Strongyloides ratti (Threadworm) Assembly and Gene Annotation

NOTE: The genome sequence and annotation for S. ratti are updated in Ensembl Metazoa infrequently. The data here corresponds with WormBase WS279. For the latest genome and annotation, please visit WormBase ParaSite (for an Ensembl-oriented view), or WormBase.

About Strongyloides ratti

The nematode Strongyloides ratti is a common gastro-intestinal parasite of the rat. The adult parasites are female only, about 2mm long and live in the mucosa of the small intestine. These parasites produce eggs that pass out of the host in its faeces. In the environment infective larval stages develop either directly or after a facultative sexual free-living adult generation. Infective larvae infect hosts by skin penetration.

S. ratti is the laboratory model of the parasite of humans, S. stercoralis. S. stercoralis is a wide-spread parasite of humans, occurring principally in the tropics and sub-tropics: some 100-200 million people are infected worldwide. Infection of immunosuppressed individuals can result in disseminated strongyloidiasis, in which worms occur throughout the body. This can be fatal unless anti-Strongyloides therapy is given. Other species of Strongyloides parasitise a wide range of vertebrates.

• S. ratti data at WormBase.
• *S. ratti data at WormBase ParaSite.
• Strongyloidiasis info by CDC.

Picture credit: Copyright Mark Viney 2023 - Reference [2]

Assembly

The reference genome was assembled by the Berriman Lab, in collaboration with Mark Viney (University of Bristol), using a combination of capillary, 454 and Illumina paired-end sequence and genetic map data, and improved using bespoke manual and automated tools (WTSI Strongyloididae Nematode Genomes Project, Hunt et al. (2016)).

Annotation

The gene predictions were made by the Berriman Lab 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.

References

1. The genomic basis of parasitism in the Strongyloides clade of nematodes.
   Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H et al. 2016. Nat. Genet.. 48:299-307. (Viney, M.E. and Lok J.B. Strongyloides spp. (May 23, 2007), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.141.1, http://www.wormbook.org.)
2. Strongyloides spp., The C. elegans Research Community, WormBook

Picture credit: Copyright Mark Viney 2023

Links

• S. ratti data at WormBase.
• *S. ratti data at WormBase ParaSite.