Adaptive evolution of the Retinoid X receptor in vertebrates

Retinoid X receptors (RXR) are transcription factors with important roles in development, reproduction, homeostasis, and cell differentiation. Different types of vertebrate RXRs (α (RXRA), ß (RXRB) and γ (RXRG)) have arisen from multiple duplication events. The adaptive evolution mechanism that has preserved duplicate RXR paralogs, as well as their role in development and adaptation, is thus far unknown. In this work, we have investigated different aspects of vertebrate RXR evolution. Codon based tests of positive selection identified that RXR was under significant positive selection immediately after the whole genome duplications in vertebrates. Amino acid based rate shift analysis also revealed significant rate shifts immediately after the whole genome duplications and functional divergence between all the pairs of RXRs. However, the extant RXR genes are highly conserved, particularly the helix involved in dimerization and the DNA-binding domain, but positively selected sites can nevertheless be found in domains for RXR regulation.

► Episodic positive selection following vertebrate whole genome duplications in RXRs. ► Functional divergence between all pairs of vertebrate RXRs detected. ► Extant RXR genes are highly conserved in dimerization and the DNA-binding domain. ► Lineage specific gene loss reduced the number of RXR genes in some teleost species.