WormBase ParaSite HomeVersion: WBPS8 (WS256)

Heligmosomoides polygyrus (Heligmosomoides bakeri)

BioProject PRJEB1203 | Data Source Wellcome Trust Sanger Institute | Taxonomy ID 6339

About Heligmosomoides polygyrus (Heligmosomoides bakeri)

The nematode Heligmosomoides polygyrus (formerly known as Nematospiroides dubius) is a common parasite found in the duodenum and small intestine of woodmice and other rodents. The laboratory strain that has been sequenced was originally isolated from Peromyscus in California (Behnke and Harris, 2010); natural parasites from European wood mice (Apodemus sp.) are somewhat distinct, giving rise to some debate about the correct name and taxonomy of this species (Cable et al, 2006; Behnke and Harris, 2010; Maizels et al, 2010), with suggestions that the laboratory strain is named H. polygyrus bakeri or H. bakeri, and the European strain H. polygyrus polygyrus. The laboratory strain has been maintained as described by Camberis et al (2003) and is often used to model human helminth infection as it can establish chronic infection in different strains of mice.

There is 1 alternative genome project for Heligmosomoides polygyrus available in WormBase ParaSite: PRJEB15396

Genome assembly: H_bakeri_Edinburgh_v1_5_4

The draft genome assembly was produced by the Parasite Genomic group at the Wellcome Trust Sanger Institute, in collaboration with Rick Maizels (Edinburgh 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various steps, including contig assembly, scaffolding, gap-filling and error-correction (Helminth Genomes Consortium, unpublished).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Trust Sanger Institute and WormBase, as part of the 50 Helminth Genomes Initiative (Helminth Genomes Consortium, unpublished).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

AssemblyH_bakeri_Edinburgh_v1_5_4, GCA_000950495.1
StrainScotland/Edinburgh
Database VersionWBPS8
Genome Size560,662,278
Data SourceWellcome Trust Sanger Institute
Annotation Version2014-06-50HGPpatch

Gene counts

Coding genes27,459
Gene transcripts27,459

Assembly Statistics

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About this species