WRKY genes in black raspberry (Rubus occidentalis L.): duplicate and conquer

Abstract

WRKY transcription factors regulate several biological processes in plants, including responses to biotic stresses and tolerance to abiotic stresses, and are part of a gene superfamily in higher plants. There are many studies on the functions of WRKY proteins in several model species, aiming at identification and functional characterization, but there has not yet been a comprehensive analysis of the RoWRKY protein family in black raspberry (Rubus occidentalis L.) as shown here. In this study, the investigation of the complete genome of the black raspberry identified 62 RoWRKY genes that were evaluated and are unevenly distributed in all seven chromosomes. The proteins encoded by these genes were classified into four groups (I, II, III and IV), with those of group II divided into five subgroups (IIa - IIe) based on their conserved domains and zinc finger domain types. Motif analysis showed that all RoWRKYs contained one or two WRKY domains and that proteins from the same group had similar motif compositions. Five pairs of RoWRKY genes in segmental duplication and two pairs in tandem duplication were detected. Analysis of the structure of RoWRKY genes showed that they have 1–11 introns, with most RoWRKY genes consisting of two introns and three exons. A cis element analysis showed that all promoters of the RoWRKYs genes contain at least one cis stress-response element. Differential expression analysis of 10 samples of RNA-seq data, reviewed RoWRKY genes from black raspberry, show preferential or specific expression in tissue samples. These findings provide a complete overview of the evolution and modification of the RoWRKYs protein family, which will help the functional characterization of these proteins in the response to biotic and abiotic stresses of black raspberry.