Genome-Wide Identification and Expression Profiling of the Polygalacturonase (PG) and Pectin Methylesterase (PME) Genes in Grapevine (Vitis vinifera L.)
Genome-Wide Identification and Expression Profiling of the Polygalacturonase (PG) and Pectin Methylesterase (PME) Genes in Grapevine (Vitis vinifera L.)
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葡萄（Vitis vinifera L.）中多聚半乳糖醛酸酶（PG）和果胶甲酯酶（PME）基因的全基因组鉴定和表达谱分析
DOI：
10.3390/ijms20133180
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发表时间：
2019-07-01
影响因子：
5.6
通讯作者：
Fang, Jinggui
中科院分区：
文献类型：
--
作者：
Khan, Nadeem;Fatima, Fizza;Fang, Jinggui
在果胶调控中，多聚半乳糖醛酸酶（PGs）和果胶甲基酯酶（PMEs）是植物初生细胞壁转化、分解网络和重塑的关键组分。在本研究中，我们确定了36 PG和47 PME基因利用现有的基因组资源的葡萄。在此，我们提供了一个全面的概述PG和PMEs，包括系统发育和共线性关系，基序和基因结构组成，基因重复，主成分分析，并在发育阶段的表达谱。PGs和PMEs的系统发育分析揭示了与拟南芥相似的结构域组成模式。共线性分析表明，纯化选择具有较高的保守性和基因重复性。重复的类型在PG（分别为10个分散的、1个近端的、12个串联的和13个节段的）和PME（分别为23个分散的、1个近端的、16个串联的和7个节段的）的基因数目方面也不同。PG和PME基因的组织特异性反应的基础上报告的转录组数据表现出不同的表达模式，在不同的器官在不同的发展阶段。在PG中，VvPG 8、VvPG 10、VvPG 13、VvPG 17、VvPG 18、VvPG 19、VvPG 20、VvPG 22和VvPG 23在发育期间的大多数组织中显示组织或器官特异性表达。类似地，在PME中，VvPME 3、VvPME 4、VvPME 5、VvPME 6、VvPME 19、VvPME 21、VvPME 23、VvPME 29、VvPME 31和VvPME 32提示高组织特异性反应。基因本体论（GO）、京都基因与基因组学百科全书（KEGG）的丰富和顺式元件预测分析也表明了PGs和PMEs在植物发育中的假定功能，如果胶和碳水化合物代谢以及胁迫活性。此外，32个PG和PME基因的qRT-PCR验证揭示了它们在葡萄藤的各种器官中的作用（即，根、茎、卷须、花序、肉、皮和叶）。因此，这些发现将带来新的见解，并鼓励对水果作物物种中PG和PME功能表征的前沿研究。
In pectin regulation, polygalacturonases (PGs) and pectin methylesterases (PMEs) are critical components in the transformation, disassembly network, and remodeling of plant primary cell walls. In the current study, we identified 36 PG and 47 PME genes using the available genomic resources of grapevine. Herein, we provide a comprehensive overview of PGs and PMEs, including phylogenetic and collinearity relationships, motif and gene structure compositions, gene duplications, principal component analysis, and expression profiling during developmental stages. Phylogenetic analysis of PGs and PMEs revealed similar domain composition patterns with Arabidopsis. The collinearity analysis showed high conservation and gene duplications with purifying selection. The type of duplications also varied in terms of gene numbers in PGs (10 dispersed, 1 proximal, 12 tandem, and 13 segmental, respectively) and PMEs (23 dispersed, 1 proximal, 16 tandem, and 7 segmental, respectively). The tissue-specific response of PG and PME genes based on the reported transcriptomic data exhibited diverged expression patterns in various organs during different developmental stages. Among PGs, VvPG8, VvPG10, VvPG13, VvPG17, VvPG18, VvPG19, VvPG20, VvPG22, and VvPG23 showed tissue- or organ-specific expression in majority of the tissues during development. Similarly, in PMEs, VvPME3, VvPME4, VvPME5, VvPME6, VvPME19, VvPME21, VvPME23, VvPME29, VvPME31, and VvPME32 suggested high tissue-specific response. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomics (KEGG) enrichment, and cis-elements prediction analysis also suggested the putative functions of PGs and PMEs in plant development, such as pectin and carbohydrate metabolism, and stress activities. Moreover, qRT-PCR validation of 32 PG and PME genes revealed their role in various organs of grapevines (i.e., root, stem, tendril, inflorescence, flesh, skins, and leaves). Therefore, these findings will lead to novel insights and encourage cutting-edge research on functional characterization of PGs and PMEs in fruit crop species.