TITLE

A non-tree-based comprehensive study of metazoan Hox and ParaHox genes prompts new insights into their origin and evolution

AUTHOR(S)
Thomas-Chollier, Morgane; Ledent, Valérie; Leyns, Luc; Vervoort, Michel
PUB. DATE
January 2010
SOURCE
BMC Evolutionary Biology;2010, Vol. 10, p73
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: Hox and the closely-related ParaHox genes, which emerged prior to the divergence between cnidarians and bilaterians, are the most well-known members of the ancient genetic toolkit that controls embryonic development across all metazoans. Fundamental questions relative to their origin and evolutionary relationships remain however unresolved. We investigate here the evolution of metazoan Hox and ParaHox genes using the HoxPred program that allows the identification of Hox genes without the need of phylogenetic tree reconstructions. Results: We show that HoxPred provides an efficient and accurate classification of Hox and ParaHox genes in their respective homology groups, including Hox paralogous groups (PGs). We analyzed more than 10,000 sequences from 310 metazoan species, from 6 genome projects and the complete UniProtKB database. The HoxPred program and all results arranged in the Datab'Hox database are freely available at http://cege.vub.ac.be/hoxpred/. Results for the genome-scale studies are coherent with previous studies, and also brings knowledge on the Hox repertoire and clusters for newly-sequenced species. The unprecedented scale of this study and the use of a non-tree-based approach allows unresolved key questions about Hox and ParaHox genes evolution to be addressed. Conclusions: Our analysis suggests that the presence of a single type of Posterior Hox genes (PG9-like) is ancestral to bilaterians, and that new Posterior PGs would have arisen in deuterostomes through independent gene duplications. Four types of Central genes would also be ancestral to bilaterians, with two of them, PG6- and PG7- like that gave rise, in protostomes, to the UbdA- and ftz/Antp/Lox5-type genes, respectively. A fifth type of Central genes (PG8) would have emerged in the vertebrate lineage. Our results also suggest the presence of Anterior (PG1 and PG3), Central and Posterior Hox genes in the cnidarians, supporting an ancestral four-gene Hox cluster. In addition, our data support the relationship of the bilaterian ParaHox genes Gsx and Xlox with PG3, and Cdx with the Central genes. Our study therefore indicates three possible models for the origin of Hox and ParaHox in early metazoans, a two-gene (Anterior/PG3 - Central/Posterior), a three-gene (Anterior/PG1, Anterior/PG3 and Central/ Posterior), or a four-gene (Anterior/PG1 - Anterior/PG3 - Central - Posterior) ProtoHox cluster.
ACCESSION #
49198013

 

Related Articles

  • The quest for natural selection in the age of comparative genomics. Anisimova, M.; Liberles, D. A. // Heredity;Dec2007, Vol. 99 Issue 6, p567 

    Continued genome sequencing has fueled progress in statistical methods for understanding the action of natural selection at the molecular level. This article reviews various statistical techniques (and their applicability) for detecting adaptation events and the functional divergence of...

  • Microevolutionary dynamics of a macroevolutionary key innovation in a Lepidopteran herbivore. Heidel-Fischer, Hanna M.; Vogel, Heiko; Heckel, David G.; Wheat, Christopher W. // BMC Evolutionary Biology;2010, Vol. 10, p60 

    Background: A molecular population genetics understanding is central to the study of ecological and evolutionary functional genomics. Population genetics identifies genetic variation and its distribution within and among populations, it reveals the demographic history of the populations studied,...

  • Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors. Nagy, Alinda; Szláma, György; Szarka, Eszter; Trexler, Mária; Bányai, László; Patthy, László // Genes;Sep2011, Vol. 2 Issue 3, p449 

    In view of the fact that appearance of novel protein domain architectures (DA) is closely associated with biological innovations, there is a growing interest in the genome-scale reconstruction of the evolutionary history of the domain architectures of multidomain proteins. In such analyses,...

  • Identifying Single Copy Orthologs in Metazoa. Creevey, Christopher J.; Muller, Jean; Doerks, Tobias; Thompson, Julie D.; Arendt, Detlev; Bork, Peer // PLoS Computational Biology;Dec2011, Vol. 7 Issue 12, Special section p1 

    The identification of single copy (1-to-1) orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes...

  • Developmental expression of homeobox genes in the ctenophore Mnemiopsis leidyi. Pang, Kevin; Martindale, Mark Q. // Development Genes & Evolution;Jun2008, Vol. 218 Issue 6, p307 

    Homeobox genes are a large family of genes that encode helix–turn–helix transcription factors that play fundamental roles in such developmental processes including body axis formation and cell specification. They have been found in a wide variety of organisms, from fungi to plants...

  • Key transitions in animal evolution: a mitochondrial DNA perspective. Lavrov, Dennis V. // Integrative & Comparative Biology;Nov2007, Vol. 47 Issue 5, p734 

    Synopsis Animal mitochondrial DNA (mtDNA) is usually depicted as a small and very economically organized molecule with almost invariable gene content, stable gene order, a high rate of sequence evolution, and several unorthodox genetic features. Sampling across different animal phyla reveals...

  • Full-genome sequence and analysis of a novel human rhinovirus strain within a divergent HRV-A clade. Rathe, Jennifer A.; Xinyue Liu; Tallon, Luke J.; Gern, James E.; Liggett, Stephen B. // Archives of Virology;Jan2010, Vol. 155 Issue 1, p83 

    Genome sequences of human rhinoviruses (HRV) have primarily been from stocks collected in the 1960s, with genomes and phylogeny of modern HRVs remaining undefined. Here, two modern isolates (hrv-A101 and hrv-A101-v1) collected ~8 years apart were sequenced in their entirety. Incorporation into...

  • Editorial [ Mini Hot Topic Genomic Platforms for "evo-devo" Guest Editor: Ralf J. Sommer ]. Sommer, Ralf J. // Current Genomics;Dec2005, Vol. 6 Issue 8, p569 

    Much of the knowledge in modern biology is based on studies of a handful of model organisms, such as the mouse Mus musculus, the fruit fly Drosophila melanogaster, the worm Caenorhabditis elegans and the weed Arabidopsis thaliana [1]. In the last 10 years genomic resources have revolutionized...

  • Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies. Aguileta, G.; Marthey, S.; Chiapello, H.; Lebrun, M.-H.; Rodolphe, F.; Fournier, E.; Gendrault-Jacquemard, A.; Giraud, T. // Systematic Biology;Aug2008, Vol. 57 Issue 4, p613 

    Phylogenies involving nonmodel species are based on a few genes, mostly chosen following historical or practical criteria. Because gene trees are sometimes incongruent with species trees, the resulting phylogenies may not accurately reflect the evolutionary relationships among species. The...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics