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WormBase ParaSite HomeVersion: WBPS19 (WS291)-  Archive: WBPS18

Hymenolepis microstoma

BioProject PRJEB124 | Data Source Wellcome Sanger Institute | Taxonomy ID 85433

About Hymenolepis microstoma

The cestode Hymenolepis microstoma, or rodent tapeworm, is an intestinal dwelling parasite of mice and rats. Adult worms live in the bile duct and small intestines, and larvae metamorphose in the haemocoel of beetles. H. microstoma is prevalent in rodents worldwide causing hymenolepiasis, but rarely infects humans. It is used as a laboratory model organism.

Genome Assembly & Annotation


The H. microstoma genome was sequenced by the Parasite Genomics group at the Wellcome Trust Sanger Institute, in collaboration with Pete Olson (Natural History Museum, London). The initial version of the genome was described in Tsai et al (2013). ParaSite releases 5-11 (January 2016 to October 2018) presented the November 2015 snapshot from GeneDB, corresponding to INSDC assembly HMIC002. Assembly presented here is the third consecutive version of the assembly. As described in Olson et al (2020), the previous assembly was improved by scaffolding a de novo PacBio assembly using Bionano's hybrid scaffolder (optical mapping). Further improvement was then carried out in gap5 using all the available optical map and sequence data.


As described in Olson et al (2020), the annotation was produced by running BRAKER, incorporating de novo gene predictions and RNASeq alignments, predicted on an unmasked assembly. The resulting predictions were then clustered using OrthoMCL and repeated predictions in low-complexity and repeat regions manually removed. A number of gene models were manually curated using Apollo.

Key Publications

Assembly Statistics

AssemblyHMN_v3, GCA_000469805.3
Database VersionWBPS19
Genome Size168,943,216
Data SourceWellcome Sanger Institute
Annotation Version2018-10-WormBase

Gene counts

Coding genes10,139
Gene transcripts11,429

Learn more about this widget in our help section

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