Studies of the ascidian genome system as a model of chordates and its evolution

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Ascidians, or sea squirts, are sessile marine invertebrate chordates. Although the adults are simple filter feeders, the fertilized eggs develop quickly into so-called tadpole larvae. The larva is composed of only〜2600 cells, which constitute a small number of organs including epidermis, central nervous system (CNS), endoderm and mesenchyme in the trunk, and notochord and muscle in the tail, representing the most simplified chordate body plan. We have decoded the draft genome of Cion intestinalis, and its〜120 Mbp euchromatic genome contains〜16,000 protein-coding genes. Among these is a fundamental set of conserved chordate genes encoding transcriptional factors and cell signaling molecules. Comparison of the Ciona genome with those of invertebrates and vertebrates suggests genetic changes which might have been associated with the evolution of chordates and vertebrates. In addition, we mapped by FISH methodology the genome information onto the 14 pairs of chromosomes of this anima. A thorough examination of Ciona gene expression (the transcriptome) is ongoing, including large scale EST analyses (〜700,000 ESTs), cDNA sequencing, in situ hybridization, and microarray analyses. Transgenic DNAs can be introduced into developing embryos using simple electroporation methods. Together with computational searching of conserved sequences between C. intestinalis and C. savignyi, this method permits rapid identification of cis-regulatory motifs governing the spatio-temporal expression of developmental genes. Together with recent advances in the methodology used to investigate gene regulation and function, these research circumstances make ascidians an appealingly simple experimental system for investigating the molecular mechanisms that underlie chordate development.