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转录组分析氧化胁迫对毛白杨悬浮细胞生长发育的影响

尹玢 陆海

尹玢, 陆海. 转录组分析氧化胁迫对毛白杨悬浮细胞生长发育的影响[J]. 北京林业大学学报, 2019, 41(9): 90-98. doi: 10.13332/j.1000-1522.20190157
引用本文: 尹玢, 陆海. 转录组分析氧化胁迫对毛白杨悬浮细胞生长发育的影响[J]. 北京林业大学学报, 2019, 41(9): 90-98. doi: 10.13332/j.1000-1522.20190157
Yin Bin, Lu Hai. Effects of oxidative stress on growth and development of suspension cells of Populus tomentosa by transcriptome analysis[J]. Journal of Beijing Forestry University, 2019, 41(9): 90-98. doi: 10.13332/j.1000-1522.20190157
Citation: Yin Bin, Lu Hai. Effects of oxidative stress on growth and development of suspension cells of Populus tomentosa by transcriptome analysis[J]. Journal of Beijing Forestry University, 2019, 41(9): 90-98. doi: 10.13332/j.1000-1522.20190157

转录组分析氧化胁迫对毛白杨悬浮细胞生长发育的影响

doi: 10.13332/j.1000-1522.20190157
基金项目: 国家自然科学基金项目(31500161)
详细信息
    作者简介:

    尹玢,博士生。主要研究方向:树木分子生物学。Email:yb891110@sina.com 地址:100083北京市海淀区清华东路35号北京林业大学生物科学与技术学院

    责任作者:

    陆海,教授,博士生导师。主要研究方向:树木分子生物学。Email:luhai1974@bjfu.edu.cn 地址:同上

  • 中图分类号: S718.43;S792.117;Q943.2

Effects of oxidative stress on growth and development of suspension cells of Populus tomentosa by transcriptome analysis

  • 摘要: 目的毛白杨是多年生木本植物,由于其固着的生长模式,毛白杨存在长期承受胁迫的可能性。氧化胁迫是常见的非生物胁迫方式,在多个物种中均有不同程度的研究,然而以毛白杨为材料在转录水平的研究目前鲜有报道。通过转录组数据探明活性氧平衡的打破对毛白杨悬浮细胞生长发育的影响。方法本研究对毛白杨悬浮细胞系进行H2O2胁迫处理,通过激光共聚焦显微镜和转录组测序技术(RNA-Seq),观察、分析了线粒体的形态学和基因表达量的差异。结果通过对转录组数据的分析得到了806个显著差异基因(P < 0.001且 |log2ratio| > 1),其中449个差异基因下调,357个差异基因上调。这些差异基因涉及细胞分裂、细胞分裂素的激活、赤霉素调控以及磷酸化途径。通过线粒体特异性染料并使用激光共聚焦显微镜观察氧化胁迫条件下毛白杨线粒体的形态学,结果表明氧化胁迫下线粒体以蠕虫状为主。结论通过分析氧化胁迫条件下细胞转录组数据,在RNA水平揭示了氧化胁迫对植物细胞生长发育的影响,为植物的应激反应和生长发育研究提供了理论基础。

     

  • 图  1  差异表达基因火山图

    x轴为差异倍数。y轴为校正后的P值。红点表示显著差异基因中上调的基因,绿点表示显著差异基因中下调的基因,蓝点表示不显著差异的基因。x, fold change. y, P-adjusted value. Red dots indicate significantly up-regulated differentially expressed genes, green dots indicate significantly down-regulated differentially expressed genes. Blue dots indicate non-significantly differentially expressed genes.

    Figure  1.  Volcano map of differentially expressed genes

    图  2  显著差异基因GO功能分布

    Figure  2.  GO function enrichment of DEGs

    图  3  上调差异基因GO功能富集

    Figure  3.  GO function enrichment of up-regulation DEGs

    图  4  下调差异基因GO功能富集

    Figure  4.  GO function enrichment of down-regulation DEGs

    图  5  线粒体形态学

    A、B、C分别是野生型细胞在未处理条件下线粒体形态(WT)、野生型细胞在AsA处理条件(1 mmol/L,3 h)下线粒体形态(WTA)、野生型细胞在H2O2处理条件(10 mmol/L,3 h)下线粒体形态(WTH);D是基于200个不同细胞的形态学定量统计。A, mitochondrial morphology of wild type cells under untreated conditions (WT). B, mitochondrial morphology of wild type cells under AsA treatment (1 mmol/L, 3 h) (WTA). C, mitochondrial morphology of wild type cells under H2O2 treatment (10 mmol/L, 3 h) (WTH). D, quantitative statistics based on 200 cells.

    Figure  5.  Mitochondrial morphology

    表  1  转录组测序数据的清本情况

    Table  1.   Details of transcriptome data

    样品名称 Sample name     WT WTH
    原始序列数据 Raw reads 55 304 398 55 500 942
    过滤后数据 Clean reads 53 555 976 53 151 550
    转化数据 Clean bases (G) 8.03 7.97
    误码率 Error rate/% 0.02 0.02
    Q20/% 96.45 95.55
    Q30/% 91.46 89.70
    G和C数量占总碱基百分比 GC content/% 44.15 44.11
    FPKM Interval (0 ~ 1) 18 797 (45.16%) 18 519 (44.49%)
    FPKM Interval (1 ~ 3) 3 648 (8.76%) 3 559 (8.55%)
    FPKM Interval (3 ~ 15) 9 969 (23.95%) 10 037 (24.11%)
    FPKM Interval (15 ~ 60) 6 850 (16.46%) 7 118 (17.10%)
    FPKM Interval (> 60) 2 360 (5.67%) 2 391 (5.74%)
    注:WT. 野生型;WTH. 过氧化氢处理的野生型;Q20. 测序质量质控值大于20的碱基数所占比;Q30. 测序质量质控值大于30的碱基数所占比;FPKM Interval. 每百万fragments中来自某一基因每千碱基长度的fragments数目,按照不同表达水平区间统计。Notes: WT, wild type; WTH, wild type treated with hydrogen peroxide; Q20, percentage of the bases with a quality value larger than 20; Q30, percentage of the bases with a quality value larger than 30; FPKM Interval,expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced.
    下载: 导出CSV

    表  2  部分表达差异基因的功能分析

    Table  2.   Functional analysis of differentially expressed genes

    基因ID Gene ID Log2X PP value 描述 Description
    POPTR_0007s01610 − 6.747 351 0.000 857 UDP-glucosyltransferase
    POPTR_0006s04680 − 2.620 479 0.000 660 UDP-glucosyltransferase
    POPTR_0001s31100 − 2.468 582 0.000 053 UDP-glucosyltransferase
    POPTR_0001s31140 − 2.256 589 0.000 003 UDP-glucosyltransferase
    POPTR_0016s01820 − 2.123 790 0.000 004 UDP-glucosyltransferase
    POPTR_0016s01610 − 1.896 713 0.000 034 UDP-glucosyltransferase
    POPTR_0015s05670 − 1.837 034 0.000 211 UDP-glucosyltransferase
    POPTR_0006s05450 − 1.828 310 0.000 210 UDP-glucosyltransferase
    POPTR_0016s01780 − 1.736 171 0.000 083 UDP-glucosyltransferase
    POPTR_0005s26040 − 3.920 826 0.000 001 Gibberellin regulated protein
    POPTR_0002s02410 − 3.852 437 0.000 001 Gibberellin regulated protein
    POPTR_0001s30500 − 2.510 387 0.000 080 Gibberellin regulated protein
    POPTR_0005s27030 − 2.205 589 0.000 019 1 Cytokinin riboside 5′-monophosphate phosphoribohydrolase
    POPTR_0001s06070 − 4.445 984 0.000 001 Metallo-dependent phosphatase
    POPTR_0003s02480 − 2.184 144 0.000 001 Metallo-dependent phosphatase
    POPTR_0012s14700 − 2.024 093 0.000 003 Trehalose-phosphatase
    POPTR_0019s10030 − 1.738 044 0.000 131 Protein phosphatase 2C
    POPTR_0008s05950 − 1.639 843 0.000 127 Protein phosphatase 2C
    POPTR_0010s20720 − 1.555 082 0.000 512 Protein phosphatase 2C
    POPTR_0003s02940 − 1.540 729 0.000 242 Pyridoxal phosphate phosphatase
    POPTR_0008s20130 − 1.479 330 0.000 421 Pyridoxal phosphate phosphatase
    下载: 导出CSV
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出版历程
  • 收稿日期:  2019-03-22
  • 修回日期:  2019-05-28
  • 网络出版日期:  2019-07-01
  • 刊出日期:  2019-09-01

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