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Comprehensive Analysis of Animal TALE Homeobox Genes: New Conserved Motifs and Cases of Accelerated Evolution

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Abstract

TALE homeodomain proteins are an ancient subgroup within the group of homeodomain transcription factors that play important roles in animal, plant, and fungal development. We have extracted the full complement of TALE superclass homeobox genes from the genome projects of seven protostomes, seven deuterostomes, and Nematostella. This was supplemented with TALE homeobox genes from additional species and phylogenetic analyses were carried out with 276 sequences. We found 20 homeobox genes and 4 pseudogenes in humans, 21 genes in mouse, 8 genes in Drosophila, and 5 genes plus one truncated gene in Caenorhabditis elegans. Apart from the previously identified TALE classes MEIS, PBC, IRO, and TGIF, a novel class is identified, termed MOHAWK (MKX). Further, we show that the MEIS class can be divided into two families, PREP and MEIS. Prep genes have previously only been described in vertebrates but are lacking in Drosophila. Here we identify orthologues in other insect taxa as well as in the cnidarian Nematostella. In C. elegans, a divergent Prep protein has lost the homeodomain. Full-length multiple sequence alignment of the protostome and deuterostome sequences allowed us to identify several novel conserved motifs within the MKX, TGIF, and MEIS classes. Phylogenetic analyses revealed fast-evolving PBC class genes; in particular, some X-linked PBC genes in nematodes are subject to rapid evolution. In addition, several instances of gene loss were identified. In conclusion, our comprehensive analysis provides a defining framework for the classification of animal TALE homeobox genes and the understanding of their evolution.

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Acknowledgments

We thank Barbara Meyer for discussion and unpublished information. We thank Christoph Dieterich, Ralf Sommer, and Ulrich Technau for comments on the Pristionchus and Nematostella sequence data. Preliminary sequence data for B. malayi are deposited regularly into the GSS division of GenBank. The sequencing effort is part of the International Brugia Genome Sequencing Project and is supported by an award from the National Institute of Allergy and Infectious Diseases, National Institutes of Health. This research was supported by the Swedish Foundation for Strategic Research and the Swedish Research Council.

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  1. Department of Biosciences and Nutrition, Karolinska Institutet, and School of Life Sciences, Södertörns Högskola, Huddinge, Sweden

    Krishanu Mukherjee & Thomas R. Bürglin

  2. Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden

    Thomas R. Bürglin

  3. School of Life Sciences, Alfred Nobels Allé 7, Huddinge, Södertörns Högskola, SE-141 89, Sweden

    Thomas R. Bürglin

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  1. Krishanu Mukherjee
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Correspondence to Thomas R. Bürglin.

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Mukherjee, K., Bürglin, T.R. Comprehensive Analysis of Animal TALE Homeobox Genes: New Conserved Motifs and Cases of Accelerated Evolution. J Mol Evol 65, 137–153 (2007). https://doi.org/10.1007/s00239-006-0023-0

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