Search Results (1,356)

Purple cowpea accumulates abundant anthocyanins in its epidermis, with R2R3-MYB transcription factors serving as potential regulators of anthocyanin accumulation. This study systematically deciphered the genome-wide characteristics of cowpea R2R3-MYB transcription factors, elucidating their critical roles in plant anthocyanin accumulation. Employing a combined strategy of HMMER Hidden Markov Model searches and BLASTP homology alignment, we successfully identified 127 non-redundant VuR2R3-MYB transcription factors. The encoded proteins exhibited remarkable physicochemical diversity: the average length reached 338.8 amino acid residues, with theoretical isoelectric points distributed between 4.79 and 10.91 residues. When performing a phylogenetic analysis with Arabidopsis homologs, 27 distinct subgroups were identified. Among them, the S4–S7 clades showed conserved protein architectures, which might play a role in regulating the phenylpropanoid pathway. An analysis of the gene architecture revealed patterns of intron/exon organization. Specifically, 85 out of 127 loci (66.9%) presented the typical two-intron configuration, whereas 18 genes had no introns. An investigation of the promoters found that, on average, each gene had 52 cis-regulatory elements. These elements were mainly light-responsive motifs and phytohormone-related elements. Chromosomal mapping indicated an uneven distribution of these genes across 11 chromosomes. Duplication analysis further showed 13 tandem repeats and 54 segmentally duplicated pairs. An analysis of evolutionary constraints demonstrated that purifying selection was predominant (Ka/Ks < 0.5) among paralogous pairs. Through comparative transcriptomics of pod color variants, 19 differentially expressed MYB regulators were identified. These included VuR2R3-MYB23 (MYB3 homolog), VuR2R3-MYB95 (MYB4 homolog), VuR2R3-MYB53 (MYB114 homolog), and VuR2R3-MYB92 (MYB5 homolog), which showed a strong correlation with the patterns of anthocyanin accumulation. Our findings are expected to contribute to elucidating the potential regulatory mechanisms through which R2R3-MYB transcription factors mediate anthocyanin biosynthesis and accumulation. Full article

Pink-flowered Oriental lily cultivars exhibit significant color fading under high temperatures, but the underlying regulatory mechanisms remain unclear. We subjected ‘Souvenir’ Oriental lily plants to temperature treatments (20 °C and 35 °C) and performed transcriptome sequencing and weighted gene co-expression network analysis (WGCNA). The high temperature (35 °C) significantly reduced the anthocyanin content in tepals. The transcriptome analysis identified 8354 differentially expressed genes, with the GO and KEGG analyses revealing a dynamic transition from early stress responses to metabolic adaptation. The WGCNA revealed a module strongly correlated with the anthocyanin content, from which we constructed a gene co-expression network using known anthocyanin-related genes, including the key transcription factor LhMYB12 and structural genes involved in the anthocyanin biosynthetic pathway (LhANS, LhDFR, LhUGT78, and LhF3′H). Through this comprehensive network analysis, we successfully identified and screened LhERF109 as a promising regulatory candidate. The transient overexpression of LhERF109 was found to enhance anthocyanin accumulation and upregulate biosynthetic genes including LhMYB12, while silencing LhERF109 expression produced the opposite effects. These findings identify LhERF109 as a positive regulator of anthocyanin biosynthesis under high temperatures, providing new targets for breeding heat-tolerant lilies with stable flower coloration. Full article

Isoflavones are important secondary metabolites in leguminous plants with significant physiological functions and economic value. However, the genetic variation, transcriptional regulation, and metabolic pathways governing isoflavone biosynthesis in Trifolium pratense remain largely unexplored. In this study, we systematically analyzed 500 accessions of T. pratense for isoflavone content and performed RNA-seq-based transcriptomic profiling to investigate the molecular mechanisms underlying isoflavone biosynthesis. Cluster analysis revealed significant genetic variation, with distinct transcriptional profiles between high- (H1, H2, H3) and low-isoflavone (L1, L2, L3) groups. GO and KEGG pathway enrichment analyses identified key metabolic pathways, including phenylpropanoid metabolism, flavonoid biosynthesis, carbohydrate metabolism, and hormone signaling, which play crucial roles in isoflavone regulation. Weighted gene co-expression network analysis (WGCNA) identified three key gene modules—MEblue, MEturquoise, and MEyellow—strongly correlated with isoflavone content. The MEturquoise and MEyellow modules were upregulated in high-isoflavone groups and were enriched in phenylpropanoid biosynthesis, lipid metabolism, and transcriptional regulation, suggesting that these pathways actively promote isoflavone accumulation. Conversely, the MEblue module, highly expressed in low-isoflavone groups, was enriched in sugar metabolism and MAPK signaling, indicating a potential metabolic flux shift away from secondary metabolism. Moreover, key rate-limiting enzymes (PAL, C4H, 4CL, CHS, and IFS) exhibited higher expression in high-isoflavone groups, highlighting their importance in precursor supply and enzymatic catalysis. Additionally, transcription factors such as MYB, WRKY, and NAC were identified as potential regulators of isoflavone biosynthesis, indicating a complex interplay between hormonal, circadian, and environmental signals. This study provides a comprehensive molecular framework for understanding isoflavone biosynthesis in T. pratense and identifies key regulatory genes and metabolic pathways that could be targeted for genetic improvement, metabolic engineering, and molecular breeding. The findings offer valuable insights into enhancing isoflavone production in legumes for agricultural, nutritional, and pharmaceutical applications. Full article

Plant U-box E3 ubiquitin ligases (PUBs) serve as crucial regulators of protein degradation and are fundamentally involved in plant developmental processes and stress response mechanisms. Despite their well-characterized roles in model plant species, the PUB gene family in the hybrid poplar (Populus alba × P. tremula var. glandulosa) remains poorly understood. By conducting a comprehensive genome-wide analysis, we identified 152 PUB genes in poplar and phylogenetically classified them into five distinct clades based on a comparative analysis with Arabidopsis thaliana and tomato PUB homologs. The structural characterization revealed that numerous PagPUB proteins possess additional functional domains, including ARM and WD40 repeats, which are indicative of potential functional diversification. Genomic distribution and synteny analyses demonstrated that the expansion of the PUB gene family predominantly resulted from whole-genome duplication (WGD) events, with evolutionary constraint analyses (Ka/Ks ratios < 1) suggesting strong purifying selection. An examination of the promoter region uncovered an abundance of stress-responsive cis-elements, particularly ABRE and MYB binding sites associated with abiotic stress and hormonal regulation. Transcriptome profiling demonstrated both tissue-specific expression patterns and dynamic regulation under diverse stress conditions, including drought, salinity, temperature extremes, and pathogen infection. Our findings provide the first systematic characterization of the PUB gene family in poplar and establish a valuable framework for elucidating their evolutionary history and functional significance in environmental stress adaptation. Full article

HD-Zip (homeodomain-leucine zipper) transcription factors play a crucial role in plant growth, development, and stress response; however, the HD-Zip gene family of Coix lacryma-jobi L. has not been identified. In this study, a total of 40 HD-Zip gene family members were identified in the genome of Coix. According to phylogenetic analysis, the Coix HD-Zip gene was divided into four subfamilies (I–IV), of which the HD-Zip I subfamily can be further divided into five branches. Moreover, HD-Zip members of the same subfamily usually share similar gene structures and conserved motifs. The transcription factor binding site enrichment analysis showed that there are many motifs for binding with transcription factors such as ERF (Ethylene responsive factor), MYB (v-myb avian myeloblastosis viral oncogene homolog), and ARF (Auxin Response Factor) in the promoter region of the ClHDZ genes. The results of qPCR (Quantitative Polymerase Chain Reaction) and expression profile analysis showed that ClHD-Zip I genes showed different levels of expression under different stress treatments. Among them, ClHDZ4 was located in the nucleus, and its expression pattern was significantly upregulated under salt, drought, and high-temperature stress. In addition, ectopic expression of ClHDZ4 enhanced the growth of yeast strains under drought, salt, or high-temperature treatment. In summary, these results laid a foundation for further research on the resistance function of the Coix HD-Zip gene. Full article

Wheat (Triticum aestivum) is one of the most important cereal crops globally, with significant economic value. The Arabidopsis Tóxicos en Levadura (ATL) gene family, which comprises members of ubiquitin ligase enzymes (E3s), functions in substrate protein tagging during ubiquitin-mediated protein modification. Recent studies have demonstrated its involvement in stress responses. However, the ATL gene family in wheat remains poorly characterized. This study aimed to identify the members of the ATL gene family in wheat and investigate their roles under salt stress. We identified 334 TaATL genes in the wheat genome, all of which contain either RING-H2, RING U-box, or RAD18 superfamily domains, exhibiting a remarkably low proportion of intron-containing genes. The Ka/Ks (non-synonymous to synonymous substitution rate) analysis and cis-acting element analysis of the TaATL gene family indicate that its sequences are highly conserved and functionally constrained, suggesting that it may participate in abiotic stress responses through the ABA, MeJA, and MYB signaling pathways. Both RNA-seq analysis and RT-qPCR data demonstrated that the expression levels of the TaATL gene family were significantly upregulated under stress conditions, indicating their crucial roles in stress responses. This study demonstrates that the targeted regulation of stress-responsive signaling pathways mediated by superior TaATL gene family members can effectively enhance wheat salt tolerance, thereby providing a viable strategy for the development of high-yielding cultivars adapted to saline agricultural ecosystems. Full article

Background: Coptis chinensis is a traditional medicinal plant rich in bioactive compounds like berberine, known for its antibacterial, anti-inflammatory, and antioxidant properties. This study aims to analyze the MYB transcription factor family in C. chinensis to better understand their roles in plant growth, development, metabolism, and stress responses. Methods: We employed bioinformatics to conduct a genome-wide identification of MYB genes in C. chinensis, followed by analyses of physicochemical properties, phylogenetic relationships, gene structures, chromosomal localization, conserved motifs, cis-acting elements, and expression patterns. Results were validated using qRT-PCR. Results: A total of 129 CcMYB genes were identified across nine chromosomes. Phylogenetic analysis categorized these genes into 19 subgroups, notably highlighting the S6 subgroup, which lacks counterparts in Arabidopsis. Comparative genomics revealed segmental duplication among gene pairs. Transcriptomic analysis indicated that CcMYB21, CcMYB40, CcMYB105, and CcMYB116 had high expression levels in stems. Importantly, CcMYB94 expression significantly increased under cadmium stress, suggesting its role in stress regulation. Conclusions: This study offers a comprehensive analysis of the MYB gene family in C. chinensis, underscoring the significance of MYB transcription factors in enhancing the plant’s medicinal value and stress tolerance, particularly against cadmium exposure. These insights pave the way for further exploration of specific MYB genes to improve stress resilience in C. chinensis. Full article

Seed germination is a complex developmental process and a critical stage in plant development. The mechanism of seed germination in Qiongzhuea tumidinoda remains unclear. In this study, the transcriptomic analysis of four germination stages was conducted to reveal the regulatory mechanism. Totals of 2352, 5523, and 4533 differentially expressed genes (DEGs) were identified in S2 vs. S1, S3 vs. S1, and S4 vs. S1, respectively. A total of 998 DEGs were identified during seed germination. Enrichment studies indicated that the DEGs were mainly involved in plant hormone signal transduction and phenylpropanoid biosynthesis pathways. In addition, 131 transcription factors were differentially expressed, of which ERFs and MYBs may play pivotal roles in seed germination. To sum up, TGA4, IAA24, SAUR32, AHK4, and HCT4 may regulate seed germination. Full article

The color of the walnut seed coat is a critical determinant of its market value; however, research into the mechanisms responsible for seed coat color formation is yet to be determined. Using two walnut clones with contrasting pale-yellow and light purple seed coats, we characterized pigmentation, particularly anthocyanin content, using spectrophotometry. We then conducted integrated transcriptomic and metabolomic analyses to identify the molecular mechanisms and pathways underlying their formation. The anthocyanin content in the light purple seed coat clone was significantly greater than that in the clone with a white seed coat. The results of comparative metabolomics indicated that four anthocyanins (delphinidin, cyanidin-3-(caffeoylglucoside), pelargonidin-3-(6″-caffeoylglucoside), and delphinidin-3-O-sophoroside) were significantly more abundant in the light purple seed coat clone. These anthocyanins were the key pigments responsible for the light purple coloration of the walnut seed coat. Furthermore, comparative transcriptomics revealed that structural genes in the anthocyanin biosynthesis pathway (e.g., phenylalanine ammonia-lyase, 4-coumarate-CoA ligase, chalcone isomerase, and bronze-1) were significantly upregulated in the purple seed coat clone. Coexpression network analysis revealed that several transcription factors (e.g., ARF, bHLH, and MYB-related) were significantly correlated with the upregulation of these structural genes and the accumulation of four key anthocyanins. These transcription factors may serve as critical regulators influencing seed coat color formation. In conclusion, these findings establish a strong theoretical foundation for walnut breeding aimed at developing diverse seed coat colors. Full article

Brassica species evolved through recurrent polyploidization and chromosomal rearrangements, forming diploid progenitors that hybridize into allopolyploids. These plants exhibit remarkable morphological diversity, with specialized edible organs including leaf-, stem-, root-, and oil-type cultivars, yet cross-species multi-organ transcriptomic studies elucidating their gene expression similarities and divergences remain lacking. To address this gap, we analyzed publicly available transcriptomes (downloaded from NCBI SRA) from eight organs (embryo, seed coat, silique, root, stem, leaf, flower and seedling) across six U’s Triangle species (Brassica rapa, B. nigra, B. oleracea, B. juncea, B. napus, B. carinata), revealing that (1) reproductive organs show higher gene expression conservation (GEC), particularly embryos (p < 0.05); (2) lineage-specific subgenome dominance patterns (BnaC/BjuB/BcaC) persist across organs; and (3) ancestral subgenomes functionally specialize, with MF2-subgenome transcription factors (YABBY/GRF) regulating embryogenesis and LF/MF1-subgenome MYBs controlling seed coat development. Comparative analyses demonstrate floral GEC exceeds that of the Arabidopsis thaliana homologs, while also exhibiting seed-specific divergence patterns. This study establishes a comprehensive Brassica multispecies expression atlas, elucidating organ-specific evolutionary conservation principles and providing molecular insights into subgenome functional partitioning, which offers valuable perspectives for understanding Brassica evolutionary mechanisms and crop improvement strategies. Full article

Quinoa (Chenopodium quinoa Willd.) has been widely grown as a cash crop. However, the molecular mechanism by which it responds to cold stress at the seed germination stage is still largely unknown. In this study, we performed a comparative transcriptomic analysis between the cold-tolerant cultivar XCq and cold-sensitive cultivar QCq in response to cold stress. A total number of 4552 and 4845 differentially expressed genes (DEGs) were identified in XCq and QCq upon the treatment of cold stress, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that the mitogen-activated protein kinase (MAPK) signaling pathway was identified only among the up-regulated DEGs in XCq.The expression of DEGs, which encoding transcription factors, such as AP2/ERF, bHLH, bZIP, MYB, ICEs, and CORs related to cold response, were higher in XCq than in QCq in response to cold stress. Weighted gene co-expression network analysis (WGCNA) showed that DEGs clustered in the co-expression modules positively correlated with the factors of quinoa variety and temperature were significantly enriched in the oxidative phosphorylation metabolic pathway. Further physiochemical analyses showed that the activities of superoxide dismutase and peroxidase as well as the contents of soluble protein and sugar, were significantly higher in XCq than in QCq. In summary, MAPK signaling and oxidative metabolism were the key pathways in quinoa upon cold stress. Our findings revealed that the enhanced activities of antioxidant enzymes alleviate the lipid peroxidation of membranes and promote the accumulation of osmotic adjustment substances, thereby enabling seeds to better resist oxidative damage under cold stress. Full article

Breast cancer (BRCA) continues to pose a serious risk to women’s health worldwide. Neoadjuvant chemotherapy (NAC) is a critical treatment strategy. Nevertheless, the heterogeneity in treatment outcomes necessitates the identification of reliable biomarkers and prognostic models. Programmed cell death (PCD) pathways serve as a critical factor in tumor development and treatment response. However, the relationship between the diverse patterns of PCD and NAC in BRCA remains unclear. We integrated machine learning and multiple bioinformatics tools to explore the association between 19 PCD patterns and the prognosis of NAC within a cohort of 921 BRCA patients treated with NAC from seven multicenter cohorts. A prognostic risk model based on PCD-related genes (PRGs) was constructed and evaluated using a combination of 117 machine learning algorithms. Immune infiltration analysis, mutation analysis, pharmacological analysis, and single-cell RNA sequencing (scRNA-seq) were conducted to explore the genomic profile and clinical significance of these model genes in BRCA. Immunohistochemistry (IHC) was employed to validate the expression of select model genes (UGCG, BTG22, TNFRSF21, and MYB) in BRCA tissues. We constructed a PRGs prognostic risk model by using a signature comprising 20 PCD-related DEGs to forecast the clinical outcomes of NAC in BRCA patients. The prognostic model demonstrated excellent predictive accuracy, with a high concordance index (C-index) of 0.772, and was validated across multiple independent datasets. Our results demonstrated a strong association between the developed model and the survival prognosis, clinical pathological features, immune infiltration, tumor microenvironment (TME), gene mutations, and drug sensitivity of NAC for BRCA patients. Moreover, IHC studies further demonstrated that the expression of certain model genes in BRCA tissues was significantly associated with the efficacy of NAC and emerged as an autonomous predictor of outcomes influencing the outcome of patients. We are the first to integrate machine learning and bulk and scRNA-seq to decode various cell death mechanisms for the prognosis of NAC in BRCA. The developed unique prognostic model, based on PRGs, provides a novel and comprehensive strategy for predicting the NAC outcomes of BRCA patients. This model not only aids in understanding the mechanisms underlying NAC efficacy but also offers insights into personalized treatment strategies, potentially improving patient outcomes. Full article

Cotton fiber length is an important measurement for application in the textile industry, and researchers are seeking to cultivate cotton plants with longer fibers. In this study, cotton fiber genes were systematically reviewed through meta-analysis in terms of extending and shortening fiber and the use of different research technologies for the first time. PubMed, Web of Science, China National Knowledge Infrastructure (CNKI), and Baidu Xueshu databases were included as literature retrieval sources. A total of 21,467 articles were retrieved, and 45 articles were used in the final analysis. Data analysis was performed using RevMan 5.4 software. To shorten cotton fiber length, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology was superior to virus-induced gene silencing (VIGS) technology and RNA interference (RNAi) technology [p = 0.002, MD = −1.05, 95% CI (−1.73, −0.37), Chi² = 39.89]. To increase cotton fiber length, CRISPR-Cas9 technology had a similar effect as VIGS technology [p = 0.12, MD = −0.59, 95% CI (−1.33, −0.15), Chi² = 0.17]. When some genes (GhLAC15, GhALDH7B4, GhMDHAR1A/GhDHAR2A, STTM-miR396b, GhMYB44, GhFP2, GhMYB7, GhKNL1, GhTCP4, GhHDA5, GhGalT1, GhKNOX6, GhXB38D, and GhBZR3) were damaged, cotton fiber length increased. Furthermore, we found that after gene interference, the fiber-shortening genes occurred more frequently than the fiber-elongating genes. Synergistic research on these genes may better promote cotton fiber elongation. Full article

The formation of flower color is closely related to anthocyanin synthesis. In this study, flowers of Bletilla striata (Orchidaceae) exhibiting distinct color morphs were collected and analyzed. The HPLC results showed significantly higher total flavonoid and anthocyanin contents in purple flowers compared to pink counterparts, with increases of 2.20-fold (p < 0.01) and 15.22-fold (p < 0.01), respectively. Cyanidin was the predominant anthocyanin in B. striata. Resequencing analyses highlighted SNP as the primary variation associated with color divergence. A comprehensive screen identified 61 genes encoding enzymes critical to the flavonoid and anthocyanin biosynthesis pathways in B. striata. Among these, 16 flower-specific genes exhibited high expression levels and harbored SNP variations. Notably, a premature stop codon was identified in a gene encoding dihydroflavonol 4-reductase (DFR), leading to truncated protein synthesis and potential disruption of anthocyanin production. Further, the heterologous overexpression of BsDFR4 in Phalaenopsis aphrodite changed petal color from white to yellow-green, demonstrating that it indeed played a regulatory role in the formation of flower color. Furthermore, yeast one-hybrid assays confirmed that transcription factors BsMYB36 and BsMYB51 could directly bind to the BsDFR4 promoter, suggesting their synergistic regulation of anthocyanin biosynthesis. These results provided a conceptual basis for insights into the formation of different flower colors in Orchidaceae. Full article

Lilies are one of the most popular ornamental flowers in the world. However, the abundant pollen produced in their anthers causes significant inconvenience for producers and consumers. Pollen abortion induced by molecular breeding techniques is one of the effective ways to solve this problem. In this study, the LoTDF1 gene, which is involved in regulating lily anther development, was identified and cloned from lily anthers based on transcriptome data. The open reading frame of LoTDF1 is 936 bp and encodes a protein with 311 amino acids. Multiple sequence alignment and phylogenetic tree analysis revealed that the LoTDF1 protein contained a conserved R2R3 domain, belonging to the MYB transcription factor family. Subcellular localization and transcriptional activation assays demonstrated that LoTDF1 localized to the nucleus and functioned as a transcription activator. The transcriptional activation domain was located within the last 195 amino acids (117–311a) of the C-terminus, and there may be more than one transcriptional activation domain in the region. The expression level of the LoTDF1 gene was highest during the pollen mother cell (PMC) stage of lily anther development (2 cm anther), followed by the tetrad stage (4 cm anther). In situ hybridization experiments further confirmed that LoTDF1 transcripts were predominantly localized in PMCs, tapetal cells, middle layer cells, dyads, and tetrads. The experiment data suggest that LoTDF1 plays a critical role in regulating early anther development in lily. LoTDF1 could be a promising candidate gene for molecular breeding strategies aimed at developing pollen-free lily cultivars to enhance commercial and consumer appeal. Full article