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二倍体及其同源四倍体酸枣的生理特征和转录组分析

李萌 郭烨 刘松珊 庞晓明 李颖岳

李萌, 郭烨, 刘松珊, 庞晓明, 李颖岳. 二倍体及其同源四倍体酸枣的生理特征和转录组分析[J]. 北京林业大学学报, 2019, 41(7): 57-67. doi: 10.13332/j.1000-1522.20190118
引用本文: 李萌, 郭烨, 刘松珊, 庞晓明, 李颖岳. 二倍体及其同源四倍体酸枣的生理特征和转录组分析[J]. 北京林业大学学报, 2019, 41(7): 57-67. doi: 10.13332/j.1000-1522.20190118
Li Meng, Guo Ye, Liu Songshan, Pang Xiaoming, Li Yingyue. Physiological characteristics and transcriptomics analysis in diploid Ziziphus jujuba Mill. var. spinosa and its autotetraploid[J]. Journal of Beijing Forestry University, 2019, 41(7): 57-67. doi: 10.13332/j.1000-1522.20190118
Citation: Li Meng, Guo Ye, Liu Songshan, Pang Xiaoming, Li Yingyue. Physiological characteristics and transcriptomics analysis in diploid Ziziphus jujuba Mill. var. spinosa and its autotetraploid[J]. Journal of Beijing Forestry University, 2019, 41(7): 57-67. doi: 10.13332/j.1000-1522.20190118

二倍体及其同源四倍体酸枣的生理特征和转录组分析

doi: 10.13332/j.1000-1522.20190118
基金项目: 中央高校基本科研业务费专项(2016ZCQ05)
详细信息
    作者简介:

    李萌。主要研究方向:经济林木良种繁育。Email:limeng@bjfu.edu.cn 地址:100083 北京市海淀区清华东路35号北京林业大学生物学院

    责任作者:

    李颖岳,教授,博士生导师。主要研究方向:经济林木良种繁育。Email:yingyueli@bjfu.edu.cn 地址:同上

Physiological characteristics and transcriptomics analysis in diploid Ziziphus jujuba Mill. var. spinosa and its autotetraploid

  • 摘要: 目的研究酸枣基因组复制后分子水平的变异机制,为深入探讨枣树多倍体性状、关键调控基因的克隆及基因工程育种提供参考。方法本实验以二倍体及其同源四倍体酸枣为研究材料,比较了二者的叶片相对含水量、叶绿素含量、可溶性糖含量以及可溶性蛋白质含量,对两种材料进行了转录组测序,并参考GO Ontology、KEGG等数据库对差异基因和转录因子进行功能分类与富集分析。结果四倍体的叶绿素含量、可溶性糖含量和可溶性蛋白质含量均显著高于二倍体植株,叶片相对含水量在两种材料中没有显著差异。二倍体与四倍体酸枣共1 329个基因具有显著差异,GO功能分析表明这些差异基因主要参与生长发育和胁迫耐受相关功能。KEGG通路分析显示,大部分差异基因富集在碳水化合物代谢、氨基酸代谢和信号传递过程,其中16个关键基因参与糖和氨基酸的代谢与转运过程,如SPS2、GAE6和PGDH3,这些基因在四倍体中具有较高的表达量;23个基因参与激素信号传导通路,其中与生长素传导、应答相关的基因如ARG7,GH3.6和IAA26在四倍体植株中表达量较高,而与油菜素内酯合成酶(CYP)、乙烯不敏感蛋白(EIN)相关的基因在四倍体植株中表达量较低。在对二倍体与四倍体差异转录因子的分析中发现,四倍体MYB转录因子家族基因表达量高于二倍体。结论四倍体叶片叶绿素含量高是植株叶色加深的原因之一,可溶性糖、可溶性蛋白质含量高为四倍体叶片变大、茎加粗提供了更多能源物质。参与糖、氨基酸代谢和激素合成、信号传导的关键基因在二倍体与四倍体中差异表达,可能与四倍体植株体内能源物质含量高、生长势强的性状相关;具有渗透调节功能的基因在四倍体中表达量较高暗示着四倍体可能具有较强的抗性。进一步对差异转录因子的分析表明,MYB转录因子在二倍体与四倍体植株中的差异表达可能会导致植物在生长发育、形态建成和抗逆过程中的差异,但二者的具体差异性状还需进一步的实验研究。

     

  • 图  1  新基因的注释信息

    Figure  1.  Annotation information of new genes

    图  2  二倍体与四倍体酸枣差异表达基因统计

    红色的点代表四倍体相对于二倍体表达量上调的基因,绿色的点代表表达量下调的基因,黑色的点代表没有差异的基因;FC代表差异倍数;FDR代表错误发现率。The red point indicates up-regulated genes in autotetraploid than that in diploid, green point indicates down-regulated genes and black point indicates unchanged genes; FC represents fold change; FDR represents false discovery rate.

    Figure  2.  Statistics of differentially expressed genes in diploid and autotetraploid sour jujube

    图  3  二倍体与四倍体酸枣差异表达基因KEGG分类

    Figure  3.  KEGG classification of differentially expressed genes in diploid and autotetraploid sour jujube

    图  4  二倍体与四倍体酸枣差异表达基因显著富集的KEGG通路

    Figure  4.  KEGG pathway with significantly enriched differentially expressed genes in diploid and autotetraploid sour jujube

    图  5  二倍体与四倍体差异基因表达量热图

    D1、D2、D3分别为二倍体酸枣的3个生物学重复;T1,T2,T3分别为四倍体酸枣的3个生物学重复。方块中不同的颜色表示基于FPKM值的基因表达水平;每行的数据分别进行标准化;蓝色表示在四倍体中表达量下调,红色表示在四倍体中表达量上调。D1, D2 and D3 are the three duplicates of diploid sour jujube; T1, T2 and T3 were the three duplicates of autotetraploid sour jujube. Different colors indicate different levels of gene expression based on the FPKM values; the data in each row were normalized and compared, separately; blue indicates down-regulation in autotetraploid, and red indicates up-regulation.

    Figure  5.  Heat map of differentially expressed genes in the diploid and autotetraploid sour jujube

    图  6  编码转录因子的差异基因数目统计

    Figure  6.  Statistics of the number of differentially expressed genes encoding transcription factors

    图  7  与内源生长素相关的表达通路

    方块内的红色背景代表基因在四倍体中上调表达,蓝色背景代表基因在四倍体中既有上调表达又有下调表达。The red background in the square indicates up-regulated expression of genes in autotetraploid than that of diploid, while the blue background indicates up-regulated and down-regulated expressed genes.

    Figure  7.  Expression pathway related to endogenous auxin

    表  1  二倍体和四倍体酸枣不同生理指标的比较

    Table  1.   Comparison of different physiological index between diploid and its autotetraploid sour jujube

    样品
    Sample
    可溶性糖
    Soluble sugar
    可溶性蛋白
    Soluble protein
    叶绿素
    Chlorophyll
    叶片相对含水量
    Leaf relative water content
    二倍体酸枣
    Diploid sour jujube
    25.03 ± 4.73a4.13 ± 0.63a29.17 ± 3.02a0.52 ± 0.01a
    四倍体酸枣
    Autotetraploid sour jujube
    41.15 ± 4.45b6.20 ± 0.62b37.10 ± 2.82b0.57 ± 0.01a
    注:表内数值表示方式为“平均值 ± 标准差”,同列不同字母表示差异显著(P < 0.05)。Notes: values in table were “mean ± SD”, different letters in the same column represent significant differences (P < 0.05).
    下载: 导出CSV

    表  2  测序结果统计

    Table  2.   Statistics of sequencing results

    样品 SampleClean readsClean bases Q30/%GC 含量 GC content/%比对率 Mapped ratio/%
    D1 25 635 963 7 620 864 926 94.57 45.34 83.31
    D2 27 771 165 8 268 560 788 94.43 45.1 83.67
    D3 29 668 511 8 501 884 148 94.62 45.41 83.38
    T1 27 572 679 7 659 547 606 94.21 45.19 82.92
    T2 27 039 014 7 346 405 010 94.52 45.46 83.27
    T3 29 816 038 8 096 301 012 94.53 45.32 82.52
    注:D1、D2、D3分别为二倍体酸枣的3个重复;T1、T2、T3分别为四倍体酸枣的3个重复。Notes: D1, D2 and D3 are three biological duplicates of diploid sour jujube; T1, T2 and T3 are three biological duplicates of autotetraploid sour jujube.
    下载: 导出CSV

    表  3  二倍体与四倍体酸枣差异表达基因的GO分类及富集分析

    Table  3.   GO classification and enrichment analysis of differentially expressed genes in diploid and autotetraploid sour jujube

    GO一级分类
    GO classify 1
    GO IDGO二级分类
    GO classify 2
    所有基因
    All gene
    差异基因
    Different gene
    富集P
    Enriched P value
    生物学过程
    Biological process
    GO:0009987 细胞过程 Cellular process 15 527 873 0.725 1
    GO:0008152 代谢过程 Metabolic process 14 536 829 0.983 6
    GO:0044699 单一生物过程 Single-organism process 14 286 851 0.004 2
    GO:0050896 胁迫应答 Response to stimulus 11 883 753 0.000 0
    GO:0065007 生物调控 Biological regulation 9 802 603 0.021 6
    GO:0032502 发育过程 Developmental process 8 154 492 0.003 7
    GO:0071840 细胞组分或生物合成
    Cellular component organization or biogenesis
    7 166 386 0.373 7
    GO:0051179 定位 Localization 6 533 378 0.054 4
    GO:0032501 多细胞生物过程 Multicellular organismal process 6 469 372 0.090 1
    GO:0000003 生殖 Reproduction 5 573 331 0.070 8
    GO:0022414 生殖过程 Reproductive process 5 536 332 0.065 2
    GO:0051704 多生物过程 Multi-organism process 4 643 249 0.002 4
    GO:0023052 信号传导 Signaling 3 681 237 0.184 7
    GO:0040007 生长 Growth 2 639 142 0.016 5
    GO:0002376 免疫系统过程 Immune system process 2 446 131 0.001 1
    GO:0098754 解毒 Detoxification 550 49
    GO:0048511 节律过程 Rhythmic process 294 26 0.064 5
    GO:0022610 生物附着 Biological adhesion 134 7 0.413 8
    GO:0040011 运动 Locomotion 73 4 0.295 6
    GO:0001906 细胞杀伤 Cell killing 15 2 0.556 6
    细胞组分
    Cellular component
    GO:0044464 细胞部位 Cell part 16 088 878 0.000 0
    GO:0005623 细胞 Cell 15 666 864 0.713 8
    GO:0043226 细胞器 Organelle 12 958 714 0.659 2
    GO:0016020 细胞膜 Membrane 8 588 489 0.740 6
    GO:0044422 细胞器部位 Organelle part 5 560 302 0.938 5
    GO:0044425 细胞膜部位 Membrane part 2 828 163 0.948 7
    GO:0032991 高分子复合物 Macromolecular complex 2 285 81 0.999 8
    GO:0030054 细胞连接点 Cell junction 2 259 154 0.438 3
    GO:0005576 胞外区 Extracellular region 2 091 173 0.000 2
    GO:0031974 膜封闭腔 Membrane-enclosed lumen 563 21 0.284 9
    GO:0099080 超分子复合物 Supramolecular complex 154 14
    GO:0044421 胞外区部位 Extracellular region part 132 11 0.428 4
    GO:0009295 拟核 Nucleoid 45 4 0.058 4
    分子功能
    Molecular function
    GO:0005488 结合 Binding 11 517 620 0.983 3
    GO:0003824 催化活性 Catalytic activity 10 913 655 0.587 2
    GO:0005215 转运活性 Transporter activity 1 496 91 0.801 3
    GO:0001071 核酸结合转录因子活性
    Nucleic acid binding transcription factor activity
    1 062 76 0.327 1
    GO:0004871 信号传导活性 Signal transducer activity 782 23 0.216 1
    GO:0060089 分子传感器活动 Molecular transducer activity 627 21 0.216 1
    GO:0005198 结构分子活动 Structural molecule activity 437 16 0.914 3
    GO:0009055 电子载体活动 Electron carrier activity 350 27 0.040 0
    GO:0098772 分子功能调节剂 Molecular function regulator 285 23
    GO:0016209 抗氧化活性 Antioxidant activity 179 15 0.489 6
    GO:0000988 转录因子活性,蛋白结合
    Transcription factor activity, protein binding
    78 3 0.763 7
    GO:0045735 营养库活动 Nutrient reservoir activity 45 1 0.154 2
    下载: 导出CSV
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  • 收稿日期:  2019-03-04
  • 修回日期:  2019-06-03
  • 网络出版日期:  2019-07-02
  • 刊出日期:  2019-07-01

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