Genome-Wide Identification and Expression Profiling of the Polygalacturonase (<i>PG</i>) and Pectin Methylesterase (<i>PME</i>) Genes in Grapevine (<i>Vitis</i> <i>vinifera</i> L.)

• Main Authors: Nadeem Khan, Fizza Fatima, Muhammad Salman Haider, Hamna Shazadee, Zhongjie Liu, Ting Zheng, Jinggui Fang
• Format: Article
• Language: English
• Published: MDPI AG 2019-06-01
• Series: International Journal of Molecular Sciences
• Subjects: polygalacturonase (PGs), pectin methylesterase (PMEs), collinearity analysis; gene duplications; expression profiling; grapevine
• Online Access: https://www.mdpi.com/1422-0067/20/13/3180

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 <i>PG</i> and 47 <i>PME</i> 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 <i>Arabidopsis</i>. 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 <i>PG</i> and <i>PME</i> genes based on the reported transcriptomic data exhibited diverged expression patterns in various organs during different developmental stages. Among PGs, <i>VvPG8, VvPG10, VvPG13, VvPG17, VvPG18, VvPG19, VvPG20, VvPG22</i>, and <i>VvPG23</i> showed tissue- or organ-specific expression in majority of the tissues during development. Similarly, in PMEs, <i>VvPME3, VvPME4, VvPME5, VvPME6, VvPME19, VvPME21, VvPME23, VvPME29, VvPME31</i>, and <i>VvPME32</i> 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 <i>PG</i> and <i>PME</i> 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.