Identification and Characterization of microRNA during Bemisia tabaci Infestations in Solanum lycopersicum and Solanum habrochaites

MicroRNAs (miRNAs) are a class of small non-coding RNAs that can regulate target gene expression during many plant growth and development processes. In recent years, several studies identified the miRNAs involved in fruit development, leaf development, and abiotic responses in tomato. However, little is known about the miRNAs that respond to insect attack. Here, miRNAs were identified by high-throughput sequencing at different stages after infections by the whitefly Bemisia tabaci in Solanum lycopersicum and Solanum habrochaites, which are susceptible and resistant to whitefly, respectively. A total of 44 known miRNA families were identified, and 33 were shared between the two species. Among these, 13 miRNA families were newly reported in tomato. After strict filtering, some novel miRNAs were also discovered. The global expression patterns of the miRNAs exhibited were different between the two species, reflecting their different responses and resistance levels to whitefly attack. Some of the predicted target genes of differentially expressed miRNAs may be involved in responding to, and defending against, diseases and insects. Thus, plant miRNAs are important in the responses to, and resistance against, insects and provide a useful resource for further investigations into the mechanism of miRNA-mediated plant–insect interactions.