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黄鳝生长差异基因发掘及其调控机制初步研究

霍欢欢 刘瑜 周秋白 郭枫 隗黎丽 彭墨 张燕萍 陈文静

霍欢欢, 刘瑜, 周秋白, 郭枫, 隗黎丽, 彭墨, 张燕萍, 陈文静. 黄鳝生长差异基因发掘及其调控机制初步研究[J]. 南方水产科学, 2020, 16(1): 1-8. doi: 10.12131/20190176
引用本文: 霍欢欢, 刘瑜, 周秋白, 郭枫, 隗黎丽, 彭墨, 张燕萍, 陈文静. 黄鳝生长差异基因发掘及其调控机制初步研究[J]. 南方水产科学, 2020, 16(1): 1-8. doi: 10.12131/20190176
HUO Huanhuan, LIU Yu, ZHOU Qiubai, GUO Feng, WEI Lili, PENG Mo, ZHANG Yanping, CHEN Wenjing. Primary study on differentially expressed genes screening of Monopterus albus and their regulation mechanism[J]. South China Fisheries Science, 2020, 16(1): 1-8. doi: 10.12131/20190176
Citation: HUO Huanhuan, LIU Yu, ZHOU Qiubai, GUO Feng, WEI Lili, PENG Mo, ZHANG Yanping, CHEN Wenjing. Primary study on differentially expressed genes screening of Monopterus albus and their regulation mechanism[J]. South China Fisheries Science, 2020, 16(1): 1-8. doi: 10.12131/20190176

黄鳝生长差异基因发掘及其调控机制初步研究

doi: 10.12131/20190176
基金项目: 国家特色淡水鱼产业体系建设专项资金 (CARS-46);国家自然科学基金项目 (31360641)
详细信息
    作者简介:

    霍欢欢 (1986—),男,博士,讲师,从事鱼类营养及免疫研究。E-mail: hhh16430@163.com

    通讯作者:

    周秋白 (1965—),男,博士,教授,从事鱼类营养研究。E-mail: zhouqiubai@163.com

  • 中图分类号: S 917.4

Primary study on differentially expressed genes screening of Monopterus albus and their regulation mechanism

  • 摘要:

    为揭示黄鳝 (Monopterus albus) 生长相关基因的调控机制,对相同亲本具有显著性生长差异的黄鳝肝脏进行了转录组测序分析。结果显示,转录组测序共得到19 149个基因,其中差异基因598个,差异基因中有303个基因显著上调,295个显著下调。KEGG通路分析发现,598个差异基因分属262条通路中,其中有38条通路显著富集。GO功能注释发现,与生长相关的差异基因有7个,分别为col1α1、nkx6.1、nnosplexina4、igfbp1、pcgf1和h3.3,这些基因表达水平的变化可能对黄鳝神经、内分泌和消化系统的发育及生理活动产生了调节作用从而影响了黄鳝的生长。结合KEGG通路分析发现,col1α1所在的利什曼病通路和nnos所在的精氨酸和脯氨酸代谢通路富集显著,说明其对黄鳝生长具有重要调节作用。

  • 图  1  差异基因火山和统计图

    红色代表上调,蓝色代表下调,黑色代表无差异,每个点代表一个基因

    Figure  1.  Volcano-plots (a) and statistics (b) of differentially expressed genes

    Up-regulated genes are in red; down-regulated ones are in blue; black represents no difference; each dot represents a gene.

    图  2  差异表达基因GO功能分类图

    1. 单生物体过程;2. 细胞过程;3. 代谢过程;4. 生物调节;5. 生物过程调节;6. 定位;7. 刺激应答;8. 发展过程;9. 多细胞生物体过程;10. 生物体细胞组成或起源;11. 信号传导;12. 正调节生物过程;13. 负调节生物过程;14;生长;15. 运动;16. 免疫系统过程;17. 行为;18多生物体过程;19. 节律过程;20. 细胞;21. 细胞部分;22. 膜;23. 膜部分;24. 细胞器;25. 复杂大分子;26. 细胞器部分;27. 细胞外区域;28. 细胞外区域部分;29. 膜封闭腔;30. 细胞连接;31. 细胞外模型;32. 超分子纤维;33. 突触;34. 突触部分;35. 结合;36. 催化活性;37. 运输活性;38. 分子功能调节;39. 信号传感活性;40. 结构分子活性;41. 分子传感活性;42. 核苷酸结合转录因子活性

    Figure  2.  GO functional classification map of differentially expressed genes

    1. Single-organism process; 2. Cellular process; 3. Metabolic process; 4. Biological regulation; 5. Regulation of biological regulation; 6. Localization; 7. Response to stimulus; 8. Developmental process; 9. Multicellular organismal process; 10. Cell compent organization or biogenesis; 11. Signaling; 12. Positive regulation of biological process; 13. Negative regulation of biological process; 14. Gowth; 15. Locomotion; 16. Immune system process; 17. Behavior; 18. Multi-organism process; 19. Rhythmic process; 20. Cell; 21. Cell part; 22. Membrane; 23. Membrane part; 24. Organelle; 25. Macromolecular complex; 26. Organelle part; 27. Extracellular region; 28. Extracellular region part; 29. Membrane-enclosed lumen; 30. Cell junction; 31. Extracellular matrix; 32. Supramolecular fiber; 33. Synapse; 34. Synapse part; 35. Binding; 36. Catalytic activity; 37. Transporter activity; 38. Molecular function regulation; 39. Signal transducer activity; 40. Structural molecule activity; 41. Molecular transducer activity; 42. Nucleic acid binding transcription factor activity

    图  3  差异表达基因qPCR验证图

    Figure  3.  Validation of differentially expressed genes by qPCR

    表  1  样品信息

    Table  1.   Information of samples

    样品
    Sample
    体质量
    Body mass/g
    全长
    Total length/cm
    实验组
    Treatment group
    AEG1 42.27 35.8
    AEG2 44.10 36.5
    AEG3 35.78 34.6
    对照组
    Control group
    ACG1 6.30 19.8
    ACG2 6.61 18.9
    ACG3 6.12 20.2
    下载: 导出CSV

    表  2  荧光定量PCR引物信息

    Table  2.   Information of primers used for qPCR

    基因
    Gene
    qPCR引物序列 (5'–3')
    Primer sequence of qPCR
    退火温度
    Annealing temperature/℃
    片段大小
    Fragment size/bp
    col1α1 F:AGTTGTTTGCGGACCGAGAT 60.0 110
    R:GCAATCTGGCATTTCCTCACA 59.2
    nkx6.1 F:GGACAAAGATGGGAAACGAAA 56.7 96
    R:GCCAGGTATTTGGTCTGTTCA 58.2
    nnos F:CTATCAGTCTGGATGCCACAAC 58.8 115
    R:CAGAGCCCAACAGAAACATTAG 57.3
    plexina4 F:TGCTGAGAACCCTGAGTGGATA 60.6 159
    R:TAGCATTTGCGGTTGTCTTCAT 58.9
    pcgf1 F:CAGCCCTTACTCAACCTCAAA 57.9 167
    R:GCATCTGGCACAGCATCTACG 61.7
    igfbp1 F:CAGAGAGCCTTGGAAAAGATTG 57.3 171
    R:CTTGCCGTTCCAGGAGTGT 59.9
    h3.3 F:ATTTTGAGTTGCGGCGATTA 56.4 181
    R:GTAACGATGGGGCTTCTTCAC 59.0
    18S F:GTGGAGCGATTTGTCTGGTTA 57.8 162
    R:CGGACATCTAAGGGCATCAC 57.7
    下载: 导出CSV

    表  3  测序结果统计

    Table  3.   Statistics of sequencing results

    样品
    Sample
    过滤后Reads
    Filtered Reads
    Q20/%Q30/%GC含量
    GC content/%
    匹配率
    Matching ratio/%
    对照组
    Control group
    ACG14120116898.0394.7546.7875.48
    ACG24104770498.0494.7746.6175.48
    ACG34092654098.0294.7848.1275.98
    实验组
    Treatment group
    AEG14100432498.0994.9646.8774.32
    AEG24098404698.1295.0047.0974.44
    AEG34099936698.0794.8847.3375.21
    下载: 导出CSV

    表  4  生长相关差异表达基因

    Table  4.   Growth-related differentially expressed genes

    基因名称
    Gene name
    基因ID
    Gene ID
    差异倍数
    Fold change
    所属通路
    Belonged pathway
    通路ID
    Pathway ID
    col1α1 109951101 −2.5 利什曼病 Ko05140
    nkx6.1 109952563 −3.3 青少年成熟性糖尿病 Ko04950
    nnos 109959109 4.0 精氨酸和脯氨酸代谢 Ko00330
    plexina4 109959815 3.4 细胞黏附分子 Ko04514
    igfbp1 109961253 2.3 p53信号通路 Ko04115
    pcgf1 109972045 3.3 干细胞潜能调节通路 Ko04550
    h3.3 109974907 2.2 癌症的转录失调 Ko05202
    下载: 导出CSV
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出版历程
  • 收稿日期:  2019-09-09
  • 修回日期:  2019-11-03
  • 录用日期:  2019-11-26
  • 网络出版日期:  2019-11-30
  • 刊出日期:  2020-02-05

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