C.savignyi assembly and gene annotation

Ciona savignyi is a tunicate sometimes known as the Pacific transparent sea squirt or solitary sea squirt. Found in shallow waters around Japan, it has spread to the west coast of North America where it is regarded as an invasive species. It has one of the highest known levels of genetic diversity of any species.


The genome of a single Ciona savignyi from San Francisco Bay was shotgun-sequenced by the Broad Institute and assembled using Arachne2. The Sidow lab at Stanford used this as a basis for the assembly.

The assembly consists of 374 Reftigs, totalling 174 Megabases, with a Contig N50 of 141Kb and Reftig N50 size of 1800Kb.

Gene annotation

The standard Ensembl mammalian pipeline was modified for annotation of the Ciona savignyi genome, owing to the lack of genomic information from closely-related species. Thus, in addition to aligning known Ciona proteins to the sequence (as per the standard pipeline), we aligned Ciona-specific cDNA and EST sequences against the genome, and then used these in conjunction with protein data from other species to build additional gene models.

More information

General information about this species can be found in Wikipedia.



AssemblyCSAV 2.0, Oct 2005
Base Pairs177,003,750
Golden Path Length177,003,750
Annotation methodFull genebuild
Genebuild startedApr 2006
Genebuild releasedJun 2006
Genebuild last updated/patchedApr 2013
Database version95.2

Gene counts

Coding genes11,616
Gene transcripts20,711


FGENESH gene prediction13,464
Genefinder gene prediction12,480
Genscan gene predictions12,655
Snap gene prediction35,571

About this species