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豹纹鳃棘鲈差异流速下肝脏转录组分析

高进 王永波 刘金叶 郭一兰 符书源

高进, 王永波, 刘金叶, 郭一兰, 符书源. 豹纹鳃棘鲈差异流速下肝脏转录组分析[J]. 南方水产科学. doi: 10.12131/20210125
引用本文: 高进, 王永波, 刘金叶, 郭一兰, 符书源. 豹纹鳃棘鲈差异流速下肝脏转录组分析[J]. 南方水产科学. doi: 10.12131/20210125
GAO Jin, WANG Yongbo, LIU Jinye, GUO Yilan, FU Shuyuan. Transcriptome analysis of Plectropomus leopardus liver under different flow velocity[J]. South China Fisheries Science. doi: 10.12131/20210125
Citation: GAO Jin, WANG Yongbo, LIU Jinye, GUO Yilan, FU Shuyuan. Transcriptome analysis of Plectropomus leopardus liver under different flow velocity[J]. South China Fisheries Science. doi: 10.12131/20210125

豹纹鳃棘鲈差异流速下肝脏转录组分析

doi: 10.12131/20210125
基金项目: 海南省重点研发计划项目 (ZDYF2019074,ZDYF2020093);2021海南省科研院所开发专项
详细信息
    作者简介:

    高进:高 进 (1991—),男,博士,助理研究员,从事水产动物基因组与数量遗传育种研究。E-mial: gaojin@hntou.edu.cn

    通讯作者:

    符书源 (1981—),男,硕士,副研究员,从事海水鱼类繁育与健康养殖技术研究。E-mail: fulank23@sohu.com

  • 中图分类号: S 917.4

Transcriptome analysis of Plectropomus leopardus liver under different flow velocity

  • 摘要: 水流速度是影响鱼类生长的重要生态环境因子之一。为探究豹纹鳃棘鲈在不同流速条件下相关基因的功能和表达情况,该研究利用RNA-Seq技术对差异流速下的豹纹鳃棘鲈肝脏组织进行转录组分析。挑选相同繁育批次中规格一致的豹纹鳃棘鲈 (Plectropomus leopardus) 幼苗,分别在正常流速 (0.1 m·s−1, Low flow velocity, LFV) 和高流速 (0.4 m·s−1, High flow velocity, HFV) 两个实验组中养殖150 d后进行肝脏转录组测序分析,探究豹纹鳃棘鲈差异流速下个体间的基因表达模式差异。结果显示,经筛选后共获得1 977个LFV-HFV显著性差异表达基因 (Differentially expressed genes, DGE),其中上调基因999个,下调基因978个。GO功能注释分类发现,共有1 124个DEGs被GO数据库注释到并归属为56个功能类别。KEGG富集分析结果显示,573个DEGs参与了154条KEGG通路,其中富集最显著的为PPAR信号通路。LFV和HFV两组鱼的肝脏组织学观察结果显示,两者之间脂肪含量差异明显,LFV组肝脏中的脂肪含量显著高于HFV组 (P<0.05)。通过转录组分析,筛选了大量豹纹鳃棘鲈差异流速下的DGEs,为深入探讨豹纹鳃棘鲈流速变化适应性的分子调控机制提供了技术支撑。
  • 图  1  不同流速下豹纹鳃棘鲈肝脏组织 (H.E染色)

    a和b: HFV和LFV低倍镜观察;c和d: HFV和LFV高倍镜观察

    Figure  1.  Liver tissues (H.E staining) of P. leopardus with different flow velocities

    a and b. Observation of sections with low magnification for HFV and LFV; c and d. Observation of sections with high magnification for HFV and LFV

    图  2  不同流速下豹纹鳃棘鲈肝脏组织 (油红O染色)

    e和f: HFV和LFV低倍镜观察;g和h: HFV和LFV高倍镜观察

    Figure  2.  Liver tissues (Oil red O staining) of P. leopardus with different flow velocities

    e and f. Observation of sections with low magnification for HFV and LFV; g and h. Observation of sections with high magnification for HFV and LFV

    图  3  豹纹鳃棘鲈基因GO分类图

    Figure  3.  Gene ontology (GO) assignment of genes of P. leopardus

    图  4  豹纹鳃棘鲈差异表达基因KEGG富集图

    Figure  4.  KEGG enrichment of differentially expressed genes of P. leopardus

    图  5  RT-PCR验证RNA-Seq结果

    Figure  5.  Validation of RNA-Seq data by using RT-qPCR

    图  6  SNP突变类型统计分布图

    Figure  6.  Statistical distribution of type of SNP mutations

    表  1  本研究所用引物及其序列

    Table  1.   Sequences of primers used in this study

    基因编号
    Gene ID
    基因
    名称
    Gene name
    引物序列
    Primer sequence
    utg000043l-1.624
    cyp7b1
    F: ACTTCATCGCCCTCTACCCTC
    R: TGAGCCTCTGACCGTCTTTG
    utg000067l-2.111
    nr1d2
    F: CCTCTGGTTTCCATTACGGG
    R: ATCAGGCATTTCTTGAAGCG
    utg000067l-3.316
    ciart
    F: TTCAGTGAGAGCGAGCACAC
    R: TTGGTTTCTTCAGGGCAGTG
    utg000134l-0.116
    cpt1a
    F: AGCACCTGACTGACCGTAAGC
    R: GCATCTCAAGTTCACTGGGTAAG
    utg000150l-1.275
    irs2
    F: TGACATCAGCGACCCTTGTG
    R: CGCCACTACTCTCTGTTGACG
    utg000157l-1.277
    scm2a
    F: GCAGCAAAGACTGGAGCAAG
    R: TCGGTGAACTCATCTGGCAC
    utg000241l-0.137
    lat3
    F: CAGGAAGAGATGTTGAACCTTGG
    R: GCGAGGAAGATGAGACCAGAC
    utg000253l-0.17
    wsb2
    F: GCCACAGGTTTGGAGAACAG
    R: AACACCAGGTCCCTCACTACAC
    utg001131l-0.55
    per1
    F: CTCAAATACGCACTTCAATGTGTC
    R: TGAGGGTGTACTCTGAGGTGATG
    utg000003l-2.243
    acod
    F: AGCAATGTTCTCCCTGAGGC
    R: CCAAAGCAAGGTCAAAGGATG
    utg000129l-0.32
    cyp2j2
    F: GGCAACTTATTCTCTGTGGATTTC
    R: GCTGTCTCCCTGATTTACCAGTG
    utg000134l-1.177
    chka
    F: CTTTCACATCACCATCATAAGGG
    R: CTTTGTTTGACTGTCGGGAATC
    utg000537l-0.141
    acsbg2
    F: GCAGCAGAAGAGCCTGACCTAC
    R: TAGATGCCAACAGCAAACCC
    utg000714l-0.135
    fasn
    F: TGAGAAACACTCTGACACGAATG
    R: TCAAAGCGTAGCCTCGGTAG
    下载: 导出CSV

    表  2  豹纹鳃棘鲈肝脏文库测序数据量统计

    Table  2.   Output statistics of P. leopardus liver library sequencing

    样品编号
    Sample ID
    有效读长
    Clean reads
    GC含量
    GC content/%
    Q30的碱基数比例
    Base ratio of Q30/%
    比对效率
    Mapping efficiency/%
    SP10-126861 07251.4295.3093.78
    SP10-235829 11051.5195.0593.53
    SP10-323503 73350.4494.9893.65
    SP40-128594 21951.5495.2393.16
    SP40-228147 72351.0495.2092.82
    SP40-324705 42451.0094.8092.77
    下载: 导出CSV

    表  3  豹纹鳃棘鲈不同流速显著差异通路中部分候选基因表达模式

    Table  3.   Expression pattern of partial candidate genes of P. leopardus in significant pathways with different flow velocities

    基因ID
    Gene ID
    log2 (差异倍数)
    log2 (Fold Change)
    FDR值
    FDR value
    登录号
    Accession ID
    基因名
    Gene name
    utg000134l-0.116 −5.33 1.87E-31 XP_008289244.1 cpt1a
    utg000043l-1.624 −3.55 9.54E-166 XP_008291411.1 cyp7b1
    utg000150l-1.275 −2.30 1.64E-132 XP_018557299.1 irs2
    utg000761l-0.82 −1.78 6.66E-125 XP_018522996.1 angptl4
    utg000248l-0.27 −1.64 1.10E-12 XP_018560228.1 socs3
    utg000172l-0.359 −1.59 4.89E-195 XP_019209058.1 cyp46a1
    utg000527l-0.63 −1.42 2.67E-13 XP_018558522.1 acsl1
    utg000455l_0.134 −1.41 9.36E-31 XP_010731808.1 aqp7
    utg000250l-2.242 −1.39 6.13E-46 XP_019119573.1 adipor2
    utg000129l-0.162 −1.21 1.22E-37 XP_018522970.1 rxrgb
    utg000097l-1.90 −1.08 1.01E-07 XP_019120297.1 traf2
    utg000349l-0.213 −1.03 1.05E-05 XP_018534038.1 dgke
    utg000794l-0.76 −1.02 1.54E-06 XP_019126544.1 prkag2
    utg000088l-2.212 −1.01 3.89E-47 XP_020505581.1 akr1a
    utg000841l-0.8 1.01 4.13E-08 XP_022072468.1 tradd
    utg000329l-0.218 1.03 8.07E-32 XP_018527840.1 abhd16a
    utg001296l-0.11 1.07 7.82E-05 XP_018525976.1 slc27a4
    utg000225l-0.155 1.11 6.08E-33 XP_018531738.1 lpin2
    utg000681l-0.96 1.12 2.09E-06 XP_018530981.1 acsl4
    utg000325l-0.118 1.16 5.97E-04 XP_005472382.1 hxk2
    utg000841l_0.93 1.51 1.23E-24 XP_018522449.1 adpgk
    utg000519l-0.406 1.82 1.04E-29 XP_018527726.1 kmt5c
    utg000454l-0.43 1.98 3.21E-12 XP_018528735.1 psat1
    utg000537l-0.141 2.39 2.05E-33 XP_020511829.1 acsbg2
    utg000393l-0.311 10.65 3.25E-128 XP_018529751.1 crhbp
    下载: 导出CSV

    表  4  SNP位点统计表

    Table  4.   Output statistics of SNP loci

    样品编号
    Sample ID
    SNP位点数
    Number of SNP
    基因区SNP
    Genic SNP
    基因间区SNP
    Intergenic SNP
    转换类型占比
    Transition/%
    颠换类型占比
    Transversion/%
    SP10-1161 388121 21840 17030.8893.78
    SP10-2178 270133 92344 34731.2293.53
    SP10-3171 685129 38942 29631.3793.65
    SP40-1168 801126 80042 00131.6993.16
    SP40-2171 772128 82142 95131.7992.82
    SP40-3165 186123 81441 37231.7992.77
    下载: 导出CSV
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计量
  • 文章访问数:  25
  • 被引次数: 0
出版历程
  • 收稿日期:  2021-04-22
  • 修回日期:  2021-07-19
  • 录用日期:  2021-07-29
  • 网络出版日期:  2021-08-11

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