The adult C. intestinalis is a diaphanous sack that clings to a rock or to the piling of a pier, sucking in water through its mouth and filtering plankton through perforations - gill slits - in its pharynx. This simple adult 'sea squirt' disguised its true evolutionary heritage so well that for a long time it languished in classifications among the mollusks, or even the "Vermes". In 1866, Kovalevsky recognized that this 'gilt-rimmed vase' (see Figure ​Figure1a)1a) and its relatives each developed from a beautiful larva that was obviously a chordate and a cousin of the vertebrates. The 'tadpole' larva has a notochord supporting a propulsive tail and a dorsal nervous system (Figure ​(Figure1b).1b). This microscopic larva settles from the plankton, glues its 'face' to a rock, and metamorphoses by resorbing its tail, restructuring its nervous system, and deploying a pair of siphons through which it will filter algae from the sea for the rest of its days.

Since Kovalevsky's revelation, ascidians have generated considerable excitement in the discussion of vertebrate origins. Classical anatomists entertained the possibility that an ancient ascidian evolved a capacity to mature its gonads while remaining in the motile larval form, skipping a sessile adult stage, and that its descendents gave rise to the first vertebrate. Contemporary biologists acknowledge the evolutionary importance of ascidians differently - their genome and embryos offer a periscopic view on early chordate biology, but the ascidians themselves are not our ancestors.

Ascidians and their two sister classes, the larvaceans (or appendicularians) and thaliaceans, define the urochordates that, together with vertebrates and cephalochordates (such as amphioxus) make up the phylum Chordata (Figure ​(Figure2).2). Urochordates split off earliest from other chordates, and the characteristics we share with them may therefore help to shape a portrait of the eochordate, the ancestor of modern chordates. Chordates, like echinoderms and hemichordates, are deuterostomes, a division of animals that are distinguished from other animals (protostomes) by the development of the embryonic blastopore into the anus rather than the mouth.

The Ciona sequence database [8] reports 116.7 Mb of unique sequence in 2,501 scaffolds longer than 3 kilobases (kb). Identification of genes and their annotation were facilitated by the Kyoto full-length cDNA project [9]. This has produced a database [10] that adds significant value to the sequence by providing expression data for thousands of sequences over several life-cycle stages. The team [2] identified 15,852 gene models in Ciona, a number comparable to other protostomes (there are 13,639 and 19,518 currently identified in D. melanogaster and C. elegans, respectively, according to the Ensembl project [11]) (Figure ​(Figure2).2). On the other hand, this number is only about half the estimated total number of gene models in the human and mouse genomes (30,000, although at the time of this writing Ensembl predicted just 22,980 and 22,444 genes, respectively) [12]. F. rubripes appears to have an upper limit of about 38,000 genes [13] (or 35,180 according to Ensembl); this larger number is due to the genome duplication event that preceded the radiation of teleost fish [14].

Rather surprisingly, 21% of Ciona genes (3,399) have no clear homolog in the fly, worm, pufferfish, or human genomes (under high-stringency Smith-Waterman alignment along 60% of the target protein). Although this group might include poorly modeled genes or genes that have been broken by the ends of contigs, some may also have evolved so rapidly that they have lost significant resemblance to their orthologs, or they may be genes specific to urochordates or to ascidians. Resolution of this last ambiguity would require the sequencing of a distant urochordate genome, such as that of a larvacean [17].

What can the Ciona sequence tell us about vertebrate innovations? It can expedite the hunt for genes that are important in the development of the embryonic tissues that are widely believed to have initiated the evolution of the vertebrates [18]. These include neural crest and ectodermal placodes, which contribute to the paired sensory organs and head skeleton that are so apparent in vertebrates but are seemingly lacking from other chordates. If these tissues evolved after vertebrate origins, what functions do crest and placode genes have in an ascidian? Might such genes reveal the evolutionary precursors of these tissues? Many genes central to these questions have already been investigated in ascidians by targeted sequencing [19], but the Ciona sequencing project has detected more peripheral players. For instance, three Ciona genes (ci0100131069, ci0100130876 and ci0100135383) appear to be homologous to vertebrate genes encoding the olfactomedm family; one vertebrate member of this family, Noelin-1, encodes a protein that makes the neural tube competent to generate neural crest cells [20]. Two ascidian genes (ci0100149361 and ci0100140298) are homologous to the vertebrate HAND1 and HAND2 genes, which are also Important In crest development [21]. And Ciona has two orthologs (ci0100136347 and ci0100130219) of the vertebrate Prox1 gene, a marker of lens, otic, olfactory, and ganglia placodes [22]. The discovery of genes with only weak homology to olfactory receptors, however, undermines the prospects of discovering an olfactory placode precursor. Nonetheless, developmental biologists will be kept busy for some time studying the expression and function of these newly revealed genes.