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A genomewide survey of developmentally relevant genes in Ciona intestinalis

III. Genes for Fox, ETS, nuclear receptors and NFκB

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Abstract

A survey against the draft genome sequence and the cDNA/EST database of Ciona intestinalis identified a number of genes encoding transcription factors regulating a variety of processes including development. In the present study, we describe almost complete sets of genes for Fox, ETS-domain transcription factors, nuclear receptors, and NFκB as well as other factors regulating NFκB activity, with their phylogenetic nature. Vertebrate Fox transcription factors are currently delineated into 17 subfamilies: FoxA to FoxQ. The present survey yielded 29 genes of this family in the Ciona genome, 24 of which were Ciona orthologues of known Fox genes. In addition, we found 15 ETS genes, 17 nuclear receptor genes, and several NFκB signaling pathway genes in the Ciona genome. The number of Ciona genes in each family is much smaller than that of vertebrates, which represents a simplified feature of the ascidian genome. For example, humans have two NFκB genes, three Rel genes, and five NFAT genes, while Ciona has one gene for each family. The Ciona genome also contains smaller numbers of genes for the NFκB regulatory system, i.e. after the split of ascidians/vertebrates, vertebrates evolved a more complex NFκB system. The present results therefore provide molecular information for the investigation of complex developmental processes, and an insight into chordate evolution.

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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). K.Y. was a Predoctoral Fellow of JSPS with a research grant (13003747). 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

    Kasumi Yagi, Yutaka Satou & Nori Satoh

  2. School of Animal and Microbial Sciences, University of Reading , Reading RG6 6AJ, UK

    Françoise Mazet & Sebastian M. Shimeld

  3. Department of Zoology and Entomology, University of Queensland, Brisbane, Qld 4072, Australia

    Bernard Degnan

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

    Daniel Rokhsar

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

    Michael Levine

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

    Yuji Kohara

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  1. Kasumi Yagi
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  2. Yutaka Satou
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  3. Françoise Mazet
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  4. Sebastian M. Shimeld
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  5. Bernard Degnan
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  6. Daniel Rokhsar
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  7. Michael Levine
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  8. Yuji Kohara
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  9. Nori Satoh
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Correspondence to Yutaka Satou.

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Edited by D. Tautz

The first two authors contributed equally to this work

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Yagi, K., Satou, Y., Mazet, F. et al. A genomewide survey of developmentally relevant genes in Ciona intestinalis . Dev Genes Evol 213, 235–244 (2003). https://doi.org/10.1007/s00427-003-0322-z

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  • DOI: https://doi.org/10.1007/s00427-003-0322-z

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