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胡杨异形叶差异表达miRNA及其靶基因功能分析

曾明 何书航 李文海 冯军 赵媛媛 郑彩霞

曾明, 何书航, 李文海, 冯军, 赵媛媛, 郑彩霞. 胡杨异形叶差异表达miRNA及其靶基因功能分析[J]. 北京林业大学学报, 2020, 42(6): 1-13. doi: 10.12171/j.1000-1522.20190464
引用本文: 曾明, 何书航, 李文海, 冯军, 赵媛媛, 郑彩霞. 胡杨异形叶差异表达miRNA及其靶基因功能分析[J]. 北京林业大学学报, 2020, 42(6): 1-13. doi: 10.12171/j.1000-1522.20190464
Zeng Ming, He Shuhang, Li Wenhai, Feng Jun, Zhao Yuanyuan, Zheng Caixia. Differential expression of miRNA and function of target genes in heteromorphic leaves of Populus euphratica[J]. Journal of Beijing Forestry University, 2020, 42(6): 1-13. doi: 10.12171/j.1000-1522.20190464
Citation: Zeng Ming, He Shuhang, Li Wenhai, Feng Jun, Zhao Yuanyuan, Zheng Caixia. Differential expression of miRNA and function of target genes in heteromorphic leaves of Populus euphratica[J]. Journal of Beijing Forestry University, 2020, 42(6): 1-13. doi: 10.12171/j.1000-1522.20190464

胡杨异形叶差异表达miRNA及其靶基因功能分析

doi: 10.12171/j.1000-1522.20190464
基金项目: 国家自然科学基金青年基金项目(31700250),国家自然科学基金项目(31870571)
详细信息
    作者简介:

    曾明,博士生。主要研究方向:木本植物生长与发育。Email:zengming1990@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:

    赵媛媛,讲师。主要研究方向:木本植物生长与发育。Email:yyzhao@bjfu.edu.cn 地址:同上

    郑彩霞,教授,博士生导师。主要研究方向:木本植物生长与发育。Email:zhengcx@bjfu.edu.cn 地址:同上

  • 中图分类号: S718.43; S792.119

Differential expression of miRNA and function of target genes in heteromorphic leaves of Populus euphratica

  • 摘要: 目的异形叶性是植物为适应环境在同一植株上产生多种形态成熟叶片的现象。胡杨是典型的木本异形叶植物,前人研究发现,胡杨异形叶片间展现出不同的生理特性及环境适应性。本研究拟通过对胡杨异形叶差异表达miRNA及其靶基因功能的分析,揭示胡杨叶片形态及其生理变化的分子调控机制。方法以成年胡杨披针形叶和锯齿卵圆形叶为实验材料,通过高通量测序对其miRNA的表达模式及差异表达miRNA的靶基因功能进行比较研究。结果共获得6个高质量的sRNA文库,各文库有效序列占原始序列的56% ~ 81%。通过比对,共鉴定517个已知miRNA和127个新预测miRNA,主要长度分布区间为20 ~ 22 nt,其中的389个miRNA匹配至54个已知的miRNA家族。两种形态叶片共同检出的miRNA有369个,与披针形叶片相比,锯齿卵圆形叶中7个miRNA上调表达,15个下调表达。通过靶基因预测及功能分析,发现差异表达miRNA参与调控胡杨异形叶的抗逆相关途径,如对盐胁迫的响应,磷酸肌醇代谢,角质、软木脂和蜡的生物合成,碱基切除修复和RNA降解等代谢途径。利用实时荧光定量PCR验证了5个差异表达miRNA的表达趋势与高通量测序结果一致,通过PCR检测发现差异表达miRNA与其靶基因存在一定的负调控关系。结论胡杨异形叶中miRNA表达模式存在差异。其中,调控植物生长发育的保守的miR167、miR166及调控植物抗逆性的miR172在锯齿卵圆形叶中表达量上调,参与植物逆境响应的保守的miR169、miR396在锯齿卵圆形叶中下调表达,推测差异表达miRNA引起了异形叶间形态的差异,同时使锯齿卵圆形叶对不利环境具有较强的耐受性。这与我们前期有关胡杨异形叶形态与生理特性的研究结果相一致。

     

  • 图  1  胡杨两种典型异形叶

    Figure  1.  Two representative types of heteromorphic leaves in P. euphratica

    图  2  胡杨异形叶小RNA测序的有效序列长度分布统计

    A. 总有效序列的长度分布;B.有效序列种类的长度分布。A, length distribution of total valid reads; B, length distribution of unique valid reads.

    Figure  2.  Length distribution of valid reads from sRNA sequencing for heteromorphic leaves in P. euphratica

    图  3  胡杨异形叶中miRNA统计分析

    a. 胡杨异形叶miRNA碱基偏好性分析;b. 胡杨异形叶miRNA家族统计;c. 胡杨异形叶小RNA测序鉴定的已知miRNA及新发现miRNA的长度分布。a, miRNA nucleotide bias analysis of heteromorphic leaves in P. euphratica; b, miRNA family statistics of heteromorphic leaves in P. euphratica; c, length distribution of known miRNAs and novel miRNAs identified from sRNA sequencing for heteromorphic leaves in P. euphratica.

    Figure  3.  Statistical analysis of miRNA identified in heteromorphicleaves of P. euphratica

    图  4  胡杨异形叶miRNA检测的韦恩图及差异表达miRNA

    A. 披针形叶片miRNA检测的韦恩图分析;B. 锯齿卵圆形叶片miRNA检测的韦恩图分析;C. 锯齿卵圆形与披针形叶片比较组中miRNA检测的韦恩图分析;D. 锯齿卵圆形与披针形叶片比较组中差异表达miRNA。A, Venn diagram of miRNA detected in lanceolate leaves; B, Venn diagram of miRNA detected in dentate broad-ovate leaves; C,Venn diagram of miRNA detected in dentate broad-ovate leaves vs lanceolate leaves group; D, differentially expressed miRNAs in dentate broad-ovate leaves vs lanceolate leaves group. Lan, lanceolate leaves; Db, dentate broad-ovate leaves.

    Figure  4.  Venn diagram of miRNA detected and differentially expressed miRNAs in heteromorphic leaves of P. euphratica

    图  5  胡杨异形叶中差异miRNA靶基因的GO注释

    Figure  5.  GO annotation of genes targeted by differentially expressed miRNA in heteromorphic leaves of P. euphratica

    图  6  差异miRNA靶基因的GO及KEGG通路富集性分析

    A. 差异miRNA靶基因的GO富集性分析;B. 差异miRNA靶基因的KEGG通路富集性分析。A, analysis of GO enrichment of genes targeted by differentially expressed miRNAs; B, analysis of KEGG pathway enrichment of genes targeted by differentially expressed miRNAs.

    Figure  6.  Analysis of GO enrichment and KEGG pathway enrichment of genes targeted by differentially expressed miRNAs

    图  7  胡杨异形叶差异表达miRNA及靶基因的表达量分析

    A. 差异miRNA的表达量分析;B. 差异miRNA的靶基因的表达量分析。图中误差棒表示平均值的标准偏差。A, analysis of expression level of the differentially expressed miRNAs; B, analysis of expression level of the target genes of differentially expressed miRNAs. Error bars show standard deviation of the average value.

    Figure  7.  Analysis of expression levels of the differentially expressed miRNAs and their target genes in heteromorphic leaves of P. euphratica

    表  1  胡杨异形叶小RNA测序统计

    Table  1.   sRNA sequencing data from heteromorphic leaves in P. euphratica

    文库 LibraryLan_1Lan_2Lan_3Db_1Db_2Db_3
    总原始读段
    Total raw reads
    10 994 672 10 095 826 9 811 531 9 849 631 10 445 363 10 587 269
    唯一原始读段
    Unique raw reads
    1 813 462 991 857 999 928 830 479 1 096 378 921 232
    总3ADT及长度筛选
    Total 3ADT & length filter
    4 491 129 3 357 910 1 750 389 1 604 935 4 096 241 1 930 624
    总垃圾读段
    Total junk reads
    28 511 11 988 15 331 15 505 12 559 16 490
    总Rfam
    Total Rfam
    168 570 95 671 79 962 93 630 53 066 112 629
    总mRNA
    Total mRNA
    300 609 128 948 131 286 148 439 143 075 196 224
    总重复序列
    Total repeats
    4 002 1 575 1 600 1 779 1 519 1 740
    总有效读段
    Total valid reads
    6 008 394 (54.65%) 6 502 632 (64.41%) 7 835 125 (79.86%) 7 988 626 (81.11%) 6 140 459 (58.79%) 8 333 317 (78.71%)
    唯一有效读段
    Unique valid reads
    1 130 544 (62.34%) 527 874 (53.22%) 745 979 (74.6%) 589 777 (71.02%) 664 491 (60.61%) 658 041 (71.43%)
    注:Lan为披针形叶;Db为锯齿卵圆形叶。下同。Notes: Lan is lanceolate leaves; Db, dentate broad-ovate leaves. The same below.
    下载: 导出CSV

    表  2  胡杨异形叶miRNA鉴定统计

    Table  2.   Statistics of miRNA identification in heteromorphic leaves of P. euphratica

    组别
    Group
    Lan_1Lan_2Lan_3Db_1Db_2Db_3总数
    Total
    组1
    Group 1
    3 4 3 3 3 4 4
    组2
    Group 2
    466 409 409 413 409 419 513
    组3
    Group 3
    114 79 97 98 90 97 127
    下载: 导出CSV

    表  3  植物发育及环境响应相关的靶基因

    Table  3.   Target genes involved in plant development and environmental response

    差异 miRNA
    Differentially expressed miRNA
    差异表达
    Differential expression
    靶基因登录号
    Accession No. of target gene
    靶基因功能注释
    Annotation of target gene
    ptc-MIR169s-p3 下调
    Down-regulated
    XM_011048135.1, XM_011048134.1,
    XM_011048132.1
    核转录因子Y
    Nuclear transcription factor Y
    XM_011024766.1, XM_011024764.1 GATA转录因子
    GATA transcription factor
    ptc-MIR396b-p3 下调
    Down-regulated
    XM_011046985.1 F-box蛋白
    F-box protein
    ptc-miR167e 上调
    Up-regulated
    XM_011030586.1, XM_011030585.1,
    XM_011030587.1, XM_011026286.1
    bHLH转录因子
    bHLH transcription factor
    XM_011027709.1, XM_011027715.1,
    XM_011027701.1, XM_011023286.1,
    XM_011023287.1
    E3泛素蛋白连接酶E3
    Ubiquitin-protein ligase
    ptc-MIR1450-p5_1ss12CG 下调
    Down-regulated
    XM_011028646.1, XM_011028647.1 阳离子质子反向运输载体
    Cation/H(+)antiporter
    XM_011033752.1, XM_011047107.1,
    XM_011047106.1
    ABC转运蛋白
    ABC transporter
    XM_011036267.1 热休克蛋白
    Heat shock protein
    ptc-MIR3627b-p3_2ss19TA20GA 下调
    Down-regulated
    XM_011044984.1 NAC转录因子
    NAC transcription factor
    下载: 导出CSV

    表  4  实时荧光定量PCR引物序列

    Table  4.   Primer sequence for quantitative real-time PCR

    miRNA/mRNA 序列 Sequence (5′−3′)
    miRNA AGCAGGGTCCGAGGTATTC
    ptc-miR167e GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACCAGATC
    ptc-miR167e CCGCGTGAAGCTGCCAGCAT
    lus-miR172j_L+1R-1 GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACGGGAAT
    lus-miR172j_L+1R-1 CCGCGTGCAGCATCATCAAG
    ptc-miR169q_R+1_1ss14CT GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACACAGGC
    ptc-miR169q_R+1_1ss14CT CCAGGCTAGCCAAGGACGATTT
    ptc-miR160b-3p GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACTATGCA
    ptc-miR160b-3p CCAGCGTG GCGTATGAGGAGC
    ptc-MIR6474-p3_1ss21GT GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACACTGTG
    ptc-MIR6474-p3_1ss21GT CCAGTCGACTATCTACGG
    XM_011030586.1 GATTTAGTGGAAGTTTTGCC
    XM_011030586.1 TAGCCTCTGTCATTTCATTG
    XM_011027061.1 ATGACGACGAGCACCCAA
    XM_011027061.1 CCATCTCAGACAATCCCTTT
    XM_011048135.1 CTGTTCAGGGAGCCATTT
    XM_011048135.1 CCATCATTCAACTCTTTCGT
    XM_011032166.1 CCAGGCATTGTTTATCGG
    XM_011032166.1 CCACAGTTGGGACATCAAGTATTA
    XM_011048960.1 AGTTAGTTTCAGAGGGTTGTG
    XM_011048960.1 CTTGTGGCAGCCATGTAG
    下载: 导出CSV
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  • 收稿日期:  2019-12-11
  • 修回日期:  2020-04-08
  • 网络出版日期:  2020-05-15
  • 刊出日期:  2020-07-01

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