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Rhabditophanes sp. KR3021

BioProject PRJEB1297 | Data Source Wellcome Trust Sanger Institute | Taxonomy ID 114890

About Rhabditophanes sp. KR3021

Rhabditophanes sp. KR3021 is a free-living species that is an outgroup to a clade of parasitic species that includes the human pathogen Strongyloides stercoralis and Strongyloides ratti, a laboratory model of nematode infection.

Genome Assembly & Annotation

Assembly

The draft genome assembly was produced by the Parasite Genomic group at the Wellcome Trust Sanger Institute, in collaboration with Dee Denver (Oregon State 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 (WTSI Strongyloididae Nematode Genomes Project, Hunt et al. (2016)).

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.

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

Assembly Statistics

AssemblyRhabditophanes_sp_KR3021_v2_0_4, GCA_000944355.1
Strainkr 3021
Database VersionWBPS9
Genome Size47,267,908
Data SourceWellcome Trust Sanger Institute
Annotation Version2015-05-WormBase

Gene counts

Coding genes13,496
Gene transcripts13,496

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About this species