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

Wang Xue; Song Shuang; Li Meiyu; Bo Wenhao; Li Yingyue; Pang Xiaoming; Cao Ming

doi:10.12171/j.1000-1522.20200338

Journal of Beijing Forestry University > 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:

PDF (1625 KB)

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

1.
Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
2.
National Foundation for Improved Cultivars of Chinese Jujube, Cangzhou 061000, Hebei, China

More Information

Received Date: November 08, 2020
Revised Date: January 01, 2021
Available Online: April 02, 2021
Published Date: April 29, 2021

Graphical Abstract

Abstract

Abstract

Objective Pectin is a major component and structural polysaccharide of the cell walls of plants. Pectin methylesterase (PME) is a key enzyme that modifies pectin, and thereby regulates cell wall rigidity and elasticity, playing a significant role in the plant development. The purpose of this study was to investigate the basic information and characteristics of ZjPMEs, which could serve as a foundation for further elucidation of the functions of ZjPME genes and screening of genes closely related to fruit texture.
Method We identified the family genes in the ‘Dongzao’ genome using bioinformatics softwares.The characteristics and expression patterns of the genes were analyzed based on RNA-seq data.
Result 46 PME genes were identified in the jujube genome, including 29 Type- ⅠZjPMEs and 17 Type-ⅡZjPMEs, which were classified into four subfamilies (Ⅰ −Ⅳ) and unevenly distributed across 10 chromosomes. Within each subfamily, the genes shared conserved gene structure and motif compositions. Expression analysis revealed that most of the genes were expressed highly in flowers, indicating the important function of PME genes in the reproductive developmental process. Furthermore, by analyzing the expression patterns of the ZjPMEs during the fruit development between ‘Dongzao’ (crisp) and ‘P15’ (firm), and between ‘Dongzao’ (consumed freshly) and ‘Junzao’ (consumed as dry fruit), we found ZjPME18 might be closely related to fruit texture. ZjPME18 showed higher expression in ‘Junzao’ and ‘P15’.
Conclusion The ZjPMEs have specific structure characteristics and expression patterns, and the expression and regulation of ZjPME18 may be closely related to the fruit texture.
- Ziziphus jujuba,
- pectin methylesterases (PMEs),
- gene family,
- expression pattern

FullText(HTML)

References (28)

References

[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.

[1]	Zhang Bo, Lu Kaiyan, Zhang Xiaoyu, Wu Rongling. Root development and genetic regulation in Populus euphratica under salt stress[J]. Journal of Beijing Forestry University, 2025, 47(1): 72-84. DOI: 10.12171/j.1000-1522.20230374
[2]	Xu Yujin, Li Xiang, Li Yan, Jiang Luping, Zhang Feifan, Wang Qi, Wang Lixing, Zhao Xiyang. Dynamic changes in seed, cone traits and nutritional components of Pinus koraiensis[J]. Journal of Beijing Forestry University, 2024, 46(7): 67-76. DOI: 10.12171/j.1000-1522.20220148
[3]	Sun Zhilin, Liu Bing, Li Xiaowei, Tian Yuzhen, Zhang Qing, Cao Qingqin. Functional research of transcription factor CmHAT1 regulating the development of somatic embryo in Castanea mollissima[J]. Journal of Beijing Forestry University, 2024, 46(5): 73-81. DOI: 10.12171/j.1000-1522.20230215
[4]	Li Yapeng, Sun Yuhan, Lin Huazhong, Fang Luming, Yu Xiaolong, Weng Jianyu, Zhang Yungen, Li Yun. Correlations between microsporogenesis and male cone development of Cunninghamia lanceolata[J]. Journal of Beijing Forestry University, 2023, 45(1): 51-58. DOI: 10.12171/j.1000-1522.20210251
[5]	Liu Yang, Li Bangtong, Du Guihua, Huang Dongxu, Zhou Xianqing, Niu Shihui, Li Wei. Expression profiles and regulation of FT/TFL1-like genes in Pinus tabuliformis[J]. Journal of Beijing Forestry University, 2018, 40(10): 60-66. DOI: 10.13332/j.1000-1522.20180040
[6]	ZHANG Min, ZHANG Wei, GONG Zai-xin, ZHENG Cai-xia. Morphologic and anatomical observations in the process of ovulate strobilus generation and development in Pinus tabuliformis[J]. Journal of Beijing Forestry University, 2017, 39(6): 1-12. DOI: 10.13332/j.1000-1522.20160411
[7]	LI Zhe-xin, NIU Shi-hui, GAO Qiong, LI Wei.. Cytological study of gibberellin regulated xylem development.[J]. Journal of Beijing Forestry University, 2014, 36(2): 68-73.
[8]	MA Yu-lei, TANG Xing-lin, LI Xiao-yuan, PAN Hui-tang, ZHANG Qi-xiang.. Effects of photoperiod and temperature on growth and development of Primula maximowiczii.[J]. Journal of Beijing Forestry University, 2013, 35(5): 97-103.
[9]	LI Guo-lei, LIU Yong, L Rui-heng, YU Hai-qun, LI Rui-sheng. Responses of understory vegetation development to regulation of tree density in Larix principisrupprechtii plantations.[J]. Journal of Beijing Forestry University, 2009, 31(1): 19-24.
[10]	BAO Ren-yan, JIANG Chun-ning, ZHENG Cai-xia, DING Kun-shan. Molecular mechanism of the regulation of female gametophyte development in plants[J]. Journal of Beijing Forestry University, 2005, 27(4): 90-96.

Cited By

Cited by

Periodical cited type(7)

1.	翁慧莹，刘益鹏，杨黔越，叶兴状，毕远洋，张国防，陈世品，刘宝. 福建柏地理分布及随气候变化的分布格局模拟. 生态学报. 2025(01): 137-146 .
2.	罗楚滢，佘济云，唐子朝. 基于SSPs气候场景的濒危植物银杉潜在分布区预测. 南京林业大学学报(自然科学版). 2024(01): 161-168 .
3.	童丽丽，程瑶，许晓岗，王洪超，田露，蒋孝禹. 未来气候变化下白花龙在我国的潜在适生区预测. 浙江林业科技. 2024(05): 1-8 .
4.	肖模佳，徐放，张炳建，曾梓锋. 国有林场珍贵树种发展策略浅析. 农业与技术. 2023(01): 42-44 .
5.	张华峰. 珍稀濒危物种金斑喙凤蝶在我国潜在适生区预测. 井冈山大学学报(自然科学版). 2023(03): 56-62 .
6.	何学高，刘欢，张婧，程炜，丁鹏，贾丰铭，李卿，刘超. 基于优化的MaxEnt模型预测青海省祁连圆柏潜在分布区. 北京林业大学学报. 2023(12): 19-31 . 本站查看
7.	刘佳琪，魏广阔，史常青，赵廷宁，钱云楷. 基于MaxEnt模型的北方抗旱造林树种适宜区分布. 北京林业大学学报. 2022(07): 63-77 . 本站查看

Other cited types(3)

Get Citation

PDF

XML

Article views (1664) PDF downloads (75) Cited by(10)

Turn off MathJax

Article Contents

Abstract

References

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