Genome-wide investigation of the nuclear factor Y gene family in Ginger (Zingiber officinale Roscoe): evolution and expression profiling during development and abiotic stresses.
Abiotic stress
Ginger
Inflorescence/Rhizome development
ZoNF-Ys
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
31 Aug 2024
31 Aug 2024
Historique:
received:
20
04
2023
accepted:
03
07
2024
medline:
1
9
2024
pubmed:
1
9
2024
entrez:
31
8
2024
Statut:
epublish
Résumé
Nuclear 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. We 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). In 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. This 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.
Sections du résumé
BACKGROUND
BACKGROUND
Nuclear 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.
METHODS
METHODS
We 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).
RESULTS
RESULTS
In 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.
CONCLUSION
CONCLUSIONS
This 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.
Identifiants
pubmed: 39217307
doi: 10.1186/s12864-024-10588-5
pii: 10.1186/s12864-024-10588-5
doi:
Substances chimiques
CCAAT-Binding Factor
0
Plant Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
820Subventions
Organisme : High-level Talents of Chong qing University of Arts and Sciences
ID : P2021YL11
Organisme : High-level Talents of Chong qing University of Arts and Sciences
ID : P2021YL11
Organisme : High-level Talents of Chong qing University of Arts and Sciences
ID : P2021YL11
Organisme : Chongqing Science and Technology support projects
ID : CSTB2022NSCQ-MSX1263
Organisme : Chongqing Science and Technology support projects
ID : CSTB2022NSCQ-MSX1263
Organisme : Chongqing Science and Technology support projects
ID : CSTB2022NSCQ-MSX1263
Organisme : Scientific and Technological Research Program of Chongqing Municipal Education Commission
ID : KJZD-M202101301
Organisme : Scientific and Technological Research Program of Chongqing Municipal Education Commission
ID : KJZD-M202101301
Organisme : Scientific and Technological Research Program of Chongqing Municipal Education Commission
ID : KJZD-M202101301
Organisme : Chongqing condiment industry system major special projects
ID : (2021-2025)-6
Organisme : Chongqing condiment industry system major special projects
ID : (2021-2025)-6
Organisme : Chongqing condiment industry system major special projects
ID : (2021-2025)-6
Organisme : Chongqing condiment industry system major special projects
ID : (2021-2025)-6
Organisme : The Yongchuan Ginger Germplasm Resource Garden of Chongqing City
ID : ZWZZ2020014
Organisme : The Yongchuan Ginger Germplasm Resource Garden of Chongqing City
ID : ZWZZ2020014
Informations de copyright
© 2024. The Author(s).
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