The dynamics of vertebrate homeobox gene evolution: gain and loss of genes in mouse and human lineages

Ying-Fu Zhong,Peter Wh Holland

doi:10.1186/1471-2148-11-169

Abstract

BackgroundHomeobox genes are a large and diverse group of genes, many of which play important roles in transcriptional regulation during embryonic development. Comparison of homeobox genes between species may provide insights into the evolution of developmental mechanisms.ResultsHere we report an extensive survey of human and mouse homeobox genes based on their most recent genome assemblies, providing the first comprehensive analysis of mouse homeobox genes and updating an earlier survey of human homeobox genes. In total we recognize 333 human homeobox loci comprising 255 probable genes and 78 probable pseudogenes, and 324 mouse homeobox loci comprising 279 probable genes and 45 probable pseudogenes (accessible at http://homeodb.zoo.ox.ac.uk). Comparison to partial genome sequences from other species allows us to resolve which differences are due to gain of genes and which are due to gene losses.ConclusionsWe find there has been much more homeobox gene loss in the rodent evolutionary lineage than in the primate lineage. While humans have lost only the Msx3 gene, mice have lost Ventx, Argfx, Dprx, Shox, Rax2, LOC647589, Tprx1 and Nanognb. This analysis provides insight into the patterns of homeobox gene evolution in the mammals, and a step towards relating genomic evolution to phenotypic evolution.

Highlights

Homeobox genes are a large and diverse group of genes, many of which play important roles in transcriptional regulation during embryonic development
Far less has been documented about the dynamics of homeobox gene evolution within the vertebrates, several studies focussed on individual genes or gene families have highlighted occasional gene duplications and gene losses
Human homeobox gene repertoire We identified 333 homeobox loci in the human genome, including 255 probable functional genes and 78 probable pseudogenes (Table 1; Additional File 1)

Summary

Introduction

Homeobox genes are a large and diverse group of genes, many of which play important roles in transcriptional regulation during embryonic development. Homeobox genes comprise a large and diverse group of genes, most of which are thought to act as transcription factors. There has been much interest in elucidating the evolutionary history of homeobox genes, partly to ascertain whether evolutionary changes in animal body organisation are reflected in changes to the homeobox gene repertoire of animals It is known, for example, that the emergence of vertebrates from their invertebrate chordate ancestors was accompanied by an expansion in the number of homeobox genes, from around 100 to over 200, through genome duplication plus retention of duplicated genes [6]. Far less has been documented about the dynamics of homeobox gene evolution within the vertebrates, several studies focussed on individual genes or gene families have highlighted occasional gene duplications and gene losses

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