Development Genes and Evolution

, Volume 213, Issue 5–6, pp 222–234 | Cite as

A genomewide survey of developmentally relevant genes in Ciona intestinalis

II. Genes for homeobox transcription factors
  • Shuichi Wada
  • Miki Tokuoka
  • Eiichi Shoguchi
  • Kenji Kobayashi
  • Anna Di Gregorio
  • Antonietta Spagnuolo
  • Margherita Branno
  • Yuji Kohara
  • Daniel Rokhsar
  • Michael Levine
  • Hidetoshi Saiga
  • Nori SatohEmail author
  • Yutaka Satou
Original Article


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.


Basal chordates Ciona intestinalis Genomewide survey Homeobox genes 



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.

Supplementary material (274 kb)
Supplementary material, approximately 281 KB.


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Copyright information

© Springer-Verlag 2003

Authors and Affiliations

  • Shuichi Wada
    • 1
  • Miki Tokuoka
    • 1
  • Eiichi Shoguchi
    • 1
  • Kenji Kobayashi
    • 1
  • Anna Di Gregorio
    • 2
  • Antonietta Spagnuolo
    • 3
  • Margherita Branno
    • 3
  • Yuji Kohara
    • 4
  • Daniel Rokhsar
    • 5
  • Michael Levine
    • 6
  • Hidetoshi Saiga
    • 7
  • Nori Satoh
    • 1
    Email author
  • Yutaka Satou
    • 1
  1. 1.Department of Zoology, Graduate School of ScienceKyoto UniversityKyoto 606-8502Japan
  2. 2.Department of Cell and Developmental BiologyWeill Medical College of Cornell UniversityNew YorkUSA
  3. 3.Laboratory of Biochemistry and Molecular BiologyStazione Zoologica Anton DohrnNaplesItaly
  4. 4.National Institute of GeneticsMishima, Shizuoka 411-8540Japan
  5. 5.U.S. DoE Joint Genome InstituteWalnut CreekUSA
  6. 6.Department of Molecular and Cellular Biology, Division of Genetics and DevelopmentUniversity of CaliforniaBerkeleyUSA
  7. 7.Department of Biological Sciences, Graduate School of ScienceTokyo Metropolitan UniversityTokyo 192-0397Japan

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