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A genomewide survey of developmentally relevant genes in Ciona intestinalis

II. Genes for homeobox transcription factors

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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.

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Acknowledgements

This research was supported by Grants-in-Aid for Scientific Research from MEXT and JSPS, Japan, to Y.S. (14704070) and N.S. (12202001), and by a CREST project of Japan Science and Technology Corporation (N.S., E.S., and S.W.). K.K. was a Postdoctoral Fellow of JSPS with a research grant (14061430). We thank Kazuko Hirayama, Chikako Imaizumi, Asako Fujimoto, and Hisayoshi Ishikawa for their technical support.

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Authors and Affiliations

  1. Department of Zoology, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan

    Shuichi Wada, Miki Tokuoka, Eiichi Shoguchi, Kenji Kobayashi, Nori Satoh & Yutaka Satou

  2. Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA

    Anna Di Gregorio

  3. Laboratory of Biochemistry and Molecular Biology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy

    Antonietta Spagnuolo & Margherita Branno

  4. National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan

    Yuji Kohara

  5. U.S. DoE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

    Daniel Rokhsar

  6. Department of Molecular and Cellular Biology, Division of Genetics and Development, University of California, Berkeley, CA 94720, USA

    Michael Levine

  7. Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Hachiohji, Tokyo 192-0397, Japan

    Hidetoshi Saiga

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  1. Shuichi Wada
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  13. Yutaka Satou
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Correspondence to Nori Satoh.

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Edited by D. Tautz

The first two authors contributed equally to this work

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Wada, S., Tokuoka, M., Shoguchi, E. et al. A genomewide survey of developmentally relevant genes in Ciona intestinalis . Dev Genes Evol 213, 222–234 (2003). https://doi.org/10.1007/s00427-003-0321-0

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