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军曹鱼响应低氧胁迫转录组SNP位点鉴定及其功能注释分析

杨二军 杨林桐 王维政 黄建盛 张健东 王忠良 陈刚

杨二军,杨林桐,王维政,等. 军曹鱼响应低氧胁迫转录组SNP位点鉴定及其功能注释分析[J]. 海洋学报,2021,44(x):1–12 doi: 10.12284/hyxb2021182
引用本文: 杨二军,杨林桐,王维政,等. 军曹鱼响应低氧胁迫转录组SNP位点鉴定及其功能注释分析[J]. 海洋学报,2021,44(x):1–12 doi: 10.12284/hyxb2021182
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,2021, 44(x):1–12 doi: 10.12284/hyxb2021182
Citation: 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,2021, 44(x):1–12 doi: 10.12284/hyxb2021182

军曹鱼响应低氧胁迫转录组SNP位点鉴定及其功能注释分析

doi: 10.12284/hyxb2021182
基金项目: 南方海洋科学与工程广东省实验室(湛江)资助项目(ZJW-2019-06);财政部和农业农村部:国家现代农业产业技术体系资助(CARS-47);广东海洋大学本科生创新创业团队项目(CCTD201804)
详细信息
    作者简介:

    杨二军(1994—),男,甘肃省陇南市人,主要研究方向海水鱼类养殖生理生态学。E-mail:931471532@qq.com

    通讯作者:

    黄建盛,副教授,主要研究方向海水鱼养殖生理生态学。E-mail:huangjs@gdou.edu.cn

    陈刚,教授,主要研究方向海水鱼养殖生理生态学。E-mail:cheng@gdou.edu.cn

  • 中图分类号: S965.399

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

  • 摘要: 为了研究低氧胁迫下军曹鱼肠道转录组中单核苷酸多态性标记(SNP)位点及SNP所在基因SNP-Unigene的作用,通过SOAPsnp软件对军曹鱼幼鱼对照组和低氧组肠道转录组测序结果进行SNP检测,并将其比对到GO、KOG、KEGG数据库进行功能注释。结果显示,军曹鱼转录组SNP位点分布在26 120条SNP-Unigene上,共检测到431 845个SNP位点,SNP平均发生频率约为1/171 bp;SNP-Unigene功能注释发现,在低氧胁迫条件下,军曹鱼SNP-Unigene主要涉及信号转导、传染病、癌症和内分泌系统等生物过程。进一步筛选到3 417条SNP-Unigene被注释到MAPK信号通路等35条与免疫相关的通路中。基于转录组差异基因分析,检测了其中7个重要免疫通路中18个免疫相关基因的SNP位点分布情况。同时,也检测了HIF-1信号通路中PIK3CA等8个差异基因的SNP位点分布情况。研究结果将为进一步挖掘免疫及低氧相关SNP的分子遗传标记奠定基础,为军曹鱼低氧适应机制的深入研究提供科学参考。
  • 图  1  SNP密度频数分布图

    Fig.  1  The density frequency distribution of SNP

    图  2  SNP的分布统计

    Fig.  2  Distribution statistics of SNP

    图  3  SNP突变类型数量统计

    Fig.  3  The numbers of different mutation types statistics of SNP

    图  4  SNP位置分析

    Fig.  4  Identification of SNP location

    图  5  SNP突变类型分析

    Fig.  5  Identification of SNP variants type

    图  6  SNP-Unigene GO功能注释分析

    Fig.  6  GO classification of SNP-Unigene

    图  7  SNP-Unigene KOG功能注释分析

    Fig.  7  KOG classification of SNP-Unigene

    图  8  SNP-Unigene的KEGG信号通路富集分析

    Fig.  8  KEGG classification of SNP-Unigene

    表  1  SNP位点数量概况

    Tab.  1  The number of the SNP sites

    组别CTHT合计
    SNP-Unigene数13 07613 04426 120
    SNP位点总数215 953215 892431 845
    纯合SNP位点数76 55076 092152 642
    下载: 导出CSV

    表  2  免疫防御相关SNP-Unigene的KEGG富集分析

    Tab.  2  KEGG enrichment analysis of immune-related SNP-Unigene

    KEGG信号通路信号通路IDSNP-Unigene数目
    MAPK信号通路ko04010262
    神经活性配体-受体相互作用ko04080228
    Rap1信号通路ko04015190
    Ras信号通路ko04014164
    Wnt信号通路ko04310144
    细胞因子-细胞因子受体相互作用ko04060137
    细胞凋亡ko04210130
    mTOR信号通路ko04150129
    吞噬体ko04145123
    趋化因子信号通路ko04062117
    血小板活化ko04611117
    FoxO信号通路ko04068117
    NOD样受体信号通路ko04621113
    白细胞经内皮迁移ko04670101
    TNF信号通路ko0466895
    Jak-STAT信号通路ko0463093
    T细胞受体信号通路ko0466092
    TRP通道的炎症介质调节ko0475089
    NF-κB信号通路ko0406481
    TGF-β信号通路ko0435080
    Fcγ-R介导的吞噬作用ko0466679
    B细胞受体信号通路ko0466273
    造血细胞系ko0464072
    Toll样受体信号通路ko0462071
    自然杀伤细胞介导的细胞毒性ko0465069
    Notch信号通路ko0433063
    PPAR信号通路ko0332056
    IL-17信号通路ko0465755
    补体和凝血级联ko0461053
    Fc ε RI信号通路ko0466447
    抗原处理与呈递ko0461247
    RIG-I样受体信号通路ko0462245
    Toll和Imd信号通路ko0462435
    肠道免疫网络Ig A的产生ko0467227
    细胞质DNA传感通路 ko04623 23
    合计3 417
    下载: 导出CSV

    表  3  CT和HT转录组中差异表达免疫防御及低氧相关基因SNP位点分析

    Tab.  3  SNP identified in differentially expressed immune and hypoxia-related genes in CT and HT transcriptomes

    基因名称低氧后表达水平CT-SNP数目HT-SNP数目
    MAPK信号通路
    IL1R1上调44
    ERBB3上调55
    CACNA1E上调44
    Wnt信号通路
    FZD3下调31
    LRP5下调55
    PLCB2上调1011
    PLCB3下调77
    NFATC4上调66
    mTOR信号通路
    LPIN1上调99
    LPIN2下调33
    DDIT4上调22
    Jak-STAT信号通路
    GHR下调88
    LEPR上调55
    IL4RA上调99
    NOD样受体信号通路
    TRPM7下调1717
    Toll和Imd信号通路
    ANK3上调1818
    NF-κB信号通路
    BTK下调33
    TNFRSF11A下调22
    HIF-1信号通路
    PIK3CA下调54
    HK1上调44
    EPAS1下调33
    GAPDH下调22
    EDN1下调11
    ENO3下调11
    ANGPT1上调44
    ANGPT2上调11
    下载: 导出CSV
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  • 收稿日期:  2021-05-12
  • 修回日期:  2021-08-12
  • 网络出版日期:  2021-09-02

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