Phylogenetic relationships of B-related phytochromes in the Brassicaceae: Redundancy and the persistence of phytochrome D

Plants use phytochrome (phy) photoreceptors to detect and respond to changes in the quantities and proportions of red (R) and far-red (FR) light in their environments. The principal mediators of responses to R and FR in Arabidopsis thaliana are phyA and phyB, which are found in all angiosperms surveyed. The present study is concerned with a phytochrome gene pair in Arabidopsis, PHYB and PHYD, which are of relatively recent origin, share high sequence identity, and are partially redundant. Our data suggest that the duplication occurred after the mustard family (Brassicaceae) diverged from its closest relatives but before the radiation of extant Brassicaceae, and that both copies have persisted for up to 40 myr. We detected no evidence of positive selection in the divergence of PHYD from PHYB; the evolution of both sequences is constrained by purifying selection. Levels of diversity at both loci are among the lowest observed at nuclear genes in A. thaliana. In common with other loci in A. thaliana, PHYB and PHYD showed elevated levels of intraspecific replacement variation, and each showed an excess of rare nucleotide polymorphisms, consistent with a recent, rapid population expansion. Our results are consistent with the functional importance of amino acid divergence in the central regions of phyB and phyD and suggest specific sites for mutagenesis that may yield insights into the functional differences of phyB and phyD.