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雌、雄海水青鳉肝脏组织差异表达基因转录组分析

张林宝 田斐 陈海刚 张喆 叶国玲 李艺彤 唐海威

张林宝, 田斐, 陈海刚, 张喆, 叶国玲, 李艺彤, 唐海威. 雌、雄海水青鳉肝脏组织差异表达基因转录组分析[J]. 南方水产科学. doi: 10.12131/20220250
引用本文: 张林宝, 田斐, 陈海刚, 张喆, 叶国玲, 李艺彤, 唐海威. 雌、雄海水青鳉肝脏组织差异表达基因转录组分析[J]. 南方水产科学. doi: 10.12131/20220250
ZHANG Linbao, TIAN Fei, CHEN Haigang, ZHANG Zhe, YE Guoling, LI Yitong, TANG Haiwei. Comparative transcriptome analysis in liver of female and male marine medaka (Oryzias melastigma)[J]. South China Fisheries Science. doi: 10.12131/20220250
Citation: ZHANG Linbao, TIAN Fei, CHEN Haigang, ZHANG Zhe, YE Guoling, LI Yitong, TANG Haiwei. Comparative transcriptome analysis in liver of female and male marine medaka (Oryzias melastigma)[J]. South China Fisheries Science. doi: 10.12131/20220250

雌、雄海水青鳉肝脏组织差异表达基因转录组分析

doi: 10.12131/20220250
基金项目: 广东省自然科学基金项目 (2017A030313220);广东省科技计划项目 (2019B121201001);中国水产科学研究院南海水产研究所公益性科研院所基本科研业务费专项资金资助 (2021SD17);农业农村部南海渔业资源开发利用重点实验室开放基金  ( FREU2020-01)
详细信息
    作者简介:

    张林宝 (1984—),女,副研究员,博士,研究方向为海洋环境毒理学。E-mail: zhanglinbao1984@163.com

    通讯作者:

    陈海刚 (1980—),男,副研究员,博士,研究方向为渔业生态环境。E-mail: hgchenes@163.com

  • 中图分类号: X 55; S 949

Comparative transcriptome analysis in liver of female and male marine medaka (Oryzias melastigma)

  • 摘要: 海水青鳉 (Oryzias melastigma) 作为雌雄异体的模式动物,在研究外来污染物毒性效应性别差异上具有优势。运用转录组学技术系统研究了雌、雄海水青鳉肝脏组织中的差异表达基因,结果显示雌、雄青鳉肝脏中有1 351个显著差异表达基因,其中683个差异表达基因在雌鱼肝脏组织高表达,668个差异表达基因在雄鱼肝脏中高表达。雌鱼肝脏中高表达的差异基因主要涉及生殖和性激素合成相关通路,如卵黄蛋白原和雌激素受体。雄鱼肝脏中高表达基因主要涉及能量代谢、细胞骨架和肌肉收缩等相关生物过程,如丙酮酸激酶、肌酸激酶、肌球蛋白和肌钙蛋白等。实时荧光定量PCR验证结果显示,除DNA错配修复蛋白基因以外,其他17个基因差异表达倍数与RNA-seq对应基因差异表达趋势基本一致,表明转录组分析数据基本可靠。研究表明,雌、雄海水青鳉肝脏中基因表达具有差异调控模式,研究获得的差异基因和调控通路将为海水青鳉对外来污染物性别差异响应分子机制研究提供一定的理论基础。
  • 图  1  雌、雄海水青鳉肝脏基因差异表达分析火山图

    Figure  1.  Volcano plot of deferential expressed genes in liver of female and male marine medaka

    图  2  qRT-PCR验证结果

    Figure  2.  Comparison of relative expression levels between RNA-Seq and qRT-PCR results

    表  1  靶基因qRT-PCR引物序列

    Table  1.   Primer sequences of tested genes used in qRT-PCR

    Gene 编号
    Gene ID
    注释结果
    Gene description
    引物序列 (5'—3')
    Primer sequence (5'–3')
    ENSOMEG00000014272 丙酮酸激酶 pyruvate kinase GATGCAGGTTCTTCCGTTAT
    GTTTCAGCGTGGTATTCGTG
    ENSOMEG00000023209 肌酸激酶 creatine kinase M-type TACAAGCCCACCGACAAGCA
    GCCAGAGCCTCAATGGACAG
    ENSOMEG00000008770 ATP依赖6-磷酸果糖激酶 ATP-dependent 6-phosphofructokinase, muscle type TCCTCCAGGGACATCAGA
    CCAGGAAAGCCTCAAAGC
    ENSOMEG00000013229 异柠檬酸脱氢酶 isocitrate dehydrogenase [NADP], mitochondrial ACATTCCTCGGCTTGTTC
    ACATTCCTCGGCTTGTTC
    ENSOMEG00000016412 葡萄糖激酶 glucokinase GCGATTTCTTGGCTTTGG
    GGAGTACATTTGGTTCGT
    ENSOMEG00000013940 肌球蛋白重链 myosin heavy chain AAGGCTAACAGTGAGGTGG
    CTCCACATCAATCATAAGGTC
    ENSOMEG00000022055 肌钙蛋白 C troponin C ACTCACCCAAACGGACCCAG
    GCCCAGCATCCTCATCACCT
    ENSOMEG00000017631 卵黄蛋白原1 vitellogenin-1 ACCCTCTACTCTGTCAACGA
    TATCTTCTGGCACTCCTCAC
    ENSOMEG00000017938 卵黄蛋白原2 vitellogenin-2 TGAAAGATGTACCGAGTGCG
    TCAATGGGTGTTTGGAGGAG
    ENSOMEG00000015512 3-β-羟基类固醇异构酶 3-beta-hydroxysteroid-Delta (8), Delta (7) -isomerase TGGAGTTCCGTGTTTGAGTT
    GGTCATTAGCCACATAGTTAGG
    ENSOMEG00000010141 17-β-羟基类固醇脱氢酶 17-beta-hydroxysteroid dehydrogenase 7 GTGCTGCCAAAGAAATCAAA
    ACATAGAAGAGGCTCCAACT
    ENSOMEG00000009991 雌激素受体 estrogen receptor ATCAGCCCAGCCTCCTCA
    GGGTCCGTTCGTCTCCAT
    ENSOMEG00000011913 脂肪酸脱羧酶2 fatty acid desaturase 2 CGGCACTGCTGGCAACTT
    GGCTGAACGGCTCCTAAA
    ENSOMEG00000009600 细胞色素P450 cytochrome P4502K1 ACGAGCCAACGAGACAATAC
    TAGCAGTCCACAAATCCCCT
    ENSOMEG00000011275 DNA复制许可因子 DNA replication licensing factor MCM6 CCACGGAAACGACGAGGTA
    TTTGGCGGTACTCGGGTCT
    ENSOMEG00000001336 DNA错配修复蛋白 DNA mismatch repair protein GGCGTCGCATCATAGTAGCT
    CCCTTCTTCCTCCTCCTCTT
    ENSOMEG00000001928 DNA修复蛋白 DNA repair protein RAD51 homolog 1 CGAGTTTGGTGTTGCCGTAG
    AGGTCAGATTTCCCAGCGTC
    ENSOMEG00000014847 DNA聚合酶 DNA polymerase epsilon subunit 2 GTGCCCAGATACATTTACAACG
    GTGACCATCCCGAGTACGATTA
    18S核糖体RNA 18S ribosomal RNA GACAAATCGCTCCACCAACT
    CCTGCGGCTTAATTTGACCC
    下载: 导出CSV

    表  2  海水青鳉肝脏转录组测序结果统计

    Table  2.   Statistics of liver transcriptome of marine medaka

    样品名称
    Sample TD
    原始数据
    Raw reads
    净序列
    Clean reads
    错误率
    Error/%
    质量值大于30
    Q30/%
    比对到基因组上的序列
    Total mapped reads to genome/%
    CF146 032 40642 172 4600.0294.3091.89
    CF246 965 05243 062 4980.0393.7691.71
    CF345 711 65241 474 5800.0393.9091.92
    CM144 214 55841 630 5220.0393.7090.06
    CM247 037 77044 496 9700.0393.9986.77
    CM347 890 61044 474 9940.0394.0087.79
    下载: 导出CSV

    表  3  雌雄海水青鳉肝脏基因表达变化倍数最高的前20个基因

    Table  3.   Top twenty significantly up-regulated genes in liver of female and male marine medaka

    基因ID
    Gene ID
    变化倍数
    log2 fold change
    基因注释
    Gene description
    雌鱼 Female
    ENSOMEG00000001115 10.20 溶质载体家族41成员 solute carrier family 41 member 1
    ENSOMEG00000003787 10.05 WAP型 (乳清酸性蛋白质) 四二硫核心 WAP-type (Whey Acidic Protein) 'four-disulfide core'
    ENSOMEG00000009600 9.90 细胞色素 P450 cytochrome P450 2K1
    novel.1314 9.90 卵黄蛋白原1 vitellogenin-1
    ENSOMEG00000017631 9.80 卵黄蛋白原1 vitellogenin-1
    ENSOMEG00000003805 9.69 WAP型 (乳清酸性蛋白质) 四二硫核心 WAP-type (Whey Acidic Protein) 'four-disulfide core'
    ENSOMEG00000014709 9.65 卵黄蛋白原1 vitellogenin-1
    ENSOMEG00000017938 9.63 卵黄蛋白原2 vitellogenin-2
    ENSOMEG00000016745 9.35 脑特异性血管生成抑制因子1 brain-specific angiogenesis inhibitor 1
    ENSOMEG00000014656 9.31 卵黄蛋白原1 vitellogenin-1
    ENSOMEG00000012102 9.20 蛋白赖氨酸6-氧化酶 protein-lysine 6-oxidase
    ENSOMEG00000016916 9.11 神经元正五肽受体 neuronal pentraxin receptor
    ENSOMEG00000013237 8.76 cornichon同源蛋白3 protein cornichon homolog 3
    ENSOMEG00000017881 8.73 ras相关蛋白 ras-related protein Rab-39B
    ENSOMEG00000014740 8.73 卵黄蛋白原1 vitellogenin-1
    ENSOMEG00000016835 8.67 细胞外丝氨酸/苏氨酸蛋白激酶 extracellular serine/threonine protein kinase FAM20C
    ENSOMEG00000016456 8.17 卵黄蛋白原1 vitellogenin-1
    ENSOMEG00000017903 7.67 ras相关蛋白 ras-related protein Rab-38
    ENSOMEG00000008961 6.89 透明带精子结合蛋白4 zona pellucida sperm-binding protein 4
    ENSOMEG00000009991 6.45 雌激素受体 estrogen receptor
    雄鱼 Nale
    ENSOMEG00000014272 13.42 丙酮酸激酶 pyruvate kinase PKM
    ENSOMEG00000015762 11.86 肌酸激酶 creatine kinase M-type
    ENSOMEG00000018541 11.74 热休克蛋白71 heat shock cognate 71 kDa protein
    ENSOMEG00000013940 11.72 肌球蛋白重链 myosin heavy chain, fast skeletal muscle
    ENSOMEG00000021803 11.30 肌球蛋白调节轻链2 myosin regulatory light chain 2, skeletal muscle isoform
    ENSOMEG00000021829 11.00 磷酸甘油酸突变酶2 phosphoglycerate mutase 2
    ENSOMEG00000005322 10.74 肌球蛋白重链 myosin heavy chain, fast skeletal muscle
    ENSOMEG00000015087 10.60 肥大细胞蛋白酶8 mast cell protease 8
    ENSOMEG00000000307 10.56 肌钙蛋白 c troponin C, skeletal muscle
    ENSOMEG00000012484 10.55 蛋白酪氨酸磷酸酶 protein tyrosine phosphatase type IVA 3
    ENSOMEG00000007501 10.50 ADP/ATP转位酶 ADP/ATP translocase 1
    ENSOMEG00000023209 10.48 肌酸激酶 creatine kinase M-type
    ENSOMEG00000008770 10.47 ATP依赖6-磷酸果糖激酶 ATP-dependent 6-phosphofructokinase, muscle type
    ENSOMEG00000002691 10.25 辛肌动蛋白结合重复序列蛋白Xin actin-binding repeat-containing protein 2
    ENSOMEG00000006520 10.24 小清蛋白 parvalbumin beta
    ENSOMEG00000008672 10.21 LIM结构域结合蛋白 LIM domain-binding protein 3
    ENSOMEG00000018391 10.15 肌球蛋白结合蛋白C myosin-binding protein C, fast-type
    ENSOMEG00000020650 9.98 ryanodine受体 ryanodine receptor 1
    ENSOMEG00000001483 9.96 结蛋白 desmin
    ENSOMEG00000015807 9.96 AMP脱氨酶 AMP deaminase 1
    下载: 导出CSV

    表  4  差异表达基因显著富集KEGG通路

    Table  4.   Significantly enriched KEGG pathways

    KEGG 通路
    KEGG pathway
    雌鱼
    Female
    雄鱼
    Male
    P通路 ID
    Pathway ID
    DNA复制与修复过程 DNA replication and repair process
     DNA复制 DNA replication 20 0 1.91×10−11 ola03030
     错配修复 Mismatch repair 11 0 5.03×10−6 ola03430
     嘧啶代谢 Pyrimidine metabolism 12 3 3.31×10−3 ola00240
     嘌呤代谢 Purine metabolism 10 13 2.52×10−2 ola00230
     核苷酸切除修复 Nucleotide excision repair 9 0 3.18×10−2 ola03420
     碱基切除修复 Base excision repair 7 1 4.95×10−2 ola03410
     脂类代谢过程 Lipid metabolism process
     甾体生物合成 Steroid biosynthesis 13 0 2.64×10−7 ola00100
     PPAR信号通路 PPAR signaling pathway 8 8 6.39×10−3 ola03320
     脂肪酸代谢 Fatty acid metabolism 12 2 1.70×10−2 ola01212
     不饱和脂肪酸生物合成 Biosynthesis of unsaturated fatty acids 7 2 2.52×10−2 ola01040
     脂肪酸生物合成 Fatty acid biosynthesis 6 0 3.78×10−2 ola00061
     萜骨架生物合成 Terpenoid backbone biosynthesis 6 0 3.78×10−2 ola00900
    氨基酸与蛋白生物合成 Amino acid and protein biosynthesis
     真核生物核糖体生物发生 Ribosome biogenesis in eukaryotes 21 1 2.64×10−7 ola03008
     内质网蛋白加工 Protein processing in endoplasmic reticulum 27 3 3.31×10−3 ola04141
     精氨酸和脯氨酸代谢 Arginine and proline metabolism 4 8 1.22×10−2 ola00330
     氨基酸生物合成 Biosynthesis of amino acids 9 7 1.30×10−2 ola01230
     氨酰 tRNA生物合成 Aminoacyl-tRNA biosynthesis 10 0 1.31×10−2 ola00970
     蛋白质输出 Protein export 7 0 1.81×10−2 ola03060
    其他 Other
     N-聚糖生物合成 N-Glycan biosynthesis 11 0 2.52×10−2 ola00510
    下载: 导出CSV
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  • 文章访问数:  39
  • 被引次数: 0
出版历程
  • 收稿日期:  2022-09-17
  • 修回日期:  2022-11-28
  • 录用日期:  2022-12-08
  • 网络出版日期:  2022-12-19

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