with long PacBio reads and optical mapping, giving a chromosome-level assembly (described in Doyle et al. (2020)).

Annotation

The gene models were made by the Parasite Genomics group at the Wellcome Sanger Institute using an automated prediction tool BRAKER1 to generate preliminary gene models, which were subsequently improved using IsoSeq, incorporating orthologs using PASA and EVidenceModeler, and ongoing manual curation. The annotation presented here is a snapshot from Spring 2020.

Downloads

• Genomic Sequence (FASTA)
• Hard-masked Genomic Sequence (FASTA)
• Soft-masked Genomic Sequence (FASTA)
• Annotations (GFF3)
• Proteins (FASTA)
• Full-length transcripts (FASTA)
• CDS transcripts (FASTA)

Tools

• Search for sequences in the genome and proteome using BLAST
• Work with lists of data using the WormBase ParaSite BioMart data-mining tool
• Programatically access WormBase ParaSite data using the REST API
• Predict the effects of variants using the Variant Effect Predictor

Key Publications

• Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston SL, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders GI, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS, Cotton JA. The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biol, 2013;14(8):R88
• Doyle SR, Tracey A, Laing R, Holroyd N, Bartley D, Bazant W, Beasley H, Beech R, Britton C, Brooks K, Chaudhry U, Maitland K, Martinelli A, Noonan JD, Paulini M, Quail MA, Redman E, Rodgers FH, Sallé G, Shabbir MZ, Sankaranarayanan G, Wit J, Howe KL, Sargison N, Devaney E, Berriman M, Gilleard JS, Cotton JA. Genomic and transcriptomic variation defines the chromosome-scale assembly of Haemonchus contortus, a model gastrointestinal worm. Commun Biol, 2020;3(1):656

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Gene Expression