Integration of DNA methylation, small RNAs, degradome and transcriptome sequencing in petunia hybrida uncovers a complex regulatory network and provides insights into anther development

Petunia hybrida, prevalently cultivated in landscaping, is a dicotyledonous herbaceous flower of high ornamental value. Annually, there is a massive worldwide market demand for petunia seeds. The normal development of anther is the necessary prerequisite for the plants to generate seeds. However, the knowledge of petunia anther development processes is still limited. Here, we combined analyses of the transcriptomics, DNA methylation, small RNAs, and the degradome to generate a comprehensive resource focused on the the molecular mechanism of petunia anther development. The results showed that the development of petunia anthers was accompanied by elevated levels of DNA methylation, suggesting that DNA methylation may regulate the anther development. A total of 33,029 unigenes and 2,053 miRNAs were identified by deep sequencing, and 1,256 genes were differentially expressed during tapetum development. In addition, prediction and analysis of miRNA targeted genes suggested that miR160a/b/c and miR597 participated in egulation of anther development through the target genes, respectively. Moreover, a co-expression regulatory network for the tapetum development was constructed based on multiomics analysis, and two hub TFs, phERF48 and phMS1, were uncovered and function validated using VIGS. Our findings revealed new insights into the regulation mechanism of petunia anther development, which will support the breeding of new sterile lines of petunia in the future.