Genome-wide systematic characterization of bZIP transcription factors and their expression profiles during seed development and in response to salt stress in peanut.
Arachis
/ genetics
Basic-Leucine Zipper Transcription Factors
/ genetics
Binding Sites
Gene Duplication
Gene Expression Profiling
Gene Expression Regulation, Developmental
Gene Expression Regulation, Plant
Genes, Plant
Genome, Plant
Introns
/ genetics
Multigene Family
Phylogeny
Plant Proteins
/ genetics
Protein Multimerization
Salt Stress
/ genetics
Seeds
/ genetics
Evolution
Expression analysis
Peanut
bZIP gene family
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
16 Jan 2019
16 Jan 2019
Historique:
received:
03
10
2018
accepted:
07
01
2019
entrez:
18
1
2019
pubmed:
18
1
2019
medline:
30
4
2019
Statut:
epublish
Résumé
Plant basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses. However, systematic investigation and analyses of the bZIP gene family in peanut are lacking in spite of the availability of the peanut genome sequence. In this study, we identified 50 and 45 bZIP genes from Arachis duranensis and A. ipaensis genomes, respectively. Phylogenetic analysis showed that Arachis bZIP genes were classified into nine groups, and these clusters were supported by several group-specific features, including exon/intron structure, intron phases, MEME motifs, and predicted binding site structure. We also identified possible variations in DNA-binding-site specificity and dimerization properties among different Arachis bZIPs by inspecting the amino acid residues at some key sites. Our analysis of the evolutionary history analysis indicated that segmental duplication, rather than tandem duplication, contributed greatly to the expansion of this gene family, and that most Arachis bZIPs underwent strong purifying selection. Through RNA-seq and quantitative real-time PCR (qRT-PCR) analyses, the co-expressed, differentially expressed and several well-studied homologous bZIPs were identified during seed development stages in peanut. We also used qRT-PCR to explore changes in bZIP gene expression in response to salt-treatment, and many candidate bZIPs in groups A, B, and S were proven to be associated with the salt-stress response. This study have conducted a genome-wide identification, characterization and expression analysis of bZIP genes in Arachis genomes. Our results provide insights into the evolutionary history of the bZIP gene family in peanut and the funcntion of Arachis bZIP genes during seed development and in response to salt stress.
Sections du résumé
BACKGROUND
BACKGROUND
Plant basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses. However, systematic investigation and analyses of the bZIP gene family in peanut are lacking in spite of the availability of the peanut genome sequence.
RESULTS
RESULTS
In this study, we identified 50 and 45 bZIP genes from Arachis duranensis and A. ipaensis genomes, respectively. Phylogenetic analysis showed that Arachis bZIP genes were classified into nine groups, and these clusters were supported by several group-specific features, including exon/intron structure, intron phases, MEME motifs, and predicted binding site structure. We also identified possible variations in DNA-binding-site specificity and dimerization properties among different Arachis bZIPs by inspecting the amino acid residues at some key sites. Our analysis of the evolutionary history analysis indicated that segmental duplication, rather than tandem duplication, contributed greatly to the expansion of this gene family, and that most Arachis bZIPs underwent strong purifying selection. Through RNA-seq and quantitative real-time PCR (qRT-PCR) analyses, the co-expressed, differentially expressed and several well-studied homologous bZIPs were identified during seed development stages in peanut. We also used qRT-PCR to explore changes in bZIP gene expression in response to salt-treatment, and many candidate bZIPs in groups A, B, and S were proven to be associated with the salt-stress response.
CONCLUSIONS
CONCLUSIONS
This study have conducted a genome-wide identification, characterization and expression analysis of bZIP genes in Arachis genomes. Our results provide insights into the evolutionary history of the bZIP gene family in peanut and the funcntion of Arachis bZIP genes during seed development and in response to salt stress.
Identifiants
pubmed: 30651065
doi: 10.1186/s12864-019-5434-6
pii: 10.1186/s12864-019-5434-6
pmc: PMC6335788
doi:
Substances chimiques
Basic-Leucine Zipper Transcription Factors
0
Plant Proteins
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
51Subventions
Organisme : National Natural Science Foundation of China
ID : 31671734
Organisme : National Natural Science Foundation of China
ID : 31461143022
Organisme : National Natural Science Foundation of China
ID : 31371662
Organisme : National Natural Science Foundation of China
ID : 31770250
Organisme : National High Technology Research and Development Program of China
ID : 2013AA102602
Organisme : Agriculture Research System of China
ID : CARS-14
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