Genome-wide identification, comprehensive characterization of transcription factors, cis-regulatory elements, protein homology, and protein interaction network of DREB gene family in Solanum lycopersicum

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Nov. 24, 2022

Tomato is a drought-sensitive crop which has high susceptibility to adverse climatic changes. Dehydration-responsive element-binding (DREB) are significant plant transcription factors that have vital role in regulating abiotic stress tolerance by networking with DRE/CRT

Language: Английский

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Genome-wide analysis of AP2/ERF transcription factors that regulate fruit development of Chinese prickly ash

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: June 15, 2024

Abstract Background AP2/ERF is a large family of plant transcription factor proteins that play essential roles in signal transduction, growth and development, responses to various stresses. The has been identified verified by functional analysis plants, but so far there no comprehensive study these factors Chinese prickly ash. Phylogenetic, motif, analyses combined with transcriptome ash fruits at different developmental stages (30, 60, 90 days after anthesis) were conducted this study. Results 146 ZbAP2/ERF genes could be classified into 15 subgroups. motif revealed the presence motifs or elements each group may explain differences between groups. ZbERF13.2 , ZbRAP2-12 ZbERF2.1 showed high levels expression early fruit development. ZbRAP2-4 ZbERF3.1 significantly expressed coloring stage (R2 G2). ZbERF16 ripening level increased as continued develop. Relative gene 6 representative ZbAP2/ERFs assessed RT-qPCR agreed results. Conclusions These screening can used candidate affect results help guide future genetic improvement enrich our understanding their regulatory functions plants.

Language: Английский

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Genome-Wide Identification of the ERF Transcription Factor Family for Structure Analysis, Expression Pattern, and Response to Drought Stress in Populus alba × Populus glandulosa

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(4), P. 3697 - 3697

Published: Feb. 12, 2023

The Ethylene Responsive Factor (ERF) transcription factor family is important for regulating plant growth and stress responses. Although the expression patterns of ERF members have been reported in many species, their role Populus alba × glandulosa, an model forest research, remains unclear. In this study, we identified 209 PagERF factors by analyzing P. glandulosa genome. We analyzed amino acid sequences, molecular weight, theoretical pI (Isoelectric point), instability index, aliphatic grand average hydropathicity, subcellular localization. Most PagERFs were predicted to localize nucleus, with only a few localized cytoplasm nucleus. Phylogenetic analysis divided proteins into ten groups, Class I X, those belonging same group containing similar motifs. Cis-acting elements associated hormones, abiotic responses, MYB binding sites promoters genes. used transcriptome data analyze genes different tissues including axillary buds, young leaves, functional cambium, xylem, roots, results indicated that are expressed all especially roots. Quantitative verification consistent data. When seedlings treated 6% polyethylene glycol 6000 (PEG6000), RT-qRCR showed nine responded drought various tissues. This study provides new perspective on roles development, responses glandulosa. Our basis research future.

Language: Английский

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Comprehensive analysis and expression profiles of the AP2/ERF gene family during spring bud break in tea plant (Camellia sinensis)

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: April 20, 2023

AP2/ERF transcription factors (AP2/ERFs) are important regulators of plant physiological and biochemical metabolism. Evidence suggests that AP2/ERFs may be involved in the regulation bud break woody perennials. Green tea is economically vital China, its production value significantly affected by time spring plant. However, relationship between remains largely unknown.A total 178 genes (CsAP2/ERFs) were identified genome Based on phylogenetic analysis, these could classified into five subfamilies. The analysis gene duplication events demonstrated whole (WGD) or segmental was primary way CsAP2/ERFs amplification. According to result Ka/Ks calculation, purification selection dominated evolution CsAP2/ERFs. Furthermore, composition structure analyses indicated different subfamilies contained a variety structures conserved motifs, potentially resulting functional differences among promoters also various signal-sensing elements, such as abscisic acid responsive light elements low temperature elements. evidence presented here offers theoretical foundation for diverse functions Additionally, expressions during analyzed RNA-seq grouped clusters A-F according their expression patterns. changes A B more synchronized with Moreover, several potential correlation genes, D-type cyclin screened out through weighted network (WGCNA). Temperature treatment experiments individually nine candidate related plant.This study provides new role plant, establishes analyzing molecular mechanism contributes improvement cultivars.

Language: Английский

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CtDREB52 transcription factor regulates UV-B-induced flavonoid biosynthesis by transactivating CtMYB and CtF3′H in Safflower (Carthamus tinctorius L.)

Plant Stress, Journal Year: 2024, Volume and Issue: 11, P. 100384 - 100384

Published: Feb. 6, 2024

The APETALA2/ethylene-responsive element binding protein (AP2/ERF) is a highly conserved transcription factors family, involved in plant growth, development, and response to diverse stress conditions. Until recently, the AP2/ERF family has not been functionally characterized safflower. In total, 187 genes were identified from safflower genome. Phylogenetic analysis divided these CtAP2/ERFs into four distinct groups: DREB, ERFs, AP2s, RAV genes. Furthermore, motifs, gene structure, cis-regulatory elements suggested important evolutionary insights potential role of CtAP2/ERFs. Moreover, comprehensive expression conducted across various flowering stages demonstrated consistent pattern CtDREB52, which exhibited significant correlation with alterations total flavonoid content. Importantly, CtDREB52 was found be responsive UV-B stress, its overexpression only promoted accumulation but also induced an early phenotype up-regulated key pathway, while silencing showed opposite effect. Further, interaction between CtDFR CtMYB enzymes confirmed through yeast two-hybrid BiFC analysis. These findings provide CtDREB52-mediated regulation biosynthesis under by interacting

Language: Английский

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Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(23), P. 15225 - 15225

Published: Dec. 3, 2022

Juglans mandshurica has strong freezing resistance, surviving temperatures as low -40 °C, making it an important freeze tolerant germplasm resource of the genus Juglans. APETALA2/ethylene responsive factor (AP2/ERF) is a plant-specific superfamily transcription factors that regulates plant development, growth, and response to biotic abiotic stress. In this study, phylogenetic analysis was used identify 184 AP2/ERF genes in J. genome, which were classified into five subfamilies (JmAP2, JmRAV, JmSoloist, JmDREB, JmERF). A significant amount discordance observed distribution throughout its 16 chromosomes. Duplication found 14 tandem 122 segmental gene pairs, indicated duplications may be main reason for JmAP2/ERF family expansion. Gene structural revealed 64 contained introns. evolution among Juglandaceae separated by 14.23 15 Mya from regia Carya cathayensis, respectively. Based on promoter mandshurica, many cis-acting elements discovered are related light, hormones, tissues, stress processes. Proteins contribute cold resistance selected further construct regulatory network based GO annotation protein interaction analysis. Expression profiling using qRT-PCR showed involved seven significantly upregulated under female flower buds phloem This study provides new light role response, paving way functional validation TFs their application genetic improvement other tree species.

Language: Английский

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GWAS Reveals a Novel Candidate Gene CmoAP2/ERF in Pumpkin (Cucurbita moschata) Involved in Resistance to Powdery Mildew

International Journal of Molecular Sciences, Journal Year: 2022, Volume and Issue: 23(12), P. 6524 - 6524

Published: June 10, 2022

Pumpkin (Cucurbita moschata Duchesne ex Poir.) is a multipurpose cash crop rich in antioxidants, minerals, and vitamins; the seeds are also good source of quality oils. However, pumpkin susceptible to fungus Podosphaera xanthii, an obligate biotrophic pathogen, which usually causes powdery mildew (PM) on both sides leaves reduces photosynthesis. The fruits infected plants often smaller than usual unpalatable. This study identified novel gene that involves PM resistance pumpkins through genome-wide association (GWAS). allelic variation CmoCh3G009850 encoding for AP2-like ethylene-responsive transcription factor (CmoAP2/ERF) was proven be involved resistance. Validation GWAS data revealed six single nucleotide polymorphism (SNP) variations CmoAP2/ERF coding sequence between resistant (IT 274039 [PMR]) 278592 [PMS]). A polymorphic marker (dCAPS) developed based diversity differentiate these two haplotypes. Genetic analysis segregating population derived from PMS PMR parents provided evidence incomplete dominant gene-mediated Further, qRT-PCR assay validated elevated expression during infection compared with PMS. These results highlighted pivotal role conferring identifies it as valuable molecular entity breeding cultivars.

Language: Английский

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Functional Characterization of AP2/ERF Transcription Factors during Flower Development and Anthocyanin Biosynthesis Related Candidate Genes in Lycoris

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(19), P. 14464 - 14464

Published: Sept. 23, 2023

The APETALA2/ethylene-responsive transcription factor (AP2/ERF) family has been extensively investigated because of its significant involvement in plant development, growth, fruit ripening, metabolism, and stress responses. To date, there little investigation into how the AP2/ERF genes influence flower formation anthocyanin biosynthesis Lycoris. Herein, 80 putative LrAP2/ERF factors (TFs) with complete open reading frames (ORFs) were retrieved from Lycoris transcriptome sequence data, which could be divided five subfamilies dependent on their protein sequences. Furthermore, our findings demonstrated that belonging to same subfamily had structural similarities conserved motifs. analyzed for playing an important role water deprivation, by means gene ontology (GO) enrichment analysis. expression pattern differed across tissues might growth development. In response methyl jasmonate (MeJA) exposure drought stress, each varied time. Moreover, a total 20 components characterized using ultra-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI-MS/MS) analysis, pelargonidin-3-O-glucoside-5-O-arabinoside was identified as major aglycone responsible coloration red petals addition, we mapped relationships between metabolites found LrAP2/ERF16 is strongly linked pelargonidin accumulation petals. These provide basic conceptual groundwork future research molecular underpinnings regulation mechanisms TFs floral

Language: Английский

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Comprehensive transcriptome analysis of AP2/ERFs in Osmanthus fragrans reveals the role of OfERF017-mediated organic acid metabolism pathway in flower senescence

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: Sept. 26, 2024

Osmanthus fragrans is an ethylene-sensitive flower, and flower senescence was mediated by ethylene-responsive transcription factors ( OfERFs ). A total of 227 were identified from O. , which classified into five subfamilies: AP2 (35), DREB (57), ERF (125), RAV (6), Soloist (4). Gene composition structural analysis indicate that members different subfamilies have gene structures conserved domains. Their promoter contains various functional responsive elements, including auxin, jasmonic acid, other elements. Among them, 124 OfAP2/ERF genes expressed at any stage flowering, 10 them may play roles in flowering or senescence. By comparative transcriptome analysis, OfAP2/ERFs affected ethephon (ETH) 5′-azacytidine (Aza) treatment divided three categories, target sets. Importantly, these sets participate similar biological processes metabolic pathways, suggesting ethylene DNA hypomethylation crosstalk a unique mechanism regulating the fragrans. Co-expression revealed several key played central role organic acid metabolism biosynthesis branched-chain amino acids (BcAAs), among OfERF017 selected for further analysis. Overexpression leads to significant enrichment decrease levels promoting . Together, results give insights characteristics

Language: Английский

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Understanding Transcription Factors and How They Affect Processes in Cucumber Sex Determination

Metabolites, Journal Year: 2023, Volume and Issue: 13(6), P. 740 - 740

Published: June 10, 2023

Plant reproduction is a fundamental process on Earth from the perspective of biodiversity, biomass gain, and crop productivity. It therefore important to understand sex determination process, many researchers are investigating molecular basis this phenomenon. However, information influence transcription factors (TFs), genes that encode DNA-binding proteins, limited, although cucumber model plant in regard. In present study, based RNA-seq data for differentially expressed (DEGs), we aimed investigate regulatory TFs may metabolic processes shoot apex containing forming flower buds. Therefore, annotation genome B10 line was supplemented with assigned families factors. By performing ontology analyses DEGs, they participate were identified, located among results. addition, have significantly overrepresented targets DEGs detected, sex-specific interactome network maps generated, indicating their effects furthermore, leading formation different-sex flowers. Among most TF comparisons NAC, bHLH, MYB, bZIP families. An interaction analysis indicated abundant DEGs' AP2/ERF, bZIP, those significant impact developmental namely AP/ERF family, followed by DOF, MADS, others. Thus, networks' central nodes key regulators identified respect male, female, hermaphrodite forms. Here, proposed first influences metabolism development cucumber. These findings help us genetics functional mechanisms underlying processes.

Language: Английский

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