Ascidians are invertebrate chordates, which diverged from the vertebrate lineage near the root of the chordate phylogenetic tree. Their larvae have a tadpole structure that closely resembles lower vertebrate larvae. They are, however, composed of a very small number of cells (2600 for Ciona intestinalis), have a stereotyped development due to invariant cleavage patterns, and are therefore simpler to study than vertebrate embryos. This, combined with the recent establishment of powerful functional genomics tools in the wake of the sequencing of the Ciona intestinalis genome, has led to the re-emergence of ascidians as a chordate model organism of great evolutionary and developmental significance. Ciona studies have provided crucial insights into chordate evolution and the function of families of chordate-specific genes. In particular, Ciona and other ascidians have emerged as excellent model organisms to address three topics of wide interest: the study of the origin of features specific for chordate body plan (notochord, neural plate, neural crests), the dissection of gene regulatory networks, and the study of neural networks and function.
The fulfillment of the sea squirt’s potential as a model organism is, however, dependent on an improved collection of gene models. The current genome assembly, though good, remains at the draft stage, and the gene models often lack reliable first and last exons because of insufficient expressed sequence tag (EST) coverage. The current Unigene collection (assembled at Kyoto University) lacks full open reading frames (ORFs) for around 30% of predicted genes–insufficient coverage for the large-scale functional genomics projects currently initiated in the ascidian community. This latest sequencing project will generate a novel set of ESTs from long-insert, Gateway-compatible cDNA libraries from mixed embryonic stages. The new data will allow the creation of a full Unigene collection, enabling advanced studies of chordate evolution and gene function.
CSP project coordinator: Patrick Lemaire (CNRS, France).