Abstract
BackgroundThe iroquois (iro/Irx) genes encode transcriptional regulators that belong to the TALE superclass of homeodomain proteins and have key functions during development in both vertebrates and insects. The Irx genes occur in one or two genomic clusters containing three genes each within the Drosophila and several vertebrate genomes, respectively. The similar genomic organization in Drosophila and vertebrates is widely considered as a result of convergent evolution, due to independent tandem gene duplications. In this study, we investigate the evolutionary history of the Irx genes at the scale of the whole metazoan kingdom.ResultsWe identified in silico the putative full complement of Irx genes in the sequenced genomes of 36 different species representative of the main metazoan lineages, including non bilaterian species, several arthropods, non vertebrate chordates, and a basal vertebrate, the sea lamprey. We performed extensive phylogenetic analyses of the identified Irx genes and defined their genomic organizations. We found that, in most species, there are several Irx genes, these genes form two to four gene clusters, and the Irx genes are physically linked to a structurally and functionally unrelated gene known as CG10632 in Drosophila.ConclusionThree main conclusions can be drawn from our study. First, an Irx cluster composed of two genes, araucan/caupolican and mirror, is ancestral to the crustaceans+insects clade and has been strongly conserved in this clade. Second, three Irx genes were probably present in the last common ancestor of vertebrates and the duplication that has given rise to the six genes organized into two clusters found in most vertebrates, likely occurred in the gnathostome lineage after its separation from sea lampreys. Third, the clustered organization of the Irx genes in various evolutionary lineages may represent an exceptional case of convergent evolution or may point to the existence of an Irx gene cluster ancestral to bilaterians.
Highlights
The iroquois genes encode transcriptional regulators that belong to the TALE superclass of homeodomain proteins and have key functions during development in both vertebrates and insects
[3,8,9,12,13]] and more than one Irx gene is observed in most bilaterian species, we wondered whether similar clustering may be found in all these species. We found these genes organized into clusters in most species (20 out of 28 bilaterian species; for the others, either there is a single gene, or the current state of the genome assembly does not allow to establish potential clusters due to very small genomic scaffolds; Figures 1 and 6; the data used to construct Figure 6 can be found in Additional file 4)
We present here a large-scale phylogenomic analysis of the Irx and Mkx genes that extends a previously published study on the evolution of Irx genes in metazoans
Summary
The iroquois (iro/Irx) genes encode transcriptional regulators that belong to the TALE superclass of homeodomain proteins and have key functions during development in both vertebrates and insects. We investigate the evolutionary history of the Irx genes at the scale of the whole metazoan kingdom. Gene duplication clearly plays an important role in generating molecular diversity. In some cases, these duplications arise through the duplication of entire chromosomes or large chromosomal regions. Duplications appear as tandem copies of genes, which form clusters of evolutionarily related genes. When did these clusters form and what are the evolutionary forces that act to maintain these genes clustered? As complete genome sequences become available, we can begin to track the evolutionary history of many other clusters of evolutionarily related genes. One gene family which displays genomic linkage of unknown functionality and origin is the iroquois (iro/Irx) family
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