Dynamic Molecular Evolution of Mammalian Homeobox Genes: Duplication, Loss, Divergence and Gene Conversion Sculpt PRD Class Repertoires

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.

PRD-Class Homeobox Genes in Bovine Early Embryos: Function, Evolution, and Overlapping Roles

“…Second, we constructed expression plasmids carrying bovine homeobox genes ARGFX or LEUTX driven by a constitutive promoter, each connected by a peptide linker to a C-terminal 3xFLAG tag to facilitate downstream analysis. We also constructed an expression plasmid carrying a mutant allele of ARGFX identified in the ARS-UCD1.2 reference genome ( Lewin et al 2021 ). This allele has a 13 base pair (bp) deletion before the homeodomain resulting in a frameshift and truncated predicted protein.…”

“…We previously identified a 13 bp deletion in the coding region of the ARGFX gene of the B. taurus reference genome ARS-UCD1.2 and showed that the indel is polymorphic, as several RNA-seq datasets exhibit the wild type (WT) allele ( Lewin et al 2021 ). Here, we investigate the frequency of the deletion allele and its effect on protein function.…”

“…The six ancestral ETCHbox genes ( ARGFX , DPRX , LEUTX , PARGFX , TPRX1 , and TPRX2 ) duplicated from the Otx-family gene CRX on the stem lineage leading to eutherians, and the ancestral eutherian ETCHbox repertoire likely consisted of one copy of each gene ( Maeso et al 2016 ). A curious property of the genes is their high propensity for duplication and loss, and the subsequent variation in the gene repertoires possessed by different eutherian species ( Maeso et al 2016 ; Royall et al 2018 ; Lewin et al 2021 ) ( fig. 1 ).…”

“…Indeed, M. musculus possesses a huge array of 66 Obox loci ( Royall et al 2018 ). The ETCHbox repertoire of European cattle ( Bos taurus ) is more similar to that of human, except that DPRX is a pseudogene and there is an extra TPRX duplicate ( Maeso et al 2016 ; Lewin et al 2021 ).…”

“…In addition to extensive gain and loss, ETCHbox genes exhibit a much faster rate of sequence change across the eutherians than do other homeobox genes ( Maeso et al 2016 ; Lewin et al 2021 ). They are an archetypal example of asymmetric evolution, as their “parent” CRX has been conserved while ETCHbox sequences have changed drastically ( Maeso et al 2016 ; Katayama et al 2018 ; Royall et al 2018 ; Lewin et al 2021 ). These features are unusual for homeobox genes, which are generally highly conserved because they perform key roles in embryonic development and tissue patterning ( Bürglin and Affolter 2016 ).…”