Identification of miRNA targets in eggplant in response to Verticillium dahliae by degradome sequencing

Verticillium wilt is a vascular disease caused by Verticillium dahliae, which has a serious impact on the yield and quality of eggplant. MiRNAs regulates plant growth, development, environmental adaptation and other life activities by controlling the expression of target genes. Although miRNAs have been systematically studied by high-throughput sequencing in eggplant (Solanum melongena L.), their target genes are not identified systematically, which would provide the basis for exploring the mechanism of miRNA mediated gene regulation in response to Verticillium wilt of eggplant. In this study, degradome sequencing was performed using two libraries separately prepared from mock-inoculated and V. dahliae-inoculated seedlings of eggplants. A total of 122 target genes for 49 miRNAs families were identified. Of them, 62 target genes were significantly induced by V. dahliae, including 34 targets were found only in the inoculated seedlings library and 28 targets were shown to be differentially expressed between both two libraries. Further analysis showed that a conserved miRNA could target various genes ranging from one up to 15 or a target gene could be cleaved by 1-5 different miRNAs. QRT-PCR analysis on five miRNAs and their target genes confirmed the reliability of the degradome sequencing data. GO analysis revealed that target genes owned diverse biological functions and transcription regulation was the largest functional category. Analysis on KEGG showed that target genes were mainly involved in plant-pathogen interaction pathway and plant hormone signal transduction pathway to resist disease. This result will provide basic information for further studying the regulatory mechanism of eggplant miRNAs in response to Verticillium wilt infection.