Adult sea squirt, image courtesy of Nori Satoh.

The sea squirt Ciona intestinalis is an unusual organism with an unusual history. For more than a century, biologists have pored over this marine invertebrate due to its peculiar anatomical features and controversial taxonomy. It is now widely accepted that this species is a primitive chordate — that is, it has a cartilaginous column resembling a spine — and so it is suitably placed to tell us about the evolutionary steps leading from invertebrates to vertebrates such as ourselves. The draft sequence of the C. intestinalis genome — which has been 18 months in the making — has now been published by Dehal and colleagues and represents the first genome of an invertebrate chordate to be published. In their paper, the authors present a preliminary analysis of the gene content of Ciona and how it compares with those of other sequenced animals.

The 160 million bp Ciona genome was sequenced using a whole-genome shotgun approach and is freely available on the web. It was found to contain ∼16,000 protein-coding genes. This is similar to the number of genes in Drosophila melanogaster (∼14,000) and Caenorhabditis elegans (∼19,000), but around half the number estimated to be present in puffer fish (∼31,000) and human (∼30,000). It has been argued that extensive gene duplication was important in the evolution of the vertebrates. Comparative studies of gene families in Ciona and the vertebrates support this idea, as most genes that are present as multiple copies in vertebrates only have a single representative in Ciona.

The two physiological innovations that characterize vertebrates are their complex central nervous system and their adaptive immune system. A major evolutionary question is how and when these features arose. Genes required for these functions are absent from the Ciona genome, suggesting that they originated specifically in the vertebrate lineage. By contrast, there are Ciona homologues of genes required for other aspects of vertebrate development that are absent in the fly and worm genomes, such as thyroid hormone production and detection, and heart development.

As well as shedding light on the origin of the vertebrates, interesting evolutionary insights can be gained from unique features of the Ciona genome. This is the first animal that has been found to have genes involved in the synthesis of cellulose. A putative cellulose synthase has been identified that is likely to be involved in the production of the outer tunic of the adult sea squirt. This gene shares homology with those found in nitrogen-fixing bacteria and so might have been acquired by an ancestor of Ciona through horizontal gene transfer from a bacterial genome. Also of interest is a new family of receptors that contain two domains — a caspase domain and a region with homology to proteins involved in Notch signalling — that have never been observed before in a single protein, thereby providing an example of domain shuffling.

This paper illustrates the power of genome projects to give insight into evolutionary processes. Sea squirts might be only distantly related to humans, but their genome sequence adds another perspective to that given by other sequenced vertebrate and invertebrate genomes. Undoubtedly, the release of the sea urchin genome, expected in the next ten months, will complement this work and will provide more information about metazoan evolution.