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

• Published in: Journal of molecular evolution Vol. 89; no. 6; pp. 396 - 414
• Main Authors: Lewin, Thomas D., Royall, Amy H., Holland, Peter W. H.
• Format: Journal Article
• Language: English
• Published: New York Springer US 01.07.2021; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Biomedical and Life Sciences; Cell Biology; Conversion; Divergence; Evolution; Evolutionary Biology; Evolutionary genetics; Gene conversion; Genes; Genomes; Homeobox; Life Sciences; Mammals; Microbiology; Molecular evolution; Original; Original Article; Plant Genetics and Genomics; Plant Sciences; Positive selection; Reproduction (copying); Etchbox; Genome evolution; Positive selection; Tandem duplication; Homeodomain
• ISSN: 0022-2844; 1432-1432
• DOI: 10.1007/s00239-021-10012-6

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.