Origin and evolution of the Rax homeobox gene by comprehensive evolutionary analysis

Abstract

Rax is one of the key transcription factors crucial for vertebrate eye development. In this study, we conducted comprehensive evolutionary analysis of Rax. We found that Bilateria and Cnidaria possess Rax, but Placozoa, Porifera, and Ctenophora do not, implying that the origin of the Rax gene dates back to the common ancestor of Cnidaria and Bilateria. The results of molecular phylogenetic and synteny analyses on Rax loci between jawed and jawless vertebrates indicate that segmental duplication of the Rax locus occurred in an early common ancestor of jawed vertebrates, resulting in two Rax paralogs in jawed vertebrates, Rax and Rax2. By analyzing 86 mammalian genomes from all four major groups of mammals, we found that at least five independent Rax2 gene loss events occurred in mammals. This study may provide novel insights into the evolution of the eye.

The rax homeobox gene is mutated in the eyeless axolotl, Ambystoma mexicanum

“…Homozygous Rax ‐null mice die at birth with brain and craniofacial malformations 64 ; however, inbred eyeless mice carrying a hypomorphic allele ( ey1 , Rax M10L ) are viable and fertile 65 . There are two vertebrate Rax families, which arose through ancestral whole genome duplications, WGD 66,67 . In partially tetraploid species ( Xenopus laevis , teleost fish), these paralogs are further duplicated.…”

“…In zebrafish, for example, rx3 is expressed in the anterior neural plate, optic vesicles, and forebrain, and corresponds to mouse Rax , whereas rx1 and rx2 are mainly localized to the neuroretina 68 . The orthologous gene (raxL, RxL, RAX2) promotes photoreceptor differentiation in chick, Xenopus and humans, 69‐73 but was lost in at least five mammalian lineages, including rodents 67 . RAX2 coding mutations cause retinal degeneration in humans 74,75 and an rx1 regulatory deletion underlies the large natural variation in cone opsin expression among Lake Malawi cichlid species with diverse visual sensitivities 76 …”

“…dor, dorsal; ven, ventral; dh, dorsal hypothalamus; le, lens; on, optic nerve; ph, pharynx; ret, retina; rpe, retinal pigment epithelium; tc, tectum; vh, ventral hypothalamus; disorg ret, disorganized retina; scale bars, 200 μm genome duplications, WGD. 66,67 In partially tetraploid species (Xenopus laevis, teleost fish), these paralogs are further duplicated. In zebrafish, for example, rx3 is expressed in the anterior neural plate, optic vesicles, and forebrain, and corresponds to mouse Rax, whereas rx1 and rx2 are mainly localized to the neuroretina.…”

“…68 The orthologous gene (raxL, RxL, RAX2) promotes photoreceptor differentiation in chick, Xenopus and humans, [69][70][71][72][73] but was lost in at least five mammalian lineages, including rodents. 67 RAX2 coding mutations cause retinal degeneration in humans 74,75 and an rx1 regulatory deletion underlies the large natural variation in cone opsin expression among Lake Malawi cichlid species with diverse visual sensitivities. 76 To test these candidates, we intercrossed carriers and prepared genomic DNA from F2 larvae, of which approximately 25% were eyeless.…”

Construction and characterization of EGFP reporter plasmid harboring putative human RAX promoter for in vitro monitoring of retinal progenitor cells identity

“…However, a more direct alternative is to use the advantage of a fluorescent reporter under control of a specific retinal promoter [ 8 ]. Retina and anterior neural fold homeobox gene ( RAX ) is one of the initial genes expressed in prospective retina derived from the anterior neural plate [ 9 ]. RAX transcription factor consists of two conserved domains of homeodomain proteins.…”