Skip to content

Research at St Andrews

Comprehensive survey and classification of homeobox genes in the genome of amphioxus, Branchiostoma floridae.

Research output: Contribution to journalArticle

Author(s)

N. Takatori, T. Butts, S. Candiani, M Pestariono, David Ellard Keith Ferrier, H. Saiga, P.W.H. Holland

School/Research organisations

Abstract

The homeobox genes comprise a large and diverse gene superfamily, many of which encode transcription factors with pivotal roles in the embryonic development of animals. We searched the assembled draft genome sequence of an amphioxus, Branchiostoma floridae, for genes possessing homeobox sequences. Phylogenetic analysis was used to divide these into gene families and classes. The 133 amphioxus homeobox genes comprise 60 ANTP class genes, 29 PRD genes (excluding Pon and Pax1/9), nine TALE genes, seven POU genes, seven LIM genes, five ZF genes, four CUT genes, four HNF genes, three SINE genes, one CERS gene, one PROS gene, and three unclassified genes. Ten of the 11 homeobox gene classes are less diverse in amphioxus than humans, as a result of gene duplication on the vertebrate lineage. Amphioxus possesses at least one member for all of the 96 homeobox gene families inferred to be present in the common ancestor of chordates, including representatives of the Msxlx, Bari, Abox, Nk7, Ro, and Repo gene families that have been lost from tunicates and vertebrates. We find duplication of several homeobox genes in the cephalochordate lineage (Mnx, Evx, Emx, Vent, Nk1, Nedx, Uncx, Lhx2/9, Hmbox, Pou3, and Irx) and several divergent genes that probably originated by extensive sequence divergence (Hx, Ankx, Lcx, Acut, Atale, Azfh, Ahbx, Muxa, Muxb, Aprd1-6, and Ahnf). The analysis reveals not only the repertoire of amphioxus homeobox genes but also gives insight into the evolution of chordate homeobox genes.

Close

Details

Original languageEnglish
Pages (from-to)579-590
Number of pages12
JournalDevelopment Genes and Evolution
Volume218
DOIs
Publication statusPublished - Dec 2008

    Research areas

  • Homeodomain, Lancelet, Molecular evolution, Molecular phylogeny, Chordate, PAIRED BOX GENE, DEVELOPMENTAL EXPRESSION, VERTEBRATE DEVELOPMENT, MAXIMUM-LIKELIHOOD, CERAMIDE SYNTHASES, IROQUOIS GENES, HOX CLUSTER, EVOLUTION, ORGANIZATION, DOMAIN

Discover related content
Find related publications, people, projects and more using interactive charts.

View graph of relations

Related by author

  1. Transcriptional regulation of the Ciona Gsx gene in the neural plate

    Hudson, C., Esposito, R., Palladino, A., Staiano, L., Ferrier, D., Faure, E., Lemaire, P., Yasuo, H. & Spagnuolo, A., 15 Apr 2019, In : Developmental Biology. 448, 2, p. 88-100 13 p.

    Research output: Contribution to journalArticle

  2. Space and time in Hox/ParaHox gene cluster evolution.

    Ferrier, D. E. K., 2019, Perspectives on Evolutionary Developmental Biology: Essays for Alessandro Minelli. Fusco, G. (ed.). Padova: Padova University Press, p. 245-258

    Research output: Chapter in Book/Report/Conference proceedingChapter

  3. Two more Posterior Hox genes and Hox cluster dispersal in echinoderms

    Szabó, R. & Ferrier, D. E. K., 27 Dec 2018, In : BMC Evolutionary Biology. 18, 13 p., 203.

    Research output: Contribution to journalArticle

  4. Amphioxus functional genomics and the origins of vertebrate gene regulation

    Marletaz, F., Firbas, P., Maeso, I., Tena, J., Bogdanovic, O., Perry, M., Wyatt, C., de la Calle-Mustienes, E., Bertrand, S., Burguera, D., Acemel, R., van Heeringen, S., Naranjo, S., Herrera-Ubeda, C., Skvortsova, K., Jimenez-Gancedo, S., Aldea, D., Marquez, Y., Buono, L., Kozmikova, I. & 41 othersPermanyer, J., Louis, A., Albuixech-Crespo, B., Le Petillon, Y., Leon Florian, A., Subirana, L., Balwierz, P. J., Duckett, P., Farahani, E., Aury, J. M., Mangenot, S., Wincker, P., Albalat, R., Benito-Gutierrez, E., Canestro, C., Castro, F., D'Aniello, S., Ferrier, D. E. K., Huang, S., Laudet, V., Marais, G., Pontarotti, P., Schubert, M., Seitz, H., Somorjai, I. M. L., Takahashi, T., Mirabeau, O., Xu, A., Yu, J-K., Carninci, P., Martinez-Morales, J., Crollius, H., Kozmik, Z., Weirauch, M., Garcia-Fernandez, J., Lister, R., Lenhard, B., Holland, P., Escriva, H., Gomez-Skarmeta, J. L. & Irimia, M., 21 Nov 2018, In : Nature. 564, 7734, p. 64-70 29 p.

    Research output: Contribution to journalArticle

  5. Horizons in evolutionary genomics: an interview with David Ferrier

    Ferrier, D. E. K., 1 Nov 2018, In : BMC Biology. 16, 3 p., 124.

    Research output: Contribution to journalArticle

Related by journal

  1. Evolution of follistatin in teleosts revealed through phylogenetic, genomic and expression analyses

    Johnston, I. A. & MacQueen, D. J., Jan 2008, In : Development Genes and Evolution. 218, 1, p. 1-14 14 p.

    Research output: Contribution to journalArticle

  2. The Mnx homeobox class defined by HB9, MNR2 and amphioxus AmphiMnx.

    Ferrier, D. E. K., Brooke, N. M., Panopoulou, G. & Holland, P. W. H., Feb 2001, In : Development Genes and Evolution. 211, p. 103-107 5 p.

    Research output: Contribution to journalArticle

ID: 419486