Genome-Wide Analysis of the R2R3-MYB Gene Family in × and Its Function Identification During Anthocyanins Biosynthesis in Pink-Flowered Strawberry.

The strawberry ( × ) is an economically important fruit throughout the world. The large gene family participates in a variety of plant functions, including anthocyanin biosynthesis. The present study is the first genome-wide analysis of the gene family in the octoploid strawberry and describes the identification and characterization of the family members using the recently sequenced × genome. Specifically, we aimed to identify the key MYBs involved in petal coloration in the pink-flowered strawberry, which increases its ornamental value. A comprehensive, genome-wide analysis of × was performed, investigating gene structures, phylogenic relationships, promoter regions, chromosomal locations, and collinearity. A total of 393 genes were identified in the × genome and divided into 36 subgroups based on phylogenetic analysis. Most genes with similar functions in the same subgroup exhibited similar exon-intron structures and motif compositions. These were unevenly distributed over 28 chromosomes. The expansion of the gene family in the × genome was found to be caused mainly by segmental duplication. The Ka/Ks analysis indicated that duplicated mostly experienced purifying selection and showed limited functional divergence after the duplication events. To elucidate which genes were associated with anthocyanin biosynthesis in the petals of the pink-flowered strawberry, we compared transcriptional changes in different flower developmental stages using RNA-seq. There were 131 differentially expressed genes identified in the petals, of which three genes, , , and , appeared likely, based on the phylogenetic analysis, to regulate anthocyanin biosynthesis. The qRT-PCR showed that these three genes were more highly expressed in petals than in other tissues (fruit, leaf, petiole and stolon) and their expressions were higher in red compared to pink and white petals. These results facilitate the clarification on the roles of the genes in petal coloration in the pink-flowered strawberry. This work provides useful information for further functional analysis on the gene family in × .