MicroRNA regulation in echolocation call frequency variation of the intermediate horseshoe bat

miRNAs(microRNAs) are non coding small RNAs with a length of about 22 nt. They are considered to play an important regulatory role in mRNA post-transcription. This regulation may involve biological phenotypic differences, development, adaptation to the environment and so on. The call frequencies of R. affinis. hainanus and R. affins. himalayanus are about 71 kHz and 87 kHz respectively. miRNA may play a role in regulating gene expression and promoting the change of call frequency, but there are few related studies. Therefore, here, we explored the role of miRNA in the change of echolocation call frequency between two subspecies. Specifically, we first annotated 365 miRNAs in R. affinis cochlea using microRNA sequencing data, including 244 miRNAs present in the identified miRNAs library and 121 potential new miRNAs. Secondly, we analyzed the expression of miRNA and mRNA and found that 67 miRNAs were differentially expressed among subspecies. We predicted the target genes of these miRNAs and identified the negatively regulated miRNA-mRNA pairs and 834 genes involved. The results of functional annotation of the target genes showed that many GO terms were related to immunity, and some terms that might be related to hearing were also found, Such as cell response to environmental stimuli, cell response to biological stimuli and cochlear development, these important terms also contain some hearing related genes, such as KCNQ1, PIEZO1, OTOG, indicating that miRNA may play a regulatory role in the difference of call frequency. Thirdly, by looking for potential miRNAs unique only to echolocation bats and predicting their target genes, such as cell stimulation to the environment, which also shows that these miRNAs may be closely related to the difference of call frequency.