Genome-wide identification and analysis of the molecular evolution and expression of type-A response regulator genes in Populus deltoids

Abstract

Cytokinins have vital effects on various plant development-related processes. Type-A response regulators (RRs) are among the most important regulators in the cytokinin signaling pathway. Specifically, RR genes are the primary cytokinin-responsive genes, encode negative regulators of cytokinin signaling. Similar sex-determining mechanisms involving a type-A RR homolog have recently been identified in sister genera Populus and Salix. Here, we aimed to identify and characterize type-A RR gene family members in Populus deltoides. On the basis of the conserved receiver domain and phylogenetic analysis, we identified 9, 11, and 14 type-A RR genes were identified in P. deltoides, Populus trichocarpa, and Salix suchowensis, respectively. The exon-intron organization and chromosomal locations of these genes in P. deltoides as well as the characteristics of the encoded proteins were analyzed in detail. Gene duplication events, molecular evolution, and phylogenetic relationships were analyzed for all identified type-A RR genes along with 10 Arabidopsis thaliana homologs. These results indicated that the expansion of the type-A RR gene family was primarily due to whole-genome and segmental duplication events. The collinear type-A ARR pairs in A. thaliana were all derived from the α-whole-genome duplication (WGD) event, whereas those in the three Salicaceae species were divided into two groups, one comprising 10 pairs derived from the p-WGD event and the other consisting of 11 pairs derived from the γ-WGD event or a more ancient duplication event. All of the duplicated paralogous gene pairs had undergone purifying selection. Although different type-A RR paralogs experienced different selection pressures, convergent evolution was detected within the receiver domain-encoding sequence, indicative of the importance of this domain for the phosphorelay-related function of the encoded proteins. Three type-A RR genes (PdRR9, PtRR11, and SsRR12) associated with sex determination in Salicaceae species formed a small subclade that lacked A. thaliana counterparts. Evaluation of gene expression in vegetative tissues and at different floral developmental stages in P. deltoides revealed the specific spatiotemporal expression of each PdRR gene, with two (PdRR8 and PdRR9) of the nine PdRR genes exhibiting the opposite sex-biased expression patterns. Diverse expression levels were detected between all eight paralogous PdRR pairs. These findings support future research to elucidate the functional divergence of type-A RR genes.