Comparative cochlear transcriptomics of echolocating bats provides new insights into different nervous activities of CF bat species

Hui Wang,Hanbo Zhao,Keping Sun,Jiang Feng,Xiaobin Huang

doi:10.1038/s41598-018-34333-7

Hui Wang, Hanbo Zhao + Show 3 more

Open Access

https://doi.org/10.1038/s41598-018-34333-7

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Abstract

The molecular mechanisms used by echolocating bats to deal with different ultrasonic signals remain to be revealed. Here, we utilised RNA-Seq data to conduct comparative cochlear transcriptomics to assess the variation of gene expression among bats with three types of echolocation: constant-frequency (CF) bats, frequency-modulated (FM) bats and click bats. Our results suggest larger differences in gene expression between CF and click bats than between CF and FM bats and small differences between FM and click bats. We identified 426 and 1,504 differentially expressed genes (DEGs) by the different methods as functionally important for CF bats, in that they showed consistent upregulation in the cochlea of two CF bats, relative to the levels in click and FM bats. Subsequently, downstream GO and KEGG enrichment analyses indicated that both the 426 and 1,504 gene sets were associated with changes in nervous activities in the cochleae of CF bats. In addition, another set of 1,764 DEGs were identified to have crucial hearing related physiological functions for laryngeally echolocating bats. Our study provides a comprehensive overview of the genetic basis of differences among echolocating bats, revealing different nervous system activities during auditory perception in the cochlea particularly in CF bats.

Highlights

The divergence of gene expression is an important component of molecular adaptation and an essential way to generate biological diversity[1,2,3]
To gain insights into the genetic bases underlying the diversity of echolocation evolved by different bat species, in this study, we explored the utility of next-generation sequencing technologies for comparative cochlear transcriptomics to assess the variation in gene expression among three types of echolocating bat: CF, FM and click bats
After filtering the adaptor sequences, regions containing “N” sequences and low-quality sequences, approximately 34.88, 33.65, 32.61 and 36.45 million clean reads were obtained for R. sinicus, A. stoliczkanus, T. melanopogon and R. leschenaultii, respectively (Table 1)

Summary

Introduction

The divergence of gene expression is an important component of molecular adaptation and an essential way to generate biological diversity[1,2,3]. CF bats have a special structure called the auditory fovea, a highly expanded frequency representation centralised to the constant frequency, which is present on the basilar membrane[20,21]. This enables CF bats to compensate for Doppler shifts of complete echo signals in order to maintain the audition of echoes within the auditory fovea, which is an important cochlear adaptation[22]. In the case of bats, to the best of our knowledge only one study has determined the genes differentially expressed in the inner ear between echolocating bats (FM type) and nonecholocating bats using RNA-Seq[28]. Our knowledge about the genetic bases of mechanisms in bat cochleae that underlie different echolocating types remains limited

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