Tables of microRNA and gene expression of an echolocating bat

MicroRNAs (miRNAs) are important post-transcriptional regulators of gene
expression and play key roles in many biological processes, such as
development and response to multiple stresses. However, little is known
about their roles in generating novel phenotypes and phenotypic variation
during the course of animal evolution. Here, we, for the first time,
characterized the miRNAs of the cochlea in an echolocating bat
(Rhinolophus affinis). We sampled eight individuals from two R. affinis
subspecies with significant echolocation call frequency differences. We
identified 365 miRNAs and 121 of them were novel. By searching sequences
of these miRNAs precursors in multiple high-quality mammal genomes, no
specific miRNAs were found to be shared by all echolocating mammals.
Together with the matched mRNA-seq data, we identified 1,766
differentially expressed genes (DEGs) between the two subspecies and 555
of them were negatively regulated by differentially expressed miRNAs
(DEMs). We found that almost half of known hearing genes in the list of
all DEGs were regulated negatively by DEMs, suggesting an important role
of miRNAs in call frequency variation of the two subspecies. These
targeted DEGs included several important hearing genes (e.g. Piezo1,
Piezo2 and CDH23) that have been shown to be important in ultrasonic
hearing of echolocating mammals.