Dataset Information

Identification of Ginger (Zingiber officinale Roscoe) Reference Genes for Gene Expression Analysis.

ABSTRACT: Quantitative real-time PCR (qRT-PCR) is widely used in the detection of gene expression level. However, there is no suitable ginger reference gene for qPCR analysis. Therefore, it is the primary task to select and validate the appropriate ginger reference gene to normalize the expression of target genes. In this study, 14 candidate reference genes were selected and analyzed in different tissues (leaf, and rhizome), different development stages, different varieties, and abiotic stress (ABA and salt stress). Expression stability was calculated using geNorm and NormFinder, Bestkeeper, and RefFinder. For abiotic stress and total conditions, 28S and COX were identified as the most stable genes. In addition, RPII was the most stable in the different development stages and different varieties. TEF2 and RPL2 were the least stably expressed in the tissue and all the conditions. In order to verify the feasibility of these genes as reference genes, we used the most stable and least stable reference genes to normalize the expression levels of ZoSPS genes under different conditions. This work can provide theoretical support for future research on ginger gene expression.

SUBMITTER: Lv Y

PROVIDER: S-EPMC7670040 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Identification of Ginger (<i>Zingiber officinale</i> Roscoe) Reference Genes for Gene Expression Analysis.

Lv Yao Y Li Yanyan Y Liu Xiaohui X Xu Kun K

Frontiers in genetics 20201103

Quantitative real-time PCR (qRT-PCR) is widely used in the detection of gene expression level. However, there is no suitable ginger reference gene for qPCR analysis. Therefore, it is the primary task to select and validate the appropriate ginger reference gene to normalize the expression of target genes. In this study, 14 candidate reference genes were selected and analyzed in different tissues (leaf, and rhizome), different development stages, different varieties, and abiotic stress (ABA and sa ...[more]

PMID: 33240331

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Project description:BackgroundMicroRNAs (miRNAs) are endogenous, non-coding small functional RNAs that govern the post-transcriptional regulatory system of gene expression and control the growth and development of plants. Ginger is an herb that is well-known for its flavor and medicinal properties. The genes involved in ginger rhizome development and secondary metabolism have been discovered, but the genome-wide identification of miRNAs and their overall expression profiles and targets during ginger rhizome development are largely unknown. In this study, we used BGISEQ-500 technology to perform genome-wide identification of miRNAs from the leaf, stem, root, flower, and rhizome of ginger during three development stages.ResultsIn total, 104 novel miRNAs and 160 conserved miRNAs in 28 miRNA families were identified. A total of 181 putative target genes for novel miRNAs and 2772 putative target genes for conserved miRNAs were predicted. Transcriptional factors were the most abundant target genes of miRNAs, and 17, 9, 8, 4, 13, 8, 3 conserved miRNAs and 5, 7, 4, 5, 5, 15, 9 novel miRNAs showed significant tissue-specific expression patterns in leaf, stem, root, flower, and rhizome. Additionally, 53 miRNAs were regarded as rhizome development-associated miRNAs, which mostly participate in metabolism, signal transduction, transport, and catabolism, suggesting that these miRNAs and their target genes play important roles in the rhizome development of ginger. Twelve candidate miRNA target genes were selected, and then, their credibility was confirmed using qRT-PCR. As the result of qRT-PCR analysis, the expression of 12 candidate target genes showed an opposite pattern after comparison with their miRNAs. The rhizome development system of ginger was observed to be governed by miR156, miR319, miR171a_2, miR164, and miR529, which modulated the expression of the SPL, MYB, GRF, SCL, and NAC genes, respectively.ConclusionThis is a deep genome-wide investigation of miRNA and identification of miRNAs involved in rhizome development in ginger. We identified 52 rhizome-related miRNAs and 392 target genes, and this provides an important basis for understanding the molecular mechanisms of the miRNA target genes that mediate rhizome development in ginger.

Project description:BackgroundProtein phosphatases type 2C (PP2C) are heavily involved in plant growth and development, hormone-related signaling pathways and the response of various biotic and abiotic stresses. However, a comprehensive report identifying the genome-scale of PP2C gene family in ginger is yet to be published.ResultsIn this study, 97 ZoPP2C genes were identified based on the ginger genome. These genes were classified into 15 branches (A-O) according to the phylogenetic analysis and distributed unevenly on 11 ginger chromosomes. The proteins mainly functioned in the nucleus. Similar motif patterns and exon/intron arrangement structures were identified in the same subfamily of ZoPP2Cs. Collinearity analysis indicated that ZoPP2Cs had 33 pairs of fragment duplicated events uniformly distributed on the corresponding chromosomes. Furthermore, ZoPP2Cs showed greater evolutionary proximity to banana's PP2Cs. The forecast of cis-regulatory elements and transcription factor binding sites demonstrated that ZoPP2Cs participate in ginger growth, development, and responses to hormones and stresses. ZoERFs have plenty of binding sites of ZoPP2Cs, suggesting a potential synergistic contribution between ZoERFs and ZoPP2Cs towards regulating growth/development and adverse conditions. The protein-protein interaction network displayed that five ZoPP2Cs (9/23/26/49/92) proteins have robust interaction relationship and potential function as hub proteins. Furthermore, the RNA-Seq and qRT-PCR analyses have shown that ZoPP2Cs exhibit various expression patterns during ginger maturation and responses to environmental stresses such as chilling, drought, flooding, salt, and Fusarium solani. Notably, exogenous application of melatonin led to notable up-regulation of ZoPP2Cs (17/59/11/72/43) under chilling stress.ConclusionsTaken together, our investigation provides significant insights of the ginger PP2C gene family and establishes the groundwork for its functional validation and genetic engineering applications.

Project description:BackgroundNuclear factor Y (NF-Y) plays a vital role in numerous biological processes as well as responses to biotic and abiotic stresses. However, its function in ginger (Zingiber officinale Roscoe), a significant medicinal and dietary vegetable, remains largely unexplored. Although the NF-Y family has been thoroughly identified in many plant species, and the function of individual NF-Y TFs has been characterized, there is a paucity of knowledge concerning this family in ginger.MethodsWe identified the largest number of NF-Y genes in the ginger genome using two BLASTP methods as part of our ginger genome research project. The conserved motifs of NF-Y proteins were analyzed through this process. To examine gene duplication events, we employed the Multiple Collinearity Scan toolkit (MCScanX). Syntenic relationships of NF-Y genes were mapped using the Dual Synteny Plotter software. Multiple sequence alignments were performed with MUSCLE under default parameters, and the resulting alignments were used to generate a maximum likelihood (ML) phylogenetic tree with the MEGA X program. RNA-seq analysis was conducted on collected samples, and statistical analyses were performed using Sigma Plot v14.0 (SYSTAT Software, USA).ResultsIn this study, the ginger genome was utilized to identify 36 NF-Y genes (10 ZoNF-YAs, 16 ZoNF-YBs, and 10 ZoNF-YCs), which were renamed based on their chromosomal distribution. Ten distinct motifs were identified within the ZoNF-Y genes, with certain unique motifs being vital for gene function. By analyzing their chromosomal location, gene structure, conserved protein motifs, and gene duplication events, we gained a deeper understanding of the evolutionary characteristics of these ZoNF-Y genes. Detailed analysis of ZoNF-Y gene expression patterns across various tissues, performed through RNA-seq and qRT-PCR, revealed their significant role in regulating ginger rhizome and flower growth and development. Additionally, we identified the ZoNF-Y family genes that responded to abiotic stresses.ConclusionThis study represents the first identification of the ZoNF-Y family in ginger. Our findings contribute to research on evolutionary characteristics and provide a better understanding of the molecular basis for development and abiotic stress response. Furthermore, it lays the foundation for further functional characterization of ZoNF-Y genes with an aim of ginger crop improvement.

Dataset Information

Identification of Ginger (Zingiber officinale Roscoe) Reference Genes for Gene Expression Analysis.

Publications

Identification of Ginger (<i>Zingiber officinale</i> Roscoe) Reference Genes for Gene Expression Analysis.

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