Supercompact Genome in the Protochordate Oikopleura dioica

Oikopleura dioica is a protochordate with a remarkably short generation time (5 days) that can be bred in the laboratory. Due to high fecundity and transparency, Oikopleura has considerable potential for genetics and embryology. We have examined the overall genome organization in Oikopleura. Flow cytometry has revealed the smallest genome known in the chordate phylum (70 Mb). We have cloned and annotated 400 small and 5 larger genomic fragments, including a 145-kb-long BAC insert. A combination of BLAST search and gene finding programs has revealed a very high gene density (1 gene per 4 kb), which correlates with the presence of very short intergenic sequences and introns. Intron positions indicate major rearrangements of gene structures during the divergence between vertebrates and Oikopleura and also during the late diversification of tunicates. The distribution of predicted genes appears rather uniform and most gene predictions have been confirmed by cloning and sequencing of corresponding cDNAs. Oikopleura is therefore a very attractive model organism for genome-based developmental studies.