Parastrongyloides trichosuri

Genome Assembly & Annotation

Assembly

The draft genome assembly was produced by the Parasite Genomic group at the Wellcome Trust Sanger Institute, in collaboration with Warwick Grant (La Trobe University), using Illumina paired-end sequencing followed by an in-house genome assembly pipeline comprising various steps, including contig assembly, scaffolding, gap-filling and error-correction, followed by some bespoke manual improvement (WTSI Strongyloididae Nematode Genomes Project, Hunt et al. (2016)).

In May 2019 Eerik Aunin reported that the genome could be contaminated with bacteria. He observed that the average GC content of scaffold peaks once around 25% and a second time around 70%. Additionally, 685 of 1810 scaffolds, almost exclusively with GC% corresponding to the second peak, are reported as bacterial in an nt BLAST against a reference bacterial database. 483 of the scaffolds match genus Brevundimonas of protobacteria, and others match about 30 different bacteria.

Annotation

The gene predictions were made by the Parasite Genomics group at the Wellcome Trust Sanger Institute as part of the Strongyloididae Nematode Genomes Project, Hunt et al. (2016). An in-house automatic pipeline (based around AUGUSTUS plus MAKER) was used to generate first-pass gene models, and this was followed by a round of targeted manual curation of selected gene families.

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

• Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H, Bennett HM, Brooks K, Harsha B, Kajitani R, Kulkarni A, Harbecke D, Nagayasu E, Nichol S, Ogura Y, Quail MA, Randle N, Xia D, Brattig NW, Soblik H, Ribeiro DM, Sanchez-Flores A, Hayashi T, Itoh T, Denver DR, Grant W, Stoltzfus JD, Lok JB, Murayama H, Wastling J, Streit A, Kikuchi T, Viney M, Berriman M. The genomic basis of parasitism in the Strongyloides clade of nematodes. Nat Genet, 2016;48(3):299-307

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