Gene expression profiles in Ciona intestinalis tailbud embryos

A set of 3423 expressed sequence tags derived from the Ciona intestinalis t ailbud embryos was categorized into 1213 independent clusters. When compare d with DNA Data Bank of Japan database, 502 clusters of them showed signifi cant matches to reported proteins with distinct function, whereas 184 lacke d sufficient information to be categorized (including reported proteins wit h undefined function) and 527 had no significant similarities to known prot eins. Sequence similarity analyses of the 502 clusters in relation to the b iosynthetic function, as well as the structure of the message population at this stage, demonstrated that 390 of them were associated with functions t hat many kinds of cells use, 85 with cell-cell communication and 27 with tr anscription factors and other gene regulatory proteins. All of the 1213 clu sters were subjected to whole-mount in situ hybridization to analyze the ge ne expression profiles at this stage. A total of 387 clusters showed expres sion specific to a certain tissue or organ; 149 showed epidermis-specific e xpression; 34 were specific to the nervous system; 29 to endoderm; 112 to m esenchyme; 32 to notochord; and 31 to muscle. Many genes were also specific ally expressed in multiple tissues. The study also highlighted characterist ic gene expression profiles dependent on the tissues. In addition, several genes showed intriguing expression patterns that have not been reported pre viously; for example, four genes were expressed specifically in the nerve c ord cells and one gene was expressed only in the posterior part of muscle c ells. This study provides molecular markers for each of the tissues and/or organs that constitutes the Ciona tailbud embryo. The sequence information will a lso be used for further genome scientific approach to explore molecular mec hanisms involved in the formation of one of the most primitive chordate bod y plans.