A genomewide survey of developmentally relevant genes in Ciona intestinalis

Abstract

Homeobox-containing genes play crucial roles in various developmental processes, including body-plan specification, pattern formation and cell-type specification. The present study searched the draft genome sequence and cDNA/EST database of the basal chordate Ciona intestinalis to identify 83 homeobox-containing genes in this animal. This number of homeobox genes in the Ciona genome is smaller than that in the Caenorhabditis elegans, Drosophila melanogaster, human and mouse genomes. Of the 83 genes, 76 have possible human orthologues and 7 may be unique to Ciona. The ascidian homeobox genes were classified into 11 classes, including Hox class, NK class, Paired class, POU class, LIM class, TALE class, SIX class, Prox class, Cut class, ZFH class and HNF1 class, according to the classification scheme devised for known homeobox genes. As to the Hox cluster, the Ciona genome contains single copies of each of the paralogous groups, suggesting that there is a single Hox cluster, if any, but genes orthologous to Hox7, 8, 9 and 11 were not found in the genome. In addition, loss of genes had occurred independently in the Ciona lineage and was noticed in Gbx of the EHGbox subclass, Sax, NK3, Vax and vent of the NK class, Cart, Og9, Anf and Mix of the Paired class, POU-I, III, V and VI of the POU class, Lhx6/7 of the LIM class, TGIF of the TALE class, Cux and SATB of the Cut class, and ZFH1 of the ZFH class, which might have reduced the number of Ciona homeobox genes. Interestingly, one of the newly identified Ciona intestinalis genes and its vertebrate counterparts constitute a novel subclass of HNF1 class homeobox genes. Furthermore, evidence for the gene structures and expression of 54 of the 83 homeobox genes was provided by analysis of ESTs, suggesting that cDNAs for these 54 genes are available. The present data thus reveal the repertoire of homeodomain-containing transcription factors in the Ciona genome, which will be useful for future research on the development and evolution of chordates.

Evolution of CUT class homeobox genes: insights from the genome of the amphioxus, Branchiostoma floridae

“…6). At present, it is difficult to decide when the change in the genomic structure of CUX/CASP or the gain and loss of SATB and COMPASS took place due to the limited genome sequence resources in the lower chordates, although previous study reported that genes encoding CUX, COMPASS and SATB were not found in the genome of Ciona intestinalis (Wada et al, 2003). Future genome sequencing of lower chordates will resolve this issue.…”

“…Recently, the genome resources of non-vertebrate deuterostomes have become available, including ascidian Ciona intestinalis (http:// genome.jgi-psf.org/Cioin2/Cioin2.home.html), sea urchin Strongylocentrotus purpuratus (http://www.ncbi.nlm.nih.gov/genome/guide/sea_urchin/) and amphioxus Branchiostoma floridae (http://genome.jgi-psf.org/Brafl1/Brafl1.home.html). In the genome of C. intestinalis, however, only ONECUT has been identified as CUT class homeobox genes (Wada et al, 2003) and in the S. purpuratus genome, two members, ONECUT and CUX, have been reported (Howard-Ashby et al, 2006), raising a possibility that other members of CUT class homeobox genes may have been lost in these animal species. Therefore, the genome resource of amphioxus is particularly important.…”

Patterning across the ascidian neural plate by lateral Nodal signalling sources

“…Interestingly, it has been observed that motoneurons may still form in isolated A4.1 explants (Okada et al, 1997). We used two motoneuron markers, Ci-ChAT, which encodes cholinergic acetyltransferase (Takamura et al, 2002;Yoshida et al, 2004), and the Ciona homologue of HB9 and MNR2 genes, which play a crucial role in motoneuron specification in other systems, and of which there is one representative in the Ciona genome, Ci-HB9/MNX (Broihier and Skeath, 2002;Odden et al, 2002;Shirasaki and Pfaff, 2002;Wada et al, 2003). Expression of these motoneuron markers was completely dependent on an intact Nodal signalling pathway ( Fig.…”

A Twist-like bHLH gene is a downstream factor of an endogenous FGF and determines mesenchymal fate in the ascidian embryos

“…In previous studies Wada et al, 2003), we identified whole gene sets for bHLH factors and homeobox transcription factors encoded in the Ciona intestinalis genome, the draft sequence of which we recently determined (Dehal et al, 2002). We comprehensively examined their expression patterns during embryogenesis, and thereby found that five bHLH genes and one homeobox gene were expressed predominantly in mesenchymal cells.…”