Characterization and comparative profiling of miRNAs among various castes of Reticuliterms flavipes

microRNAs (miRNAs) are short RNA molecules that regulate gene expression at post-transcriptional level in eukaryotes. Most research efforts on insect miRNA have been focused on holometabolous insects, owing to the availability of their complete genomes. On the other hand, miRNA studies on hemimetabolans were largely missing except for a handful of recent reports on Locusta migratoria and Acyrthosiphon pisum. Our model organism, the eastern subterranean termite Reticulitermes flavipes, is the most common termite found in North America. Termites have been attracting increasing attention in ecological, economical and biological fields due to their eusocial and wood-eating characteristics. Hence, the profiling of R. flavipes miRNAs not only offered a novel perspective to study the biology of the otherwise cryptic termites, but also provided insights on the function and evolution of miRNA in hemimetabolans. Using small RNA high-throughput sequencing data, we characterized phylogenetically conserved miRNAs as well as termite-specific miRNAs in R. flavipes. To overcome the lacking of termite genome sequences, conserved miRNAs were identified by sequence similarity against miRBase whereas termite-specific novel miRNAs were detected by searching legitimate putative precursor miRNAs in R. flavipes EST database. Comparisons among worker, soldier, queen and other developing stages of termites exhibited great variability in miRNA expression profile, suggesting that miRNAs may play a critical role in larval development as well as caste transition in termites.