Abstract
The majority of homeobox genes are highly conserved across animals, but the eutherian-specific ETCHbox genes, embryonically expressed and highly divergent duplicates of CRX, are a notable exception. Here we compare the ETCHbox genes of 34 mammalian species, uncovering dynamic patterns of gene loss and tandem duplication, including the presence of a large tandem array of LEUTX loci in the genome of the European rabbit (Oryctolagus cuniculus). Despite extensive gene gain and loss, all sampled species possess at least two ETCHbox genes, suggesting their collective role is indispensable. We find evidence for positive selection and show that TPRX1 and TPRX2 have been the subject of repeated gene conversion across the Boreoeutheria, homogenising their sequences and preventing divergence, especially in the homeobox region. Together, these results are consistent with a model where mammalian ETCHbox genes are dynamic in evolution due to functional overlap, yet have collective indispensable roles.
Highlights
Homeobox genes encode a diverse set of transcription factors found across the Eukaryota, each of which has a characteristic DNA-binding homeodomain of around 60 amino acids (Duboule 1994; Derelle et al 2007; Holland et al 2007)
There are a smaller number of fast-evolving, taxon-specific homeobox genes found in some animals, including genes expressed during nematode (Bürglin and Cassata 2002; Mukherjee and Bürglin 2007), lepidopteran (Chai et al 2008; Ferguson et al 2014), spiralian (Paps et al 2015; Morino et al 2017) and mammalian (Maeso et al 2016) embryonic development
All genes are located in the same syntenic position as in humans, with Leucine-Twenty Homeobox (LEUTX), Tetra-Peptide Repeat Homeobox 1 (TPRX1), Tetra-Peptide Repeat Homeobox 2 (TPRX2) and Divergent Paired-Related Homeobox (DPRX) in a loose cluster on chromosome 18, and ARGFX separate from the cluster on chromosome 1
Summary
Homeobox genes encode a diverse set of transcription factors found across the Eukaryota, each of which has a characteristic DNA-binding homeodomain of around 60 amino acids (Duboule 1994; Derelle et al 2007; Holland et al 2007). There are a smaller number of fast-evolving, taxon-specific homeobox genes found in some animals, including genes expressed during nematode (Bürglin and Cassata 2002; Mukherjee and Bürglin 2007), lepidopteran (Chai et al 2008; Ferguson et al 2014), spiralian (Paps et al 2015; Morino et al 2017) and mammalian (Maeso et al 2016) embryonic development. We consider these genes to be fast-evolving on the basis of extensive amino acid change over relatively short timescales, following their origin by gene duplication. The amino acid divergence from the deduced parental gene is so great as to cloud insights into their origins, unless additional information such as chromosomal location is used
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