Transcriptome analysis reveals enrichment of genes associated with auditory system in swimbladder of channel catfish

Yujia Yang, Xiaozhu Wang, Yang Liu, Qiang Fu, Changxu Tian, Chenglong Wu, Huitong Shi, Zihao Yuan, Suxu Tan, Shikai Liu, Dongya Gao, Rex Dunham, Zhanjian "John" Liu

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

In aquatic organisms, hearing is an important sense for acoustic communications and detection of sound-emitting predators and prey. Channel catfish is a dominant aquaculture species in the United States. As channel catfish can hear sounds of relatively high frequency, it serves as a good model for study auditory mechanisms. In catfishes, Weberian ossicles connect the swimbladder to the inner ear to transfer the forced vibrations and improve hearing ability. In this study, we examined the transcriptional profiles of channel catfish swimbladder and other four tissues (gill, liver, skin, and intestine). We identified a total of 1777 genes that exhibited preferential expression pattern in swimbladder of channel catfish. Based on Gene Ontology enrichment analysis, many of swimbladder-enriched genes were categorized into sensory perception of sound, auditory behavior, response to auditory stimulus, or detection of mechanical stimulus involved in sensory perception of sound, such as coch, kcnq4, sptbn1, sptbn4, dnm1, ush2a, and col11a1. Six signaling pathways associated with hearing (Glutamatergic synapse, GABAergic synapse pathways, Axon guidance, cAMP signaling pathway, Ionotropic glutamate receptor pathway, and Metabotropic glutamate receptor group III pathway) were over-represented in KEGG and PANTHER databases. Protein interaction prediction revealed an interactive relationship among the swimbladder-enriched genes and genes involved in sensory perception of sound. This study identified a set of genes and signaling pathways associated with auditory system in the swimbladder of channel catfish and provide resources for further study on the biological and physiological roles in catfish swimbladder.

Original languageEnglish (US)
Pages (from-to)30-39
Number of pages10
JournalComparative Biochemistry and Physiology - Part D: Genomics and Proteomics
Volume27
DOIs
StatePublished - Sep 1 2018

Fingerprint

Air Sacs
Ictaluridae
Gene Expression Profiling
Genes
Acoustic waves
Audition
Hearing
Catfishes
Synapses
Aquatic organisms
Ionotropic Glutamate Receptors
Aquaculture
Metabotropic Glutamate Receptors
Auditory Perception
Aquatic Organisms
Gene Ontology
Aptitude
Liver
Inner Ear
Ontology

Keywords

  • Auditory system
  • Fish
  • Genome
  • Swimbladder
  • Transcriptome

ASJC Scopus subject areas

  • Biochemistry
  • Physiology
  • Molecular Biology
  • Genetics

Cite this

Transcriptome analysis reveals enrichment of genes associated with auditory system in swimbladder of channel catfish. / Yang, Yujia; Wang, Xiaozhu; Liu, Yang; Fu, Qiang; Tian, Changxu; Wu, Chenglong; Shi, Huitong; Yuan, Zihao; Tan, Suxu; Liu, Shikai; Gao, Dongya; Dunham, Rex; Liu, Zhanjian "John".

In: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, Vol. 27, 01.09.2018, p. 30-39.

Research output: Contribution to journalArticle

Yang, Yujia ; Wang, Xiaozhu ; Liu, Yang ; Fu, Qiang ; Tian, Changxu ; Wu, Chenglong ; Shi, Huitong ; Yuan, Zihao ; Tan, Suxu ; Liu, Shikai ; Gao, Dongya ; Dunham, Rex ; Liu, Zhanjian "John". / Transcriptome analysis reveals enrichment of genes associated with auditory system in swimbladder of channel catfish. In: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics. 2018 ; Vol. 27. pp. 30-39.
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AU - Fu, Qiang

AU - Tian, Changxu

AU - Wu, Chenglong

AU - Shi, Huitong

AU - Yuan, Zihao

AU - Tan, Suxu

AU - Liu, Shikai

AU - Gao, Dongya

AU - Dunham, Rex

AU - Liu, Zhanjian "John"

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AB - In aquatic organisms, hearing is an important sense for acoustic communications and detection of sound-emitting predators and prey. Channel catfish is a dominant aquaculture species in the United States. As channel catfish can hear sounds of relatively high frequency, it serves as a good model for study auditory mechanisms. In catfishes, Weberian ossicles connect the swimbladder to the inner ear to transfer the forced vibrations and improve hearing ability. In this study, we examined the transcriptional profiles of channel catfish swimbladder and other four tissues (gill, liver, skin, and intestine). We identified a total of 1777 genes that exhibited preferential expression pattern in swimbladder of channel catfish. Based on Gene Ontology enrichment analysis, many of swimbladder-enriched genes were categorized into sensory perception of sound, auditory behavior, response to auditory stimulus, or detection of mechanical stimulus involved in sensory perception of sound, such as coch, kcnq4, sptbn1, sptbn4, dnm1, ush2a, and col11a1. Six signaling pathways associated with hearing (Glutamatergic synapse, GABAergic synapse pathways, Axon guidance, cAMP signaling pathway, Ionotropic glutamate receptor pathway, and Metabotropic glutamate receptor group III pathway) were over-represented in KEGG and PANTHER databases. Protein interaction prediction revealed an interactive relationship among the swimbladder-enriched genes and genes involved in sensory perception of sound. This study identified a set of genes and signaling pathways associated with auditory system in the swimbladder of channel catfish and provide resources for further study on the biological and physiological roles in catfish swimbladder.

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KW - Fish

KW - Genome

KW - Swimbladder

KW - Transcriptome

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