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Identification and functional analysis of SNP from transcriptome of cobia (Rachycentron canadum) in response to hypoxia stress
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Erjun Yang1, Lintong Yang1, Weizheng Wang1, Jiansheng Huang1, 2, 3, *, Jiandong Zhang1, 2, 3, Zhongliang Wang1, 2, 3, Gang Chen1, 2, 3, *
Haiyang Xuebao | 2022, 44(1) : 113 - 124
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Haiyang Xuebao | 2022, 44(1): 113-124
• Article •
Identification and functional analysis of SNP from transcriptome of cobia (Rachycentron canadum) in response to hypoxia stress
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Erjun Yang1, Lintong Yang1, Weizheng Wang1, Jiansheng Huang1, 2, 3, *, Jiandong Zhang1, 2, 3, Zhongliang Wang1, 2, 3, Gang Chen1, 2, 3, *
Affiliations
  • 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
Published: 2022-01-15 doi: 10.12284/hyxb2022006
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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
Erjun Yang, Lintong Yang, Weizheng Wang, Jiansheng Huang, Jiandong Zhang, Zhongliang Wang, Gang Chen. 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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Article Info
doi: 10.12284/hyxb2022006
  • Receive Date：2021-05-12
  • Online Date：2026-02-01
  • Published：2022-01-15
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  • Received：2021-05-12
  • Revised：2021-08-12
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Affiliations
    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
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表12种不同金属材料的力学参数
科
Family		 属数
Number of
genus		 种数
Number of
species		 占总种数比例
Percentage of
total species (%)		 属
Genus		 种数
Number of
species		 占总种数比例
Percentage of total
species (%)
鹅膏菌科Amanitaceae 2 11 5.26 鹅膏菌属 Amanita 10 4.78
小菇科 Mycenaceae 2 12 5.74 丝盖伞属 Inocybe 5 2.39
多孔菌科 Polyporaceae 8 14 6.70 蜡蘑属 Laccaria 5 2.39
红菇科 Russulaceae 3 23 11.00 小皮伞属 Marasmius 6 2.87
小菇属 Mycena 11 5.26
光柄菇属 Pluteus 5 2.39
红菇属 Russula 17 8.13
栓菌属 Trametes 5 2.39
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