Comprehensive analysis of the R2R3-MYB transcription factor gene family in Populus trichocarpa

Abstract

The MYB proteins constitute one of the most important transcription factor families in plants, and are involved in various plant-specific processes, such as development, metabolism, and stress responses. Populus is a major industrial tree species for building, papermaking, furniture, and biofuels. This study presents a systematic genome-wide analysis of the MYB family in Populus. In total, 354 genes were identified as candidate MYB genes and divided into four subfamilies, of which 196 R2R3-MYBs were then investigated further. These Populus R2R3-MYBs were classified into 45 subgroups based on comparative phylogenetic analysis with Arabidopsis thaliana, which were solidly backed by highly conserved intron/exon structures and motifs outside the MYB domain. Many types of cis-regulatory elements were detected in the promoter region, mainly related to development, light response, phytohormone response, and environmental stress response, directly reflecting the functional diversification of Populus R2R3-MYB members. Collinearity analysis revealed that purifying selection became a primary driving force during R2R3-MYB gene evolution, and that segmental and tandem duplications played critical roles in the expansion of this family in Populus. Expression profiles from publicly available RNA-Seq data and real-time quantitative PCR analysis displayed distinct expression patterns of PtrMYB genes among tissues and organs, as well as in response to drought stress. Overall, this work establishes a solid foundation for further functional dissection of MYB gene families, as well as breeding improvement for stress resistance and wood properties in Populus.