Integration of DNA Methylation, MicroRNAome, Degradome, and Transcriptome Provides Insights into Petunia Anther Development

Abstract Petunia hybrida is an annual herb flower that is prevalently cultivated both in public landscaping and home gardening. Anthers are vital reproductive organs for plants, but the molecular mechanism controlling petunia anther development remains elusive. In this work, we combined DNA methylation, microRNAome, degradome, and transcriptome data to generate a comprehensive resource focused on exploring the complex molecular mechanism of petunia anther development. This study shows that DNA methylation could have an important impact in repressing the anther expressed genes in the late stages of anther maturation. A total of 8096 anther-preferential genes and 149 microRNAs (miRNAs) were identified that highly expressed in the five typical petunia anthers developmental stages. Gene Ontology enrichment analysis of differentially expressed genes as well as miRNAs target genes revealed that metabolic, cellular, and single-organism processes were significantly activated during the anther maturation processes. Moreover, a co-expression regulatory network for five typical anther development stages was constructed based on transcriptomic data, in which two hub transcription factors, PhERF48 and PhMS1, were demonstrated to be important regulatory genes for male fertility. Further more, two DNA demethylase proteins (PhDME and PhDML3) and three Methyl-CpG-binding-domain proteins (PhMBD2, PhMBD3, and PhMBD4) were identified as potential critical DNA methylation regulators in petunia anther development. Our results provide new knowledge regarding the regulatory mechanism of petunia anther development, which will support the breeding of novel sterile petunia lines in the future.