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A genomewide survey of bHLH transcription factors in the coral Acropora digitifera identifies three novel orthologous families, pearl, amber, and peridot

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Abstract

Decoding the genome of the coral, Acropora digitifera, enabled us to characterize a nearly full set of 70 basic helix-loop-helix (bHLH) transcription factors in this organism. This number is comparable to 68 bHLH genes in the sea anemone, Nematostella vectensis, and larger than those in most other invertebrate metazoans. The 70 bHLH genes were assigned to 29 orthologous families previously reported. In addition, we identified three novel HLH orthologous families, which we designated pearl, amber, and peridot, increasing the number of orthologous families to 32. Pearl and amber orthologues were found in genomes and expressed sequenced tags (ESTs) of Mollusca and Annelida in addition to Cnidaria. Peridot orthologues were found in genomes and ESTs of Cephalochordata and Hemichordata in addition to Cnidaria. These three genes were likely lost in the clades of Drosophila melanogaster, Caenorhabditis elegans, and Homo sapiens during animal evolution.

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Acknowledgments

The authors thank all members of the marine genomics laboratory for their helpful discussions. Drs. Chuya Shinzato and Takeshi Takeuchi are acknowledged for providing EST data for A. digitifera and P. fucata, respectively. This study was supported by OIST Internal Research Fund for marine genomics.

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Authors and Affiliations

  1. Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan

    Fuki Gyoja, Takeshi Kawashima & Nori Satoh

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  1. Fuki Gyoja
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  2. Takeshi Kawashima
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  3. Nori Satoh
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Correspondence to Fuki Gyoja.

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Communicated by H. Nishida

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Figure S1

A molecular phylogenetic tree of group C HLH factors generated by the neighbor-joining method based on the alignment of the bHLH, PAS, and PAS_3 domains. The number noted at a given branch indicates the percentage of times that a node was supported in 1,000 bootstrap pseudoreplications. When the given node was also supported by maximum likelihood method, the bootstrap value is shown in parentheses. A rooted tree is shown for simplicity. Proteins are designated by accession number, abbreviation of species and orthologous familiy names (Simiotato et al., 2007) (PDF 143 kb)

Figure S2

The alignment of amino acid sequences of the pearl, amber, and peridot proteins. For IDs for each proteins, see Fig. 1 or Fig. 2 (PDF 62 kb)

Table S1

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Gyoja, F., Kawashima, T. & Satoh, N. A genomewide survey of bHLH transcription factors in the coral Acropora digitifera identifies three novel orthologous families, pearl, amber, and peridot. Dev Genes Evol 222, 63–76 (2012). https://doi.org/10.1007/s00427-012-0388-6

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  • DOI: https://doi.org/10.1007/s00427-012-0388-6

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