Transcriptome sequencing of cochleae from constant-frequency and frequency-modulated echolocating bats

Abstract

Echolocating bats are fascinating for their ability to ‘see’ the world in the darkness. Ultrahigh frequency hearing is essential for echolocation. In this study we collected cochlear tissues from constant-frequency (CF) bats (two subspecies of Rhinolophus affinis, Rhinolophidae) and frequency-modulated (FM) bats (Myotis ricketti, Vespertilionidae) and applied PacBio single-molecule real-time isoform sequencing (Iso-seq) technology to generate the full-length (FL) transcriptomes for the three taxa. In total of 10103, 9676 and 10504 non-redundant FL transcripts for R. a. hainanus, R. a. himalayanus and Myotis ricketti were obtained respectively. These data present a comprehensive list of transcripts involved in ultrahigh frequency hearing of echolocating bats including 26342 FL transcripts, 24833 of which are annotated by public databases. No further comparative analyses were performed on the current data in this study. This data can be reused to quantify gene or transcript expression, assess the level of alternative splicing, identify novel transcripts and improve genome annotation of bat species.

Full-Length Transcriptome of Myotis pilosus as a Reference Resource and Mining of Auditory and Immune Related Genes

“…These physiological processes are related to the adaptive evolution of echolocation and high-frequency hearing in laryngeal echolocation bats [20], but more transcripts directly related to auditory perception were not detected, possibly due to the specificity of cochlear tissue resulting in relatively few genes detected in the cochlea. Ma et al [10]. reported a relatively low quality of transcriptome assembly in the cochlea due to the highly specialized cochlear tissue, and the same results were also reported in a single-cell RNA-seq study of the mouse cochlea [21].…”

“…The analysis of transcriptome completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO) showed that 39.3% (385) were complete duplicated BUSCOs; 40.3% (395) were complete single-copy BUSCOs; 1.7% (17) were fragmented BUSCO archetypes, and 18.5% (181) were missing BUSCOs (Figure S2). We also discovered that CCS length was longer than in other bats such as Rhinolophus afnis hainanus and Rhinolophus afnis himalayanus (Figure S3) [10].…”

“…The sequencing of the skin tissue of the marine mammal Sperm whale [8] and the sequencing of the head kidney tissue of Atlantic salmon, for example, demonstrate that the broad applicability of the full-length transcriptome and the stable and efficient solution of the follow-up series requires the analysis of genomics [9]. Ma et al used the approach to perform full-length sequencing of the cochlear tissues of echolocating bats such as M. pilosus, providing only the transcriptome map and annotation information [10]. However, no further comparative analyses were performed.…”

The Genomics of Auditory Function and Disease

“…As transcriptomic analyses require tissue samples, most such studies to date have used tissues from animal models such as mice ( 71 , 84 , 100 , 145 ), rats ( 125 ), zebrafish ( 183 ), or chickens ( 11 ). Additional model organisms studied include Xenopus ( 130 ), bats ( 103 ), and guinea pigs ( 158 ). Nevertheless, the comparative analysis of cell types from the auditory systems of divergent organisms has proved priceless and has enabled the identification of evolutionarily conserved as well as divergent pathways.…”

Untargeted metabolomics of the cochleae from two laryngeally echolocating bats

“…Transcriptomic approaches have been usually used to uncover candidate genes and biological pathways underlying the genetic bases of adaptations for high-frequency hearing in echolocating bats ( Dong et al, 2013 ; Wang et al, 2018 ; Ma et al, 2020 ). A study involving comparative inner ear transcriptomic analysis between M. ricketti (FM echolocating bat) and Cynopterus sphinx (non-echolocating bat) demonstrated that the genes upregulated in Myotis ricketti were particularly associated with cochlear morphogenesis, inner ear morphogenesis, and sensory perception of sound categories, which are consistent with the morphological and physiological differentiation of the inner ear between these two species ( Dong et al, 2013 ).…”