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Syphacia muris

BioProject PRJEB524 | Data Source Wellcome Trust Sanger Institute | Taxonomy ID 451379

About Syphacia muris

The nematode Syphacia muris, or rat pinworm, is a parasite of rats. The nematode Syphacia muris (Nematoda: Oxyuridae) is a ubiquitous nematode that commonly infects laboratory rodents (mainly rats). The direct transmission of this gastrointestinal nematode by contaminated food, water and bedding facilitates transmission in animal holdings. This results in continual re-exposure to the parasite, making the control of pinworms quite difficult and rodent colonies are frequently infected. Syphacia muris inhabits the caecum and the colon of the host.

Genome assembly: S_muris_Valencia_v1_0_4

The draft genome assembly was produced by the Parasite Genomic group at the Wellcome Trust Sanger Institute, in collaboration with Rafael Toledo (Universidad de Valencia), 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various steps, including contig assembly, scaffolding, gap-filling and error-correction (Helminth Genomes Consortium, unpublished).

Gene annotation

The gene predictions were made by the Parasite Genomics group at the Wellcome Trust Sanger Institute and WormBase, as part of the 50 Helminth Genomes Initiative (Helminth Genomes Consortium, unpublished). An in-house pipeline was developed that used MAKER to generate high-quality annotations by integrating evidence from multiple sources: ab initio gene predictions from AUGUSTUS, GeneMark-ES, and SNAP; projected annotation from C. elegans (using GenBlastG) and the taxonomically nearest reference helminth genome (using RATT); and ESTs, mRNAs and proteins from related organisms aligned to the genome using BLAST, with refinement of alignments using Exonerate.

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

Statistics

AssemblyS_muris_Valencia_v1_0_4, GCA_000939275.1
StrainSpain/Valencia
Database VersionWBPS8
Genome Size99,093,317
Data SourceWellcome Trust Sanger Institute
Annotation Version2014-06-50HGPpatch

Gene counts

Coding genes11,118
Gene transcripts11,118

Assembly Statistics

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About this species