Dataset Information

Genome-wide identification and expression analysis of citrus fruitlet abscission-related polygalacturonase genes.

ABSTRACT: Polygalacturonases (PGs) encoded by a relatively large gene family are involved in plant organ abscission, but few data is available in citrus. Here, to explore the role of PGs in citrus fruitlet abscission (CFA), we have obtained 38 citrus PG (CitPG) members, based on the citrus genome sequences. The ORF length varied from 378 to 2418 bp, encoding proteins with theoretical pI and molecular mass ranging from 4.83 to 9.92 and from 13,951.71 to 85,542.28, respectively. Most CitPGs contained no less than 3 introns, suggesting a high probability of alternative splicing. Phylogenetic tree revealed that all PGs could be divided into three groups, in which 9 CitPGs, including CitPG2, CitPG3, CitPG10, CitPG24, CitPG27, CitPG29, CitPG30, CitPG33 and CitPG34 possessed a close relationship with abscission-associated PGs, indicating their role in CFA. Expression analysis further demonstrated that CitPG2, CitPG29 and CitPG34 might be involved in CFA, the expression levels of which could be induced by ethylene, inhibited by IAA and increased during CFA. The findings in this study have provided a foundation for future studies to elucidate the roles of CitPGs in CFA.

SUBMITTER: Ge T

PROVIDER: S-EPMC6548785 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-wide identification and expression analysis of citrus fruitlet abscission-related polygalacturonase genes.

Ge Ting T Huang Xue X Pan Xiaoting X Zhang Jing J Xie Rangjin R

3 Biotech 20190604 7

Polygalacturonases (PGs) encoded by a relatively large gene family are involved in plant organ abscission, but few data is available in citrus. Here, to explore the role of PGs in citrus fruitlet abscission (CFA), we have obtained 38 citrus PG (CitPG) members, based on the citrus genome sequences. The ORF length varied from 378 to 2418 bp, encoding proteins with theoretical pI and molecular mass ranging from 4.83 to 9.92 and from 13,951.71 to 85,542.28, respectively. Most <i>CitPGs</i> contained ...[more]

PMID: 31218174

Similar Datasets

Project description:The high level of physiological fruitlet abscission in litchi (Litchi chinensis Sonn.) causes severe yield loss. Cell separation occurs at the fruit abscission zone (FAZ) and can be triggered by ethylene. However, a deep knowledge of the molecular events occurring in the FAZ is still unknown. Here, genome-wide digital transcript abundance (DTA) analysis of putative fruit abscission related genes regulated by ethephon in litchi were studied. More than 81 million high quality reads from seven ethephon treated and untreated control libraries were obtained by high-throughput sequencing. Through DTA profile analysis in combination with Gene Ontology and KEGG pathway enrichment analyses, a total of 2730 statistically significant candidate genes were involved in the ethephon-promoted litchi fruitlet abscission. Of these, there were 1867 early-responsive genes whose expressions were up- or down-regulated from 0 to 1 d after treatment. The most affected genes included those related to ethylene biosynthesis and signaling, auxin transport and signaling, transcription factors (TFs), protein ubiquitination, ROS response, calcium signal transduction, and cell wall modification. These genes could be clustered into four groups and 13 subgroups according to their similar expression patterns. qRT-PCR displayed the expression pattern of 41 selected candidate genes, which proved the accuracy of our DTA data. Ethephon treatment significantly increased fruit abscission and ethylene production of fruitlet. The possible molecular events to control the ethephon-promoted litchi fruitlet abscission were prompted out. The increased ethylene evolution in fruitlet would suppress the synthesis and polar transport of auxin and trigger abscission signaling. To the best of our knowledge, it is the first time to monitor the gene expression profile occurring in the FAZ-enriched pedicel during litchi fruit abscission induced by ethephon on the genome-wide level. This study will contribute to a better understanding for the molecular regulatory mechanism of fruit abscission in litchi.

Project description: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.

Dataset Information

Genome-wide identification and expression analysis of citrus fruitlet abscission-related polygalacturonase genes.

Publications

Genome-wide identification and expression analysis of citrus fruitlet abscission-related polygalacturonase genes.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets