Characterization and Divergence Analysis of Duplicated R2R3-MYB Genes in Watermelon

Watermelon (Citrullus lanatus) is an economically important cucurbit (Cucurbitaceae) crop cultivated globally for its nutritional benefits. Fruit development in watermelon is characterized by fast fruit expansion attributed to unique biological processes. Myeloblastosis (MYB) family genes play important roles in plant growth and development, especially R2R3-MYB-type genes. However, the evolution of R2R3-MYB family genes in the watermelon genome and whether they participate in the regulation of watermelon fruit development remain unknown. To address these questions, duplication modes of R2R3-MYB family genes were identified and their expression profiles were investigated during watermelon fruit development. A total of 48 duplicated gene pairs were identified among the 89 R2R3-MYBs in watermelon. Segmental and transposed duplication events play major roles in the R2R3-MYB family gene expansion process. The ratio of nonsynonymous mutation and synonymous mutation analysis indicated that all the duplicated R2R3-MYBs experienced negative selection. Gene structures and cis-element compositions in promoter sequences exhibited abundant divergences between the R2R3-MYB duplicated genes. Transcriptome analyses of seed, rind, and flesh during fruit development showed that only two duplicated gene pairs had significantly similar expression patterns, whereas divergent expression profiles were found between the remaining duplicated gene pairs. Tissue-specific and development stage-specific divergent expression patterns demonstrated that neo-functionalization occurred between watermelon R2R3-MYB duplicated genes. The current study provides valuable information for further functional analyses of R2R3-MYBs in watermelon.