Comprehensive genomic analysis of the RNase T2 gene family in Rosaceae and expression analysis in Pyrus bretschneideri

Abstract

RNase T2s exist widely in eukaryotes and prokaryotes, playing various physiological roles in plants. At present, the genomes of Chinese white pear and six other Rosaceae fruit crops have been sequenced. However, no comprehensive analysis has investigated the evolutionary characteristics of the RNase T2 family in Rosaceae species. Here, 93 RNase T2s were identified in seven Rosaceae species (Pyrus bretschneideri, Rubus occidentalis, Fragaria vesca, Malus domestica, Prunus persica, Prunus avium, and Prunus mume). On the basis of phylogenetic analysis and structural characteristics, the RNase T2 family can be divided into four classes (I, II, III, and IV). Class IV is a new class first identified among seven Rosaceae species. Intron–exon analysis further revealed a homologous intron in RNase T2s except for class IV. Although purifying selection was the major force acting on the RNase T2 family, some positively selected sites and protein regions were still found in class IV sequences by using PAML and sliding windows. Tandem and proximal gene duplications made a major contribution to the expansion of the PbrRNase T2 family. Expression analysis identified some PbrRNase T2 genes highly expressed in pear and several transcription factors that might regulate these genes. In conclusion, the study of the RNase T2 family in seven Rosaceae species will help us to better understand the molecular evolution of RNase T2 genes and facilitate further functional analysis in the future.