高级检索

留言板

尊敬的读者、作者、审稿人, 关于本刊的投稿、审稿、编辑和出版的任何问题, 您可以本页添加留言。我们将尽快给您答复。谢谢您的支持!

姓名
邮箱
手机号码
标题
留言内容
验证码

枣果胶甲酯酶基因家族鉴定及基于RNA-Seq表达分析

王雪 宋爽 李美育 薄文浩 李颖岳 庞晓明 曹明

王雪, 宋爽, 李美育, 薄文浩, 李颖岳, 庞晓明, 曹明. 枣果胶甲酯酶基因家族鉴定及基于RNA-Seq表达分析[J]. 北京林业大学学报, 2021, 43(4): 8-16. doi: 10.12171/j.1000-1522.20200338
引用本文: 王雪, 宋爽, 李美育, 薄文浩, 李颖岳, 庞晓明, 曹明. 枣果胶甲酯酶基因家族鉴定及基于RNA-Seq表达分析[J]. 北京林业大学学报, 2021, 43(4): 8-16. doi: 10.12171/j.1000-1522.20200338
Wang Xue, Song Shuang, Li Meiyu, Bo Wenhao, Li Yingyue, Pang Xiaoming, Cao Ming. Identification and expression analysis based on RNA-Seq of the pectin methylesterase gene family in Ziziphus jujuba[J]. Journal of Beijing Forestry University, 2021, 43(4): 8-16. doi: 10.12171/j.1000-1522.20200338
Citation: Wang Xue, Song Shuang, Li Meiyu, Bo Wenhao, Li Yingyue, Pang Xiaoming, Cao Ming. Identification and expression analysis based on RNA-Seq of the pectin methylesterase gene family in Ziziphus jujuba[J]. Journal of Beijing Forestry University, 2021, 43(4): 8-16. doi: 10.12171/j.1000-1522.20200338

枣果胶甲酯酶基因家族鉴定及基于RNA-Seq表达分析

doi: 10.12171/j.1000-1522.20200338
基金项目: 国家科技计划重大专项课题(2018YFD1000607)
详细信息
    作者简介:

    王雪。主要研究方向:经济林木良种繁育。Email:wangxue1660@163.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:

    庞晓明,教授。主要研究方向:经济林木良种繁育。Email:xmpang@163.com 地址:同上

Identification and expression analysis based on RNA-Seq of the pectin methylesterase gene family in Ziziphus jujuba

  • 摘要:   目的  果胶是植物细胞壁的主要成分和结构多糖。果胶甲酯酶(PME)是一种重要的果胶修饰酶,具有调节细胞壁弹性和通透性的作用,在植物的生长发育过程中发挥作用。本研究探讨枣果胶甲酯酶基因家族的基本信息和特点,为进一步阐明ZjPMEs基因的功能、筛选果实质地密切相关基因奠定基础。  方法  本研究基于‘冬枣’基因组,鉴定枣基因组中的果胶甲酯酶基因;基于RNA-Seq数据,分析枣果胶甲酯酶基因家族的特征以及表达模式。  结果  共鉴定出46个枣果胶甲酯酶基因,不均匀分布在10条染色体上。系统演化分析表明这些基因包含29个Type- Ⅰ型和17个Type- Ⅱ型成员,进一步可以划分为4个亚家族。在每个亚家族中,基因共享保守的基因结构和基序组成。基因表达分析显示该家族基因在花中表达丰度较高,可能在枣的生殖发育过程起重要作用。通过分析该家族基因在不同质地的‘冬枣’(酥脆)和‘P15’(硬质)以及在不同用途的‘冬枣’(鲜食)和‘骏枣’(制干)果实发育过程中的表达模式,筛选出与枣果实质地关系密切的基因ZjPME 18,该基因在‘P15’和‘骏枣’果实中表达量较高。  结论  枣果胶甲酯酶基因家族具有特定的结构特征及表达模式,ZjPME 18的表达与调控可能与枣果实质地密切相关。

     

  • 图  1  ZjPME基因在枣树染色体上的分布

    Figure  1.  Chromosomal distribution of ZjPME genes

    图  2  枣与拟南芥、草莓、桃 PME家族成员的系统发育树

    Zj. 枣;AT. 拟南芥;Fa. 草莓;PR. 桃。Zj, Ziziphus jujuba; AT, Arabidopsis; Fa, strawberry; PR, peach.

    Figure  2.  Phylogenetic trees of PME family members of jujube, Arabidopsis, strawberry and peach

    图  3  ZjPMEs蛋白多重序列比对

    Figure  3.  Multiple sequence alignment of ZjPMEs protein

    图  4  ZjPMEs基因结构和蛋白结构域

    Figure  4.  Gene structure and protein domain of ZjPMEs

    图  5  ‘冬枣’不同组织中ZjPME基因 RNA-seq 数据

    Figure  5.  RNA-seq data showing ZjPME gene expression in different tissues of ‘Dongzao’

    图  6  ‘冬枣’和‘骏枣’果实发育不同阶段 ZjPME 基因 RNA-seq 数据

    DZ. ‘冬枣’;JZ. ‘骏枣’;DZ1. 幼果期;DZ2. 膨大期;DZ3. 半红期;DZ4. 全红期;JZ1. 膨大期;JZ2. 半红期;JZ3. 全红期。DZ, ‘Dongzao’; JZ, ‘Junzao’; DZ1, young fruit stage; DZ2, enlarged fruit stage; DZ3, half red fruit stage; DZ4, full red fruit stage; JZ1, enlarged fruit stage; JZ2, half red fruit stage; JZ3, full red fruit stage.

    Figure  6.  RNA-seq data showing ZjPME gene expression in different fruit development stages of ‘Dongzao’ and ‘Junzao’

    图  7  ‘冬枣’和‘P15’果实发育各时期图片

    Figure  7.  Picture in different fruit development stages of ‘Dongzao’ and ‘P15’

    图  8  ‘冬枣’和‘P15’果实中 ZjPME 基因 RNA-seq 数据

    1 ~ 4 分别为花后 40 d、80 d、白熟期、半红期;DR.‘冬枣’果肉;PP.‘P15’果肉;DP.‘冬枣’果皮;PP. ‘P15’果皮。1−4 are 40 d, 80 d after anthesis, white mature fruit stage and half red fruit stage; DR, ‘Dongzao’ sarcocarp; PR, ‘P15’ sarcocarp; DP, ‘Dongzao’ pericarp; PP, ‘P15’ pericarp.

    Figure  8.  RNA-seq data showing ZjPME gene expression in different fruit development stages of ‘Dongzao’ and ‘P15’

    图  9  ‘冬枣’和‘P15’果肉中ZjPME18基因RNA-seq数据

    Ⅰ ~ Ⅳ分别为花后40 d、80 d、白熟期、半红期;不同小写字母表示显著性差异(P < 0.05)。下同。Ⅰ−Ⅳ are 40 d after anthesis, 80 d after anthesis, white mature fruit and half red fruit; different lowercase letters represent significant differences (P < 0.05). The same below.

    Figure  9.  RNA-seq data showing ZjPME18 expression in different fruit development stages of ‘Dongzao’ and ‘P15’

    图  10  ‘冬枣’和‘P15’果皮中ZjPME18基因RNA-seq数据

    Ⅰ ~ Ⅳ分别为花后40 d、80 d、白熟期、半红期。Ⅰ−Ⅳ are 40 d after anthesis, 80 d after anthesis, white mature fruit and half red fruit.

    Figure  10.  RNA-seq data showing ZjPME18 expression in different fruit development stages of ‘Dongzao’ and ‘P15’

    表  1  枣果胶甲酯酶基因家族基因信息

    Table  1.   Identified gene member of ZjPME family in Z. jujuba

    基因名称
    Gene name
    基因编号
    Gene ID
    类型
    Type
    编码序列
    CDS/bp
    氨基酸个数
    Amino acid
    number
    分子量
    Molecular
    mass
    (MW)/kDa
    等电点
    Isoelectric
    point (pI)
    总平均疏水性
    Total average
    hydrophobicity
    (GRAVY)
    不稳定系数
    Instability
    coefficient (Ⅱ)
    信号肽
    Singnal P
    亚细胞定位
    Subcellular
    localization
    ZjPME01 LOC107419067 1 1 644 547 60.35 9.55 −0.19 33.90 N/A 细胞壁 Cell wall
    ZjPME02 LOC107434427 1 1 761 586 64.36 8.57 −0.22 35.40 N/A 细胞壁 Cell wall
    ZjPME03 LOC107434488 2 1 080 359 40.59 9.22 −0.34 29.39 1-25 细胞壁 Cell wall
    ZjPME04 LOC107410548 2 654 217 24.41 9.24 −0.21 33.60 N/A 细胞壁 Cell wall
    ZjPME05 LOC107411637 2 1 260 419 46.76 6.25 −0.16 44.90 1-23 细胞壁 Cell wall
    ZjPME06A LOC107411638 2 957 318 34.79 4.79 −0.15 34.26 N/A 细胞壁 Cell wall
    ZjPME06B LOC107411638 2 1 098 365 40.15 4.97 −0.08 34.14 1-20 细胞壁 Cell wall
    ZjPME07 LOC107411741 2 1 020 339 37.68 5.03 −0.16 31.80 1-25 细胞壁 Cell wall
    ZjPME08 LOC107411742 2 1 032 343 38.24 7.14 −0.22 42.26 1-33 细胞壁 Cell wall
    ZjPME09 LOC107411833 1 1 812 603 67.70 8.74 −0.21 40.59 N/A 细胞壁 Cell wall
    ZjPME10 LOC107411914 1 1 659 552 61.56 9.16 −0.28 37.29 1-17 细胞壁 Cell wall
    ZjPME11 LOC107411835 1 1 608 535 59.51 8.97 −0.33 36.17 N/A 细胞壁 Cell wall
    ZjPME12 LOC107412882 1 1 740 579 64.31 7.16 −0.23 34.78 1-26 细胞壁 Cell wall
    ZjPME13 LOC107412879 1 1 728 575 63.56 9.17 −0.20 33.45 N/A 细胞壁 Cell wall
    ZjPME14 LOC107413713 2 1 161 386 42.82 7.65 −0.16 34.64 N/A 细胞壁 Cell wall
    ZjPME15 LOC107414312 1 1 581 526 58.38 9.16 −0.24 33.63 1-23 细胞壁 Cell wall
    ZjPME16 LOC107414333 1 1 581 526 59.43 9.49 −0.24 36.15 1-25 细胞壁 Cell wall
    ZjPME17 LOC107414790 1 1 821 606 66.08 9.04 −0.20 32.91 N/A 细胞壁 Cell wall
    ZjPME18 LOC107415956 2 951 316 35.30 6.70 −0.24 43.65 N/A 细胞壁 Cell wall
    ZjPME19 LOC107416847 2 1 344 447 49.29 8.38 −0.13 39.75 N/A 细胞壁 Cell wall
    ZjPME20 LOC107418947 2 1 035 344 38.23 9.26 −0.16 27.79 1-28 细胞壁 Cell wall
    ZjPME21 LOC107420185 2 1 029 342 37.43 7.56 −0.14 36.51 1-25 细胞壁 Cell wall
    ZjPME22 LOC107420876 2 645 214 24.00 9.24 −0.19 28.44 N/A 细胞壁 Cell wall
    ZjPME23 LOC107421295 1 1 647 548 60.83 8.83 −0.27 44.54 1-25 细胞壁 Cell wall
    ZjPME24 LOC107421294 1 1 704 567 62.72 7.06 −0.15 33.04 1-26 细胞壁 Cell wall
    ZjPME25 LOC107423848 1 1 809 602 66.00 7.14 −0.20 26.79 N/A 细胞壁 Cell wall
    ZjPME26A LOC107423846 1 1 551 516 56.82 6.94 −0.16 28.08 1-32 细胞壁 Cell wall
    ZjPME26B LOC107423846 1 1 512 503 55.42 6.04 −0.13 28.66 1-32 细胞壁 Cell wall
    ZjPME27 LOC107423814 1 1 620 539 59.35 5.67 −0.19 38.91 1-24 细胞壁 Cell wall
    ZjPME28 LOC107423815 1 1 887 628 68.80 9.11 −0.35 37.73 N/A 细胞壁 Cell wall
    ZjPME29 LOC107423820 1 1 632 543 59.24 9.10 −0.25 39.78 1-22 细胞壁 Cell wall
    ZjPME30 LOC107425602 1 1 731 576 62.44 8.49 −0.22 40.08 N/A 细胞壁 Cell wall
    ZjPME31 LOC107426082 2 1 212 403 44.97 9.35 −0.21 30.60 N/A 细胞壁 Cell wall
    ZjPME32 LOC107426184 1 1 698 565 61.63 9.13 −0.18 25.63 1-24 细胞壁 Cell wall
    ZjPME33 LOC107426315 1 1 671 556 61.10 8.56 −0.13 31.71 1-27 细胞壁 Cell wall
    ZjPME34 LOC107426316 1 1 671 556 61.04 8.55 −0.13 31.28 1-27 细胞壁 Cell wall
    ZjPME35 LOC107426244 1 1 689 562 62.08 8.90 −0.23 33.15 1-24 细胞壁 Cell wall
    ZjPME36 LOC107429290 1 1 611 536 59.01 6.60 −0.16 33.42 1-26 细胞壁 Cell wall
    ZjPME37 LOC107432053 2 1 266 421 46.58 6.50 −0.02 32.55 1-24 细胞壁 Cell wall
    ZjPME38 LOC107432169 2 1 077 358 38.82 5.29 −0.06 30.70 1-20 细胞壁 Cell wall
    ZjPME39 LOC107433143 1 1 728 575 62.81 6.05 −0.29 29.72 N/A 细胞壁 Cell wall
    ZjPME40 LOC107406578 2 1 119 372 40.90 8.61 −0.19 23.20 N/A 细胞壁 Cell wall
    ZjPME41 LOC107403317 2 1 095 364 40.57 8.73 −0.24 29.55 1-27 细胞壁 Cell wall
    ZjPME42 LOC107409045 1 1 737 578 65.20 8.59 −0.32 31.18 N/A 细胞壁 Cell wall
    ZjPME43 LOC107405035 1 1 701 566 62.82 9.25 −0.25 30.83 N/A 细胞壁 Cell wall
    ZjPME44 LOC107405028 1 1 695 564 62.16 8.97 −0.19 33.28 1-25 细胞壁 Cell wall
    ZjPME45 LOC107406424 1 1 350 449 49.52 9.40 −0.21 30.31 N/A 细胞壁 Cell wall
    ZjPME46 LOC107406889 1 1 515 504 55.46 9.49 −0.15 38.66 N/A 细胞壁 Cell wall
    下载: 导出CSV
  • [1] Daher F B, Braybrook S A. How to let go: pectin and plant cell adhesion[J]. Frontiers in Plant Science, 2015, 6: 523.
    [2] Cosgrove D J. Diffuse growth of plant cell walls[J]. Plant Physiology, 2018, 176(1): 16−27. doi: 10.1104/pp.17.01541
    [3] Pelloux J, Rusterucci C, Mellerowicz E J. New insights into pectin methylesterase structure and function[J]. Trends Plant Science, 2007, 12(6): 267−277. doi: 10.1016/j.tplants.2007.04.001
    [4] Wolf S, Rausch T, Greiner S. The N-terminal pro region mediates retention of unprocessed type- Ⅰ PME in the Golgi apparatus[J]. The Plant Journal, 2009, 58(3): 361−375. doi: 10.1111/j.1365-313X.2009.03784.x
    [5] Pelletier S, van Orden J, Wolf S, et al. A role for pectin de-methylesterification in a developmentally regulated growth acceleration in dark-grown Arabidopsis hypocotyls[J]. New Phytologist, 2010, 188(3): 726−739. doi: 10.1111/j.1469-8137.2010.03409.x
    [6] Pilling J, Willmitzer L, Fisahn J. Expression of a Petunia inflata pectin methyl esterase in Solanum tuberosum L. enhances stem elongation and modifies cation distribution[J]. Planta, 2000, 210(3): 391−399. doi: 10.1007/PL00008147
    [7] Levesque-Tremblay G, Müller K, Mansfield S D, et al. Highly methyl esterified seeds is a pectin methyl esterase involved in embryo development[J]. Plant Physiology, 2015, 167(3): 725−737. doi: 10.1104/pp.114.255604
    [8] Jiang L, Yang S L, Xie L F, et al. VANGUARD1 encodes a pectin methylesterase that enhances pollen tube growth in the Arabidopsis style and transmitting tract[J]. The Plant Cell, 2005, 17(2): 584−596. doi: 10.1105/tpc.104.027631
    [9] Bosch M, Cheung A Y, Hepler P K. Pectin methylesterase, a regulator of pollen tube growth[J]. Plant Physiology, 2005, 138(3): 1334−1346. doi: 10.1104/pp.105.059865
    [10] Pombo M A, Dotto M C, Martínez G A, et al. UV-C irradiation delays strawberry fruit softening and modifies the expression of genes involved in cell wall degradation[J]. Postharvest Biology and Technology, 2009, 51(2): 141−148. doi: 10.1016/j.postharvbio.2008.07.007
    [11] Wei J, Ma F, Shi S, et al. Changes and postharvest regulation of activity and gene expression of enzymes related to cell wall degradation in ripening apple fruit[J]. Postharvest Biology and Technology, 2010, 56(2): 147−154. doi: 10.1016/j.postharvbio.2009.12.003
    [12] Tieman D M, Harriman R W, Ramamohan G, et al. An antisense pectin methylesterase gene alters pectin chemistry and soluble solids in tomato fruit[J]. The Plant Cell, 1992, 4(6): 667−679. doi: 10.2307/3869525
    [13] Xue C, Guan S C, Chen J Q, et al. Genome wide identification and functional characterization of strawberry pectin methylesterases related to fruit softening[J]. BMC Plant Biology, 2020, 20(1): 1−17. doi: 10.1186/s12870-019-2170-7
    [14] Li M J. Genetic diversity of Chinese jujube (Ziziphus jujuba Mill.)[C]//XXVI International Horticultural Congress: plant genetic resources. Toronto: The Fabric of Horticultures Future 623, 2002: 351−355.
    [15] Gao Q H, Wu C S, Wang M. The jujube (Ziziphus jujuba Mill.) fruit: a review of current knowledge of fruit composition and health benefits[J]. Journal of Agricultural and Food Chemistry, 2013, 61(14): 3351−3363. doi: 10.1021/jf4007032
    [16] Liu M J, Zhao J, Cai Q L, et al. The complex jujube genome provides insights into fruit tree biology[J]. Nature Communications, 2014, 5(1): 1−12.
    [17] Huang J, Zhang C, Zhao X, et al. The jujube genome provides insights into genome evolution and the domestication of sweetness/acidity taste in fruit trees[J]. PLoS Genetics, 2016, 12(12): e1006433. doi: 10.1371/journal.pgen.1006433
    [18] Chen C, Chen H, He Y, et al. TBtools, a toolkit for biologists integrating various biological data handling tools with a user-friendly interface[J/OL]. BioRxiv, [2020−01−06]. https://www.biorxiv.org/content/10.1101/289660v1.
    [19] Louvet R, Cavel E, Gutierrez L, et al. Comprehensive expression profiling of the pectin methylesterase gene family during silique development in Arabidopsis thaliana[J]. Planta, 2006, 224(4): 782−791. doi: 10.1007/s00425-006-0261-9
    [20] Wang M, Yuan D, Gao W, et al. A comparative genome analysis of PME and PMEI families reveals the evolution of pectin metabolism in plant cell walls[J]. PLoS ONE, 2013, 8(8): e72082. doi: 10.1371/journal.pone.0072082
    [21] Haas B J, Wortman J R, Ronning C M, et al. Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release[J]. BMC Biology, 2005, 3(1): 7. doi: 10.1186/1741-7007-3-7
    [22] 吴丽萍, 唐岩, 李颖岳, 等. 枣和酸枣基因组大小测定[J]. 北京林业大学学报, 2013, 35(3):77−83.

    Wu L P, Tang Y, Li Y Y, et al. Estimation of genome size of Ziziphus jujuba and Z. acdiojujuba[J]. Journal of Beijing Forestry University, 2013, 35(3): 77−83.
    [23] Tian G W, Chen M H, Zaltsman A, et al. Pollen-specific pectin methylesterase involved in pollen tube growth[J]. Developmental Biology, 2006, 294(1): 83. doi: 10.1016/j.ydbio.2006.02.026
    [24] He X, Zhang J. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution[J]. Genetics, 2005, 169(2): 1157−1164. doi: 10.1534/genetics.104.037051
    [25] Zhang L, Xue J A, Yu H Q, et al. Expression and function analysis of pectin methylesterase genes which regulate and control the petal falling in Arabidopsis[J]. Plant Physiology Communications, 2012, 48(4): 350−358.
    [26] Brummell D A, Harpster M H. Cell wall metabolism in fruit softening and quality and its manipulation in transgenic plants[J]. Plant Cell Walls, 2001: 311−340.
    [27] Ng J K T, Schröder R, Sutherland P W, et al. Cell wall structures leading to cultivar differences in softening rates develop early during apple (Malus × domestica) fruit growth[J]. BMC Plant Biology, 2013, 13(1): 183. doi: 10.1186/1471-2229-13-183
    [28] 李欢. 枣果实成熟软化的细胞壁物质代谢及其基因表达研究[D]. 咸阳: 西北农林科技大学, 2017.

    Li H. Study on cell wall metabolism and gene expression of ripening and softening jujube fruit[D]. Xianyang: Northwest A&F University, 2017.
  • 加载中
图(10) / 表(1)
计量
  • 文章访问数:  449
  • HTML全文浏览量:  139
  • PDF下载量:  29
  • 被引次数: 0
出版历程
  • 收稿日期:  2020-11-09
  • 修回日期:  2021-01-02
  • 网络出版日期:  2021-04-17
  • 刊出日期:  2021-04-30

目录

    /

    返回文章
    返回