Abstract
BackgroundVertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Comparison of genomic organisation in different lineages can often allow the evolutionary history of such regions to be traced. A classic example of this is the Hox genes, where the presence of a single continuous Hox cluster in amphioxus and four vertebrate clusters has allowed the genomic evolution of this region to be established. Fox transcription factors of the C, F, L1 and Q1 classes are also organised in clusters in both amphioxus and humans. However in contrast to the Hox genes, only two clusters of paralogous Fox genes have so far been identified in the Human genome and the organisation in other vertebrates is unknown.ResultsTo uncover the evolutionary history of the Fox clusters, we report on the comparative genomics of these loci. We demonstrate two further paralogous regions in the Human genome, and identify orthologous regions in mammalian, chicken, frog and teleost genomes, timing the duplications to before the separation of the actinopterygian and sarcopterygian lineages. An additional Fox class, FoxS, was also found to reside in this duplicated genomic region.ConclusionComparison of loci identifies the pattern of gene duplication, loss and cluster break up through multiple lineages, and suggests FoxS1 is a likely remnant of Fox cluster duplication.
Highlights
Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes
The Neighbour of COX (NOC) genes are found on the chromosome 16 and 14 (NOC4 and NOC9) and the C Oxidase Subunit 4 (COX4) genes are found on chromosome 16 and 20 (COX4I1 and COX4I2 respectively) though their exact positions relative to the other genes differ
Genomic organisation of human (Hs) Fox cluster paralogons and the putative orthologous counterparts we have identified in Mus musculus (Mm), Xenopus tropicalis (Xt), Gallus gallus (Gg), Danio rerio (Dr), Tetraodon nigroviridis (Tn) and Fugu rubripes (Fr)
Summary
Vertebrate genomes contain numerous duplicate genes, many of which are organised into paralagous regions indicating duplication of linked groups of genes. Phylogenetic analysis of the forkhead domains has lead to placement of most of these genes into 20 subclasses named FoxA to FoxS, with a small number of 'orphan' genes of unclear relationships defying classification [5,6]. These studies show vertebrate genomes contain more Fox genes than the genomes of other animals, suggesting an expansion that mirrors the increase in gene numbers seen for other gene families [7]. The 2R hypothesis predicts that a 1:4 ratio of genes should have been present in an ancestral vertebrate when compared to an invertebrate, and that in molecular (page number not for citation purposes)
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