Comparative transcriptome analysis of the swimbladder reveals expression signatures in response to low oxygen stress in channel catfish, ictalurus punctatus

Yujia Yang, Qiang Fu, Xiaozhu Wang, Yang Liu, Qifan Zeng, Yun Li, Sen Gao, Lisui Bao, Shikai Liu, Dongya Gao, Rex Dunham, Zhanjian "John" Liu

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Channel catfish is the leading aquaculture species in the US, and one of the reasons for its application in aquaculture is its relatively high tolerance against hypoxia. However, hypoxia can still cause huge economic losses to the catfish industry. Studies on hypoxia tolerance, therefore, are important for aquaculture. Fish swimbladder has been considered as an accessory respiration organ surrounded by a dense capillary countercurrent exchange system. In this regard, we conducted RNA-Seq analysis with swimbladder samples of catfish under hypoxic and normal conditions to determine if swimbladder was responsive to low oxygen treatment and to reveal genes, their expression patterns, and pathways involved in hypoxia responses in catfish. A total of 155 differentially expressed genes (DEGs) were identified from swimbladder of adult catfish, whereas a total of 2,127 DEGs were identified from swimbladder of fingerling catfish under hypoxic condition as compared with untreated controls. Subsequent pathway analysis revealed that many DEGs under hypoxia were involved in HIF signaling pathway (nos2, eno2, camk2d2, prkcb, cdkn1a, eno1, and tfrc), MAPK signaling pathway (voltage-dependent calcium channel subunit genes), PI3K/Akt/mTOR signaling pathway (itga6, g6pc, and cdkn1a), Ras signaling pathway (efna3 and ksr2), and signaling by VEGF (fn1, wasf3, and hspb1) in catfish swimbladder. This study provided insights into regulation of gene expression and their involved gene pathways in catfish swimbladder in response to low oxygen stresses.

Original languageEnglish (US)
Pages (from-to)636-647
Number of pages12
JournalPhysiological Genomics
Volume50
Issue number8
DOIs
StatePublished - Aug 21 2018

Fingerprint

Air Sacs
Ictaluridae
Catfishes
Gene Expression Profiling
Oxygen
Aquaculture
Genes
Gene Expression Regulation
Calcium Channels
Phosphatidylinositol 3-Kinases
Vascular Endothelial Growth Factor A
Industry
Respiration
Fishes
Economics
Hypoxia
RNA
Gene Expression

Keywords

  • Fish
  • Hypoxia
  • Low oxygen
  • RNA-Seq
  • Swimbladder
  • Transcriptome

ASJC Scopus subject areas

  • Physiology
  • Genetics

Cite this

Comparative transcriptome analysis of the swimbladder reveals expression signatures in response to low oxygen stress in channel catfish, ictalurus punctatus. / Yang, Yujia; Fu, Qiang; Wang, Xiaozhu; Liu, Yang; Zeng, Qifan; Li, Yun; Gao, Sen; Bao, Lisui; Liu, Shikai; Gao, Dongya; Dunham, Rex; Liu, Zhanjian "John".

In: Physiological Genomics, Vol. 50, No. 8, 21.08.2018, p. 636-647.

Research output: Contribution to journalArticle

Yang, Yujia ; Fu, Qiang ; Wang, Xiaozhu ; Liu, Yang ; Zeng, Qifan ; Li, Yun ; Gao, Sen ; Bao, Lisui ; Liu, Shikai ; Gao, Dongya ; Dunham, Rex ; Liu, Zhanjian "John". / Comparative transcriptome analysis of the swimbladder reveals expression signatures in response to low oxygen stress in channel catfish, ictalurus punctatus. In: Physiological Genomics. 2018 ; Vol. 50, No. 8. pp. 636-647.
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AU - Fu, Qiang

AU - Wang, Xiaozhu

AU - Liu, Yang

AU - Zeng, Qifan

AU - Li, Yun

AU - Gao, Sen

AU - Bao, Lisui

AU - Liu, Shikai

AU - Gao, Dongya

AU - Dunham, Rex

AU - Liu, Zhanjian "John"

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N2 - Channel catfish is the leading aquaculture species in the US, and one of the reasons for its application in aquaculture is its relatively high tolerance against hypoxia. However, hypoxia can still cause huge economic losses to the catfish industry. Studies on hypoxia tolerance, therefore, are important for aquaculture. Fish swimbladder has been considered as an accessory respiration organ surrounded by a dense capillary countercurrent exchange system. In this regard, we conducted RNA-Seq analysis with swimbladder samples of catfish under hypoxic and normal conditions to determine if swimbladder was responsive to low oxygen treatment and to reveal genes, their expression patterns, and pathways involved in hypoxia responses in catfish. A total of 155 differentially expressed genes (DEGs) were identified from swimbladder of adult catfish, whereas a total of 2,127 DEGs were identified from swimbladder of fingerling catfish under hypoxic condition as compared with untreated controls. Subsequent pathway analysis revealed that many DEGs under hypoxia were involved in HIF signaling pathway (nos2, eno2, camk2d2, prkcb, cdkn1a, eno1, and tfrc), MAPK signaling pathway (voltage-dependent calcium channel subunit genes), PI3K/Akt/mTOR signaling pathway (itga6, g6pc, and cdkn1a), Ras signaling pathway (efna3 and ksr2), and signaling by VEGF (fn1, wasf3, and hspb1) in catfish swimbladder. This study provided insights into regulation of gene expression and their involved gene pathways in catfish swimbladder in response to low oxygen stresses.

AB - Channel catfish is the leading aquaculture species in the US, and one of the reasons for its application in aquaculture is its relatively high tolerance against hypoxia. However, hypoxia can still cause huge economic losses to the catfish industry. Studies on hypoxia tolerance, therefore, are important for aquaculture. Fish swimbladder has been considered as an accessory respiration organ surrounded by a dense capillary countercurrent exchange system. In this regard, we conducted RNA-Seq analysis with swimbladder samples of catfish under hypoxic and normal conditions to determine if swimbladder was responsive to low oxygen treatment and to reveal genes, their expression patterns, and pathways involved in hypoxia responses in catfish. A total of 155 differentially expressed genes (DEGs) were identified from swimbladder of adult catfish, whereas a total of 2,127 DEGs were identified from swimbladder of fingerling catfish under hypoxic condition as compared with untreated controls. Subsequent pathway analysis revealed that many DEGs under hypoxia were involved in HIF signaling pathway (nos2, eno2, camk2d2, prkcb, cdkn1a, eno1, and tfrc), MAPK signaling pathway (voltage-dependent calcium channel subunit genes), PI3K/Akt/mTOR signaling pathway (itga6, g6pc, and cdkn1a), Ras signaling pathway (efna3 and ksr2), and signaling by VEGF (fn1, wasf3, and hspb1) in catfish swimbladder. This study provided insights into regulation of gene expression and their involved gene pathways in catfish swimbladder in response to low oxygen stresses.

KW - Fish

KW - Hypoxia

KW - Low oxygen

KW - RNA-Seq

KW - Swimbladder

KW - Transcriptome

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