Lottia gigantea Assembly and Gene Annotation

About Lottia gigantea

Lottia gigantea, the owl limpet, is a sea snail that is found along rocky inter-tidal regions of the Californian coast. Mature limpets are territorial, often returning to the same location on the rock (the "home scar"), to which the shape of the shell becomes extremely well-fitted. Underlying this territoriality is the cultivation of an algal film, across an area proportional to the size of the limpet. Owl limpets defend their "gardens" against intruding owl limpets and other species, using a range of tactics including brute force shoving and pinching the intruder's soft-body between shell and rock [1].

L. gigantea has many characteristics that are representative of molluscs and, more generally, lophotrochozoans, and its genome was sequenced alongside two annelids (Capitella teleta and Helobdella robusta) 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, ecology, and conservation.

Picture credit (Creative Commons BY 2.0): Jerry Kirkhart 2007

Assembly

The Lottia gigantea genome (v1.0, July 2007) was sequenced to 8.9x coverage, and assembled with the JGI software, Jazz. After quality control, the paired-end reads assembled into 4,469 scaffolds, giving a genome size of approximately 360 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 'LotgiT' and 'LotgiP', respectively. Genes have been renamed to have the format 'LotgiGxxx', 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. Territorial behavior of the owl limpet, Lottia gigantea.
    Stimson J. 1970. Ecology. 51(1):113-8.
  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.

Statistics

Summary

AssemblyLotgi1, INSDC Assembly GCA_000327385.1, Jan 2013
Database version94.1
Base Pairs298,896,825
Golden Path Length359,505,668
Genebuild byJGI
Genebuild methodImported from JGI
Data sourceJGI

Gene counts

Coding genes23,349
Non coding genes1,151
Small non coding genes1,150
Long non coding genes1
Gene transcripts24,500

About this species