Identification and functional analysis of SNP from transcriptome of cobia (<i>Rachycentron canadum</i>) in response to hypoxia stress

Yang Erjun; Yang Lintong; Wang Weizheng; Huang Jiansheng; Zhang Jiandong; Wang Zhongliang; Chen Gang

doi:10.12284/hyxb2022006

Volume 44 Issue 1

Jan. 2022

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Yang Erjun，Yang Lintong，Wang Weizheng, et al. Identification and functional analysis of SNP from transcriptome of cobia (Rachycentron canadum) in response to hypoxia stress[J]. Haiyang Xuebao，2022, 44(1)：113–124 doi: 10.12284/hyxb2022006

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Yang Erjun，Yang Lintong，Wang Weizheng, et al. Identification and functional analysis of SNP from transcriptome of cobia (Rachycentron canadum) in response to hypoxia stress[J]. Haiyang Xuebao，2022, 44(1)：113–124 doi: 10.12284/hyxb2022006

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Identification and functional analysis of SNP from transcriptome of cobia (Rachycentron canadum) in response to hypoxia stress

doi: 10.12284/hyxb2022006

Yang Erjun^1
,,
Yang Lintong¹,
Wang Weizheng¹,
Huang Jiansheng^{1, 2, 3
,
,},
Zhang Jiandong^{1, 2, 3},
Wang Zhongliang^{1, 2, 3},
Chen Gang^{1, 2, 3
,
,}

1.
Fishery College, Guangdong Ocean University, Zhanjiang 524088, China
2.
Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang 524025, China
3.
Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang 524088, China

Received Date: 2021-05-12
Rev Recd Date: 2021-08-12

Available Online: 2021-09-02

Publish Date: 2022-01-14

Abstract

Abstract

In order to mine single nucleotide polymorphism (SNP) sites relates to hypoxia stress and study the function of the gene SNP-Unigene from Rachycentron canadum. SOAPsnp software is mainly used to detect the SNP of the intestinal transcriptome sequencing results of cobia juveniles under hypoxia stress conditions, and then annotation of them in the databases of GO, KOG, and KEGG are compared. The results show that the transcriptome SNP locus are distributed on 26 120 SNP-Unigene, with a total of 431 845 SNP sites are detected, the average frequency of SNP occurrence is about 1/171 bp. SNP-Unigene functional annotation showes that the cobia is mainly involved in signal transduction, infectious disease, cancer and endocrine system under hypoxia stress. Further, 3 417 SNP-Unigene are annotated to 35 immune-related pathways including MAPK signaling pathway. Based on the transcriptome differential gene analysis, the distribution of SNP sites of 18 immune-related genes in 7 important immune pathways is examined. At the same time, the distribution of SNP sites of 8 differential genes such as PIK3CA in the HIF-1 signaling pathway is also detected. The research results will lay the foundation for further mining of the molecular genetic markers of immune and hypoxia-related SNPs, and provide a scientific reference for the in-depth study of cobia’s hypoxia adaptation mechanism.
- Rachycentron canadum,
- hypoxia stress,
- transcriptomics,
- immune gene,
- SNP

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References(59)

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