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.

Download C.savignyi genome sequence (FASTA)


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.