Helobdella robusta (Freshwater leech) Assembly and Gene Annotation

About Helobdella robusta

Helobdella robusta is a freshwater leech, a type of annelid with anterior and posterior suckers that are used for locomotion and feeding (on blood or soft body parts). Leeches are hermaphroditic, and some species, including H. robusta, show a considerable degree of parental care. During oviposition, up to 100 eggs are attached to the mother in cocoons, and an adhesive gland ensures that the hatchlings remain attached; the young leeches continue to cling on after their suckers develop, during which time they feed on snails killed by their mother [1].

H. robusta has many characteristics that are representative of annelids and, more generally, lophotrochozoans, and its genome was sequenced alongside another annelid (Capitella teleta) and a mollusc (Lottia gigantea) to provide insight into metazoan evolution [2]. The genomic data also promotes the use of this species as a model organism for studies of evolutionary development.

Picture credit (Creative Commons BY-SA 3.0): Ajna Rivera

Assembly

The Helobdella robusta genome (v1.0, September 2007) was sequenced to 7.9x coverage, and assembled with the JGI software, Jazz. After quality control, the paired-end reads assembled into 1,991 scaffolds, giving a genome size of approximately 235 Mb.

Annotation

The protein-coding genes displayed in Ensembl Genomes are imported from JGI. Non-coding RNA genes were added using the Ensembl Genomes pipeline, and BLAST hits and protein features have been computed. The IDs of genes, transcripts and translations must be unique across species in Ensembl Genomes (to allow cross-species comparisons), which means that the JGI IDs cannot be used without slight modifications. The JGI transcript and protein IDs have been given the prefixes 'HelroT' and 'HelroP', respectively. Genes have been renamed to have the format 'HelroG*xxx*', where xxx is the original JGI transcript ID; the original JGI gene ID is stored as a cross-reference. Searching on the original JGI IDs will return the expected result (and potentially results from other species).

References

1. Description of the Californian leech Helobdella robusta sp.nov., and comparison with Helobdella triserialis on the basis of morphology, embryology, and experimental breeding.
   Shankland M, Bissen ST, Weisblat DA. 1992. Canadian Journal of Zoology. 70(6):1258-63.
2. Insights into bilaterian evolution from three spiralian genomes.
   Simakov O, Marletaz F, Cho SJ, Edsinger-Gonzales E, Havlak P, Hellsten U, Kuo DH, Larsson T, Lv J, Arendt D et al. 2013. Nature. 493:526-531.

More information

General information about this species can be found in Wikipedia.