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Strongyloides stercoralis

BioProject PRJEB528 | Data Source Wellcome Trust Sanger Institute | Taxonomy ID 6248

About Strongyloides stercoralis

The nematode Strongyloides stercoralis, or human threadworm, is a wide-spread, minute gastro-intestinal parasite of humans, occurring principally in the tropics and sub-tropics. Infection of immunosuppressed individuals can result in disseminated strongyloidiasis, in which worms occur throughout the body and can be fatal.

Genome assembly: S_stercoralis_PV0001_v2_0_4

The draft genome assembly was produced by the Parasite Genomic group at the Wellcome Trust Sanger Institute, in collaboration with James B. Lok (University of Pennsylvania School of Veterinary Medicine), 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)).

Gene 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.

What can I find? Protein-coding and non-coding genes, splice variants, cDNA and protein sequences, non-coding RNAs.

Comparative genomics

What can I find? Orthologues, paralogues, and gene trees across multiple species.

More information and statistics

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

Statistics

AssemblyS_stercoralis_PV0001_v2_0_4, GCA_000947215.1
StrainPV0001
Database VersionWBPS8
Genome Size42,674,651
Data SourceWellcome Trust Sanger Institute
Annotation Version2015-05-WormBase

Gene counts

Coding genes13,098
Gene transcripts13,098

Assembly Statistics

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This widget has been derived from the assembly-stats code developed by the Lepbase project at the University of Edinburgh

About this species