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杨树miRNA的靶基因预测及低氮胁迫表达分析

霍晓薇 徐千惠 王延伟

霍晓薇, 徐千惠, 王延伟. 杨树miRNA的靶基因预测及低氮胁迫表达分析[J]. 北京林业大学学报, 2019, 41(8): 28-37. doi: 10.13332/j.1000-1522.20190205
引用本文: 霍晓薇, 徐千惠, 王延伟. 杨树miRNA的靶基因预测及低氮胁迫表达分析[J]. 北京林业大学学报, 2019, 41(8): 28-37. doi: 10.13332/j.1000-1522.20190205
Huo Xiaowei, Xu Qianhui, Wang Yanwei. Prediction of miRNA target genes in poplar and the expression analysis under low nitrogen stress[J]. Journal of Beijing Forestry University, 2019, 41(8): 28-37. doi: 10.13332/j.1000-1522.20190205
Citation: Huo Xiaowei, Xu Qianhui, Wang Yanwei. Prediction of miRNA target genes in poplar and the expression analysis under low nitrogen stress[J]. Journal of Beijing Forestry University, 2019, 41(8): 28-37. doi: 10.13332/j.1000-1522.20190205

杨树miRNA的靶基因预测及低氮胁迫表达分析

doi: 10.13332/j.1000-1522.20190205
基金项目: 国家自然科学基金项目(31670671、31470668)
详细信息
    作者简介:

    霍晓薇。主要研究方向:林木抗逆分子遗传。Email:hxw_vv@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科学与技术学院

    责任作者:

    王延伟,博士,副教授。主要研究方向:林木抗逆分子遗传。Email:ywwang@bjfu.edu.cn 地址:同上

  • 中图分类号: S792.95

Prediction of miRNA target genes in poplar and the expression analysis under low nitrogen stress

  • 摘要: 目的鉴定杨树受低氮胁迫后miRNA的靶基因,分析靶基因在氮胁迫后的差异表达并探讨其功能,为揭示杨树低氮胁迫下miRNA的调控功能提供参考,并为树木低氮营养高效利用育种提供重要的候选基因。方法根据miRNA的保守性及与靶基因的严谨互补配对关系,以杨树miRNA为探针利用靶基因预测软件psRNATarget,通过与毛白杨转录组的基因序列进行比对鉴定靶基因,进一步开展毛白杨受低氮胁迫后靶基因的差异表达分析及功能注释。结果获得了131个miRNA家族的242个miRNA成员对应的3 024个靶基因,分别参与了植物激素信号转导、次生代谢产物的生物合成、氨基酸合成代谢、碳代谢和RNA运输等通路。57个靶基因在低氮胁迫处理后发生显著变化,其中受到诱导(29个)和抑制(28个)的基因数目相当。14个低氮胁迫响应的miRNA,其对应的11个靶基因也发生了显著的差异表达变化,其中miRNA和靶基因表达量发生相反变化的有8个miRNA。本研究发现参与植物激素信号转导的靶基因(2个)及参与代谢途径的靶基因(6个)发生了差异表达。miR162的靶基因编码ABC转运蛋白,miR393运用于靶基因KAT2调节Na+和K+动态平衡,miR399的靶基因PIF3编码光敏色素互作因子PIFs蛋白,这些miRNA及靶基因可能在杨树响应低氮胁迫中发挥重要作用。结论本文鉴定到了毛白杨中一批低氮胁迫响应miRNA的靶基因,可调控杨树对氮逆境胁迫信号的反应。这些miRNA及靶基因为进一步揭示miRNA及靶基因在低氮胁迫下的调控功能提供了研究线索,为树木氮营养的高效利用改良提供了重要候选基因。

     

  • 图  1  靶基因数量分布图(靶基因数量 ≥ 40)

    Figure  1.  Distribution map of target gene number(more than 40)

    图  2  靶基因的GO分类

    Figure  2.  GO classification of the target genes

    图  3  差异表达靶基因功能分类

    Figure  3.  Functional classification of the target genes with differential expression

    图  4  miR162、miR396与靶基因互补位点图

    Figure  4.  The complementary sites of miR162, miR396 and the corresponding target genes

    表  1  前10显著富集的KEGG通路

    Table  1.   Top 10 significantly enriched KEGG pathways

    KEGG通路
    KEGG pathway
    差异表达基因数目
    Number of differentially expressed genes
    全部基因数目
    Total number of genes
    植物激素信号转导 Plant hormone signal transduction 85 (5.34%) 1131 (3.87%)
    植物−病原体相互作用 Plant-pathogen interaction 83 (5.21%) 1233 (4.22%)
    RNA转运 RNA transport 57 (3.58%) 849 (2.91%)
    剪接 Spliceosome 51 (3.2%) 886 (3.03%)
    内质网中的蛋白质加工 Protein processing in endoplasmic reticulum 37 (2.32%) 854 (2.92%)
    核糖体 Ribosome 75 (4.71%) 1650 (5.65%)
    次生代谢物的生物合成 Biosynthesis of secondary metabolites 158 (9.92%) 3446 (11.79%)
    碳代谢 Carbon metabolism 27 (1.69%) 863 (2.95%)
    代谢途径 Metabolic pathways 287 (18.02%) 6238 (21.35%)
    氨基酸的生物合成 Biosynthesis of amino acids 19 (1.19%) 699 (2.39%)
    下载: 导出CSV

    表  2  差异表达靶基因相关KEGG通路

    Table  2.   Differentially expressed target genes associated with the KEGG pathway

    通路ID  
    Pathway ID  
    KEGG通路
    KEGG pathway
    差异表达基因数量
    Number of differentially expressed genes
    差异表达基因
    Differentially expressed genes
    ko03022 基础转录因子
    Basal transcription factors
    2 (6.25%) CL570.Contig1_All, CL570.Contig3_All
    ko04120 泛素介导的蛋白水解
    Ubiquitin mediated proteolysis
    3 (9.38%) CL3618.Contig2_All, CL8020.Contig1_All, CL8020.Contig2_All
    ko00430 牛磺酸和亚牛磺酸代谢
    Taurine and hypotaurine metabolism
    1 (3.13%) CL1398.Contig4_All
    ko03040 剪接
    Spliceosome
    3 (9.38%) CL4501.Contig2_All, CL68.Contig2_All, Unigene22460_All
    ko00563 糖基磷脂酰肌醇 (GPI)-锚生物合成
    Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
    1 (3.13%) CL4201.Contig2_All
    ko00130 泛醌和其他萜类化合物−醌生物合成
    Ubiquinone and other terpenoid-quinone biosynthesis
    1 (3.13%) Unigene20018_All
    ko00510 N-聚糖生物合成
    N-Glycan biosynthesis
    1 (3.13%) Unigene3286_All
    ko04712 昼夜节律−植物
    Circadian rhythm-plant
    1 (3.13%) CL3618.Contig2_All
    ko03013 RNA转运
    RNA transport
    2 (6.25%) Unigene13760_All, Unigene38123_All
    ko00630 乙醛酸和二羧酸代谢
    Glyoxylate and dicarboxylate metabolism
    1 (3.13%) CL10733.Contig3_All
    ko04141 内质网中的蛋白质加工
    Protein processing in endoplasmic reticulum
    2 (6.25%) Unigene3286_All, Unigene34173_All
    ko00620 丙酮酸代谢
    Pyruvate metabolism
    1 (3.13%) CL10733.Contig3_All
    ko04075 植物激素信号转导
    Plant hormone signal transduction
    2 (6.25%) CL1120.Contig2_All, CL1130.Contig3_All
    ko03018 RNA降解
    RNA degradation
    1 (3.13%) Unigene38123_All
    ko04626 植物−病原体相互作用
    Plant-pathogen interaction
    2 (6.25%) CL4959.Contig2_All, Unigene36128_All
    ko03015 mRNA监测途径
    mRNA surveillance pathway
    1 (3.13%) Unigene38123_All
    ko00240 嘧啶代谢
    Pyrimidine metabolism
    1 (3.13%) CL6853.Contig2_All
    ko00230 嘌呤代谢
    Purine metabolism
    1 (3.13%) CL6853.Contig2_All
    ko01200 碳代谢
    Carbon metabolism
    1 (3.13%) CL10733.Contig3_All
    ko01100 代谢途径
    Metabolic pathways
    6 (18.75%) CL10733.Contig3_All, CL1398.Contig4_All, CL4201.Contig2_All, CL6853.Contig2_All, Unigene20018_All, Unigene3286_All
    ko01110 次生代谢物的生物合成
    Biosynthesis of secondary metabolites
    3 (9.38%) CL10733.Contig3_All, CL6853.Contig2_All, Unigene20018_All
    ko03010 核糖体
    Ribosome
    1 (3.13%) Unigene24651_All
    下载: 导出CSV

    表  3  参与代谢途径通路的靶基因

    Table  3.   Target genes involved in metabolic pathways

    基因编号
    Gene ID
    miRNA
    miRNA
    同源基因
    Homologous gene
    基因名称
    Gene name
    基因功能
    Gene function
    CL10733.Contig3_All miR7838 ATCG01180.1 RRN23S.2 叶绿体编码的23S核糖体
    RNA chloroplast-encoded 23S ribosomal RNA
    CL1398.Contig4_All miR1445 AT5G12200.1 PYD2 编码具有二氢嘧啶酰胺水解酶活性的蛋白质
    Encodes a protein with dihydropyrimidine amidohydrolase activity
    CL6853.Contig2_All miR393a-3p
    miR393b-3p
    AT3G27250.1 AITR1 假设蛋白质
    Hypothetical protein
    CL4201.Contig2_All miR399a AT1G66430.1 FRK3 含有无菌α基序结构域的蛋白质
    Sterile alpha motif domain-containing protein
    Unigene20018_All miR156g-j AT5G54320.1 假设蛋白(DUF295)
    hypothetical protein (DUF295)
    Unigene3286_All miR399i AT1G09530.1 PAP3 转录因子与光感受器phyA和phyB相互作用
    Transcription factor interacting with photoreceptors phyA and phyB
    下载: 导出CSV

    表  4  参与植物激素信号传导的靶基因

    Table  4.   Target genes involved in plant hormone signaling pathways

    miRNA miRNA靶基因编号 Target gene No.同源基因 Homologous gene基因功能 Gene function
    ptc-miR530a CL1120.Contig2_All Potri.006G272400.1 剪接因子 RSZp22(RSZP22)
    Splicing factor RSZp22 (RSZP22)
    ptc-miR396a,b CL1130.Contig3_All Potri.001G215800.1 DNAJ 热休克N-末端结构域蛋白
    DNAJ heat shock N-terminal domain-containing protein
    下载: 导出CSV

    表  5  低氮胁迫下差异表达的杨树miRNA和靶基因

    Table  5.   Differentially expressed miRNAs and target genes

    miRNA miRNA上调/下调* Up/down regulation差异倍数 Fold change靶基因编号 Target gene No.上调/下调 Up/down regulation
    miR482c-3p 0.67 Unigene31509_All
    miR482c-5p 0.67 Unigene30684_All
    miR168a-5p 0.58 Unigene13760_All
    miR168b-5p
    miR162a 0.65 Unigene18608_All
    miR162b
    miR393a-3p 2.56 CL6853.Contig2_All
    miR393b-3p
    miR399a 0.49 CL4201.Contig2_All
    miR6445a 0.54 Unigene37079_All
    miR6445b
    miR396a 1.7 CL1130.Contig3_All
    miR396b
    miR6445a 0.54 CL8486.Contig3_All
    miR6445b
    miR6427-3p 0.54 CL4139.Contig1_All
    miR6427-3p 0.54 Unigene24651_All
    注:* miRNA在毛白杨受低氮胁迫后的差异表达结果参考本实验室前期研究结果[37]。Note: * means miRNA differentially expressed results of Populus tomentosa under low nitrogen stress referring to the research results of our laboratory in the early stage[37].
    下载: 导出CSV

    表  6  miRNA和靶基因变化趋势呈负相关的预测结果

    Table  6.   Prediction of negative correlation between miRNA and target gene change trends

    miRNA
    miRNA
    靶基因编号
    Target gene No.
    同源基因(拟南芥)
    Homologous gene (Arabidopsis thaliana)
    功能
    Function
    miR482c-3p Unigene31509_All AT5G56670.1 核糖体蛋白S30家族蛋白
    Ribosomal protein S30 family protein
    miR482c-5p Unigene30684_All AT3G52105.1
    miR168a-5p,b-5p Unigene13760_All
    miR162a,b Unigene18608_All AT1G70610.1 (TAP1) 与抗原加工蛋白相关的转运蛋白1
    Transporter associated with antigen processing protein 1
    miR396a,b CL1130.Contig3_All AT5G22080.1 伴随DnaJ结构域超家族蛋白
    Chaperone DnaJ-domain superfamily protein
    下载: 导出CSV
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出版历程
  • 收稿日期:  2019-04-30
  • 修回日期:  2019-05-20
  • 网络出版日期:  2019-07-08
  • 刊出日期:  2019-08-01

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