Characterization of <scp>microRNA</scp> and gene expression in the cochlea of an echolocating bat (<i>Rhinolophus affinis</i>)

Li, Qianqian; Chen, Wenli; Mao, Xiuguang

doi:10.1002/ece3.9025

Cited by 2 publications

(1 citation statement)

References 90 publications

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“…Sex differences in echolocation pulse frequency have been found in many bat species [13,14]. Studies of echolocation pulses usually focused on the cochlea which is essential for hearing and echolocation [15][16][17][18]. Horseshoe bats (Rhinolophus) comprise over 100 recognized species [19] and emit a constant frequency (CF) in echolocation pulses which can be accurately assessed by researchers [14].…”

Section: Introductionmentioning

confidence: 99%

Sex Differences in Cochlear Transcriptomes in Horseshoe Bats

Wu,

Duan,

Lan

et al. 2024

Animals

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Sexual dimorphism of calls is common in animals, whereas studies on the molecular basis underlying this phenotypic variation are still scarce. In this study, we used comparative transcriptomics of cochlea to investigate the sex-related difference in gene expression and alternative splicing in four Rhinolophus taxa. Based on 31 cochlear transcriptomes, we performed differential gene expression (DGE) and alternative splicing (AS) analyses between the sexes in each taxon. Consistent with the degree of difference in the echolocation pulse frequency between the sexes across the four taxa, we identified the largest number of differentially expressed genes (DEGs) and alternatively spliced genes (ASGs) in R. sinicus. However, we also detected multiple DEGs and ASGs in taxa without sexual differences in echolocation pulse frequency, suggesting that these genes might be related to other parameters of echolocation pulse rather than the frequency component. Some DEGs and ASGs are related to hearing loss or deafness genes in human or mice and they can be considered to be candidates associated with the sexual differences of echolocation pulse in bats. We also detected more than the expected overlap of DEGs and ASGs in two taxa. Overall, our current study supports the important roles of both DGE and AS in generating or maintaining sexual differences in animals.

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Section: Introductionmentioning

confidence: 99%

Sex Differences in Cochlear Transcriptomes in Horseshoe Bats

Wu,

Duan,

Lan

et al. 2024

Animals

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The roles of different gene expression regulators in acoustic variation in the intermediate horseshoe bat revealed by long-read and short-read RNA sequencing data

Li,

Wu,

Mao

2023

Current Zoology

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Gene expression changes contribute greatly to phenotypic variations in nature. Studying patterns of regulators of gene expression is important to fully understand the molecular mechanism underlying phenotypic variations. In horseshoe bats, the cochleae are finely tuned to echoes of call frequency. Here, using 2 recently diverged subspecies of the intermediate horseshoe bat (Rhinolophus affinis hainanus and R. a. himalayanus) with great acoustic variations as the system, we aim to explore relative roles of different regulators of gene expression (differential gene expression, alternative splicing (AS) and long non-coding RNAs (lncRNAs)) in phenotypic variation with a combination of Illumina short-read and Nanopore long-read RNA-seq data from the cochlea. Compared to R. a. hainanus, R. a. himalayanus exhibited much more upregulated differentially expressed genes (DEGs) and multiple of them may play important roles in the maintenance and damage repair of auditory hair cells. We identified 411 differentially expressed lncRNAs and their target DEGs upregulated in R. a. himalayanus were also mainly involved in a protective mechanism for auditory hair cells. Using 3 different methods of AS analysis, we identified several candidate alternatively spliced genes (ASGs) that expressed different isoforms which may be associated with acoustic divergence of the 2 subspecies. We observed significantly less overlap than expected between DEGs and ASGs, supporting complementary roles of differential gene expression and AS in generating phenotypic variations. Overall, our study highlights the importance of a combination of short-read and long-read RNA-seq data in examining the regulation of gene expression changes responsible for phenotypic variations.

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Characterization of microRNA and gene expression in the cochlea of an echolocating bat (Rhinolophus affinis)

Cited by 2 publications

References 90 publications

Sex Differences in Cochlear Transcriptomes in Horseshoe Bats

Sex Differences in Cochlear Transcriptomes in Horseshoe Bats

The roles of different gene expression regulators in acoustic variation in the intermediate horseshoe bat revealed by long-read and short-read RNA sequencing data

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