Systematic analysis of the R2R3-MYB transcription factor gene family in Stevia rebaudiana

MYB transcription factor (TF) genes are crucial for modulating secondary metabolite biosynthesis in plants. Stevia is a valuable economic crop, and the steviol glycosides produced in its leaves are the most prevalent natural sweeteners. The present research offers a thorough genomic examination of Stevia's MYB TF gene superfamily. We identified 310 genes as putative MYB genes, out of which 176 R2R3-MYB genes were chosen for subsequent analysis. A comparative phylogenetic analysis classified these Stevia R2R3-MYB genes into nine subfamilies, with exon-intron structures and motif compositions strongly supporting this classification. Furthermore, due to its significant expansion, subfamily VIII was divided into 17 clades, and clade VIII-E was unique to Stevia. Synteny analysis revealed that the expansion of members in each subfamily, or each clade within subfamily VIII, was mainly facilitated by whole-genome duplication (WGD) as well as dispersed duplication events. Promoter detection identified multiple classes of cis-regulatory elements that are associated with responses to light, phytohormones, and environmental stressors. Expression analysis revealed that different subfamilies or clades of R2R3-MYB genes exhibited diverse expression profiles across multiple tissue types and at various phases of leaf growth. Meanwhile, SrMYB32, 15, 114/168, 163, 125/126, 33, 153/154 showed significant expression differences in two Stevia varieties with different steviol glycosides content. The present research lays a firm basis for future functional analysis of R2R3-MYBs that play important roles in the biosynthesis of steviol glycosides.