Search Results (573)

Background: Flowers are important plant organs, and their development is correlated with yield in woody fruit trees. For Pyrus pyrifolia cultivar ‘Sucui 1’, the research on how DNA methylation accurately regulates the expression of TFs and affects the specific regulatory mechanism of flower bud wizening will help reduce wizened buds. Methods: Here, the DNA methylomes and transcriptomes of two types of flower buds from the Pyrus pyrifolia cultivar ‘Sucui 1’ were compared. Results: 320 differentially expressed transcription factors (TFs), in 43 families, were obtained from the wizened bud transcriptome versus the normal bud transcriptome. Most were members of the AP2/ERF, bHLH, C2H2, CO-like, MADS, MYB, and WRKY families, which are involved in flower development. As a whole, the methylation level of TFs in the ‘Sucui 1’ genome increased once flower bud wizening occurred. A cytosine methylation analysis revealed that the methylation levels of the same gene regions in TFs from two kinds of buds were similar. However, differentially methylated regions were found in gene promoter sequences. The combined whole-genome bisulfite sequencing and RNA-Seq analyses revealed 162 TF genes (including 164 differentially methylated regions) with both differential expression and methylation differences between the two flower bud types. Among them, 126 were classified as ^mCHH-type methylation genes. Furthermore, the transcriptional down regulation of PpbHLH40, PpERF4, PpERF061, PpLHW, PpMADS6, PpZF-HD11, and PpZFP90 was accompanied by increased DNA methylation. However, PpbHLH130, PpERF011, and PpMYB308 displayed the opposite trend. The expression changes for these TFs were negatively correlated with their methylation states. Conclusions: Overall, our results offer initial experimental evidence of a correlation between DNA methylation and TF transcription in P. pyrifolia in response to bud wizening. This enriched our understanding of epigenetic modulations in woody trees during flower development. Full article

Jasmonic acid (JA) is a regulator of plant resistance to phytophagous insects, and exogenous JA treatment induces plant insect resistance. This study investigated the mechanism of exogenous JA-induced resistance of Hemerocallis citrina Baroni (daylily) to Thrips palmi at the biochemical and molecular levels. Daylily leaves sprayed with JA showed significantly higher levels of secondary metabolites—tannins, flavonoids, and total phenols, and activity of defense enzymes—peroxidase, phenylalanine ammonia lyase, polyphenol oxidase, and protease inhibitor (PI) than control leaves; the most significant effects were observed with 1 mmol L⁻¹ JA. Owing to an improved defense system, significantly fewer T. palmi were present on the JA-treated plants than control plants. The JA-treated leaves had a smoother wax layer and fewer stomata, which was unfavorable for insect egg attachment. The differentially expressed genes (DEGs) were significantly enriched in insect resistance pathways such as lignin and wax biosynthesis, cell wall thickening, antioxidant enzyme synthesis, PI synthesis, secondary metabolite synthesis, and defense hormone signaling. A total of 466 DEGs were predicted to be transcription factors, mainly bHLH and WRKY family members. Weighted gene co-expression network analysis identified 13 key genes; TRINITY_DN16412_c0_g1 and TRINITY_DN6953_c0_g1 are associated with stomatal regulation and lipid barrier polymer synthesis, TRINITY_DN7582_c0_g1 and TRINITY_DN11770_c0_g1 regulate alkaloid synthesis, and TRINITY_DN7597_c1_g3 and TRINITY_DN1899_c0_g1 regulate salicylic acid and ethylene biosynthesis. These results indicate that JA treatment of daylily improved its resistance to T. palmi. These findings provide a scientific basis for the utilization of JA as an antagonist to control T. palmi in daylily. Full article

Pomegranate (Punica granatum L.) is an ancient fruit crop that has been cultivated worldwide and is known for its attractive appearance and functional metabolites. Fruit color is an important index of fruit quality, but the color formation pattern in the peel of evergreen pomegranate and the relevant molecular mechanism is still unknown. In this study, the contents of pigments including anthocyanins, carotenoids, and chlorophyll in the peel of ‘Danruo No. 1’ pomegranate fruit during three developmental stages were measured, and RNA-seq was conducted to screen key genes regulating fruit color formation. The results show that pomegranate fruit turned from green to red during development, with a dramatic increase in a* value, indicating redness and anthocyanins concentration, and a decrease of chlorophyll content. Moreover, carotenoids exhibited a decrease–increase accumulation pattern. Through RNA-seq, totals of 30, 18, and 17 structural genes related to anthocyanin biosynthesis, carotenoid biosynthesis and chlorophyll metabolism were identified from differentially expressed genes (DEGs), respectively. Transcription factors (TFs) such as MYB, bHLH, WRKY and AP2/ERF were identified as key candidates regulating pigment metabolism by K-means analysis and weighted gene co-expression network analysis (WGCNA). The results provide an insight into the theory of peel color formation in evergreen pomegranate fruit. Full article

Blueberries (Vaccinium spp.) are extremely sensitive to drought stress. Flavonoids are crucial secondary metabolites that possess the ability to withstand drought stress. Therefore, improving the drought resistance of blueberries by increasing the flavonoid content is crucial for the development of the blueberry industry. To explore the underlying molecular mechanism of blueberry in adaptation to drought stress, we performed an integrated analysis of the metabolome and transcriptome of blueberry leaves under drought stress. We found that the most enriched drought-responsive genes are mainly involved in flavonoid biosynthesis and plant hormone signal transduction pathways based on transcriptome data and the main drought-responsive metabolites come from the flavonoid class based on metabolome data. The UDP-glucose flavonoid 3-O-glucosyl transferase (UFGT), flavonol synthase (FLS), and anthocyanidin reductase (ANR-2) genes may be the key genes for the accumulation of anthocyanins, flavonols, and flavans in response to drought stress in blueberry leaves, respectively. Delphinidin 3-glucoside and delphinidin-3-O-glucoside chloride may be the most important drought-responsive flavonoid metabolites. VcMYB1, VcMYBPA1, MYBPA1.2, and MYBPA2.1 might be responsible for drought-induced flavonoid biosynthesis and VcMYB14, MYB14, MYB102, and MYB108 may be responsible for blueberry leaf drought tolerance. ABA responsive elements binding factor (ABF) genes, MYB genes, bHLH genes, and flavonoid biosynthetic genes might form a regulatory network to regulate drought-induced accumulation of flavonoid metabolites in blueberry leaves. Our study provides a useful reference for breeding drought-resistant blueberry varieties. Full article

Natural rubber is a crucial industrial material, and it is primarily harvested from the latex of the rubber tree Hevea brasiliensis by tapping the tree trunk. During the regular tapping process, mechanical damage seriously affects latex reproduction and rubber yield, but the molecular mechanisms on tapping stimulation remain unclear. In this study, we firstly determined the changed physiological markers on latex regeneration, overall latex yield, and latex flow time during the tapping process. Then, we combined proteomics and transcriptomics analyses of latex during tapping and identified 3940 differentially expressed genes (DEGs) and 193 differentially expressed proteins (DEPs). Among them, 773 DEGs and 120 DEPs displayed a persistent upregulation trend upon tapping. It is interesting that, in the detected transcription factors, basic helix-loop-helix (bHLH) family members occupied the highest proportion among all DEGs, and this trend was similarly observed in DEPs. Notably, 48 genes and 34 proteins related to natural rubber biosynthesis were identified, and most members of small rubber particle protein (SRPP) and rubber elongation factor (REF) showed a positive response to tapping stimulation. Among them, SRPP6 and REF5 showed significant and sustained upregulation at the gene and protein levels following tapping, indicating their pivotal roles for post-tapping rubber biosynthesis. Our results deepen the comprehension of the regulation mechanism underlying tapping and provide candidate genes and proteins for improving latex production in the Hevea rubber tree in future. Full article

Background: Sweet potato (Ipomoea batatas (L.) Lam.) is widely cultivated as an important food crop. However, the molecular regulatory mechanisms affecting root tuber development are not well understood. Methods: The aim of this study was to systematically reveal the regulatory network of sweet potato root enlargement through transcriptomic and metabolomic analysis in different early stages of sweet potato root development, combined with phenotypic and anatomical observations. Results: Using RNA-seq, we found that the differential genes of the S1 vs. S2, S3 vs. S4, and S4 vs. S5 comparison groups were enriched in the phenylpropane biosynthesis pathway during five developmental stages and identified 67 differentially expressed transcription factors, including AP2, NAC, bHLH, MYB, and C2H2 families. Based on the metabolome, K-means cluster analysis showed that lipids, organic acids, organic oxides, and other substances accumulated differentially in different growth stages. Transcriptome, metabolome, and prophetypic data indicate that the S3-S4 stage is the key stage of root development of sweet potato. Weighted gene co-expression network analysis (WGCNA) showed that transcriptome differential genes were mainly enriched in fructose and mannose metabolism, pentose phosphate, selenium compound metabolism, glycolysis/gluconogenesis, carbon metabolism, and other pathways. The metabolites of different metabolites are mainly concentrated in amino sugar and nucleotide sugar metabolism, flavonoid biosynthesis, alkaloid biosynthesis, pantothenic acid, and coenzyme A biosynthesis. Based on WGCNA analysis of gene-metabolite correlation, 44 differential genes and 31 differential metabolites with high correlation were identified. Conclusions: This study revealed key gene and metabolite changes in early development of sweet potato root tuber and pointed out potential regulatory networks, providing new insights into sweet potato root tuber development and valuable reference for future genetic improvement. Full article

Camellia hainanica is one of the camellia plants distributed in tropical regions, and its regeneration system and genetic transformation are affected by callus browning. However, the underlying mechanism of Camellia hainanica callus browning formation remains largely unknown. To investigate the metabolic basis and molecular mechanism of the callus browning of Camellia hainanica, histological staining, high-throughput metabolomics, and transcriptomic assays were performed on calli with different browning degrees (T1, T2, and T3). The results of histological staining revealed that the brown callus cells had obvious lignification and accumulation of polyphenols. Widely targeted metabolomics revealed 1190 differentially accumulated metabolites (DAMs), with 53 DAMs annotated as phenylpropanoids and flavonoids. Comparative transcriptomics revealed differentially expressed genes (DEGs) of the T2 vs. T1 associated with the biosynthesis and regulation of flavonoids and transcription factors in Camellia hainanica. Among them, forty-four enzyme genes associated with flavonoid biosynthesis were identified, including phenylalaninase (PAL), 4-coumaroyl CoA ligase (4CL), naringenin via flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), Chalcone synthase (CHS), Chalcone isomerase (CHI), hydroxycinnamoyl-CoA shikimate transferase (HCT), Dihydroflavonol reductase (DFR), anthocyanin reductase (LAR), anthocyanin synthetase (ANS), and anthocyanin reductase (ANR). Related transcription factors R2R3-MYB, basic helix-loop-helix (bHLH), and WRKY genes also presented different expression patterns in T2 vs. T1. These results indicate that the browning of calli in Camellia hainanica is regulated at both the transcriptional and metabolic levels. The oxidation of flavonoids and the regulation of related structural genes and transcription factors are crucial decisive factors. This study preliminarily revealed the molecular mechanism of the browning of the callus of Camellia hainanensis, and the results can provide a reference for the anti-browning culture of Camellia hainanica callus. Full article

The flavonoids play important roles in plant salt tolerance. Blueberries (Vaccinium spp.) are extremely sensitive to soil salt increases. Therefore, improving the salt resistance of blueberries by increasing the flavonoid content is crucial for the development of the blueberry industry. To explore the underlying molecular mechanism, we performed an integrated analysis of the metabolome and transcriptome of blueberry leaves under salt stress. We identified 525 differentially accumulated metabolites (DAMs) under salt stress vs. control treatment, primarily including members of the flavonoid class. We also identified 20,920 differentially expressed genes (DEGs) based on transcriptome data; of these, 568 differentially expressed transcription factors (TFs) were annotated, and bHLH123, OsHSP20, and HSP20 TFs might be responsible for blueberry leaf salt tolerance. DEGs involved in the flavonoid biosynthesis pathway were significantly enriched at almost all stages of salt stress. Salt treatment upregulated the expression of most flavonoid biosynthetic pathway genes and promoted the accumulation of flavonols, flavonol glycosides, flavans, proanthocyanidins, and anthocyanins. Correlation analysis suggested that 4-coumarate CoA ligases (4CL5 and 4CL1) play important roles in the accumulation of flavonols (quercetin and pinoquercetin) and flavan-3-ol (epicatechin and prodelphinidin C2) under salt stress, respectively. The flavonoid 3′5′-hydroxylases (F3′5′H) regulate anthocyanin (cyanidin 3-O-beta-D-sambubioside and delphinidin-3-O-glucoside chloride) biosynthesis, and leucoanthocyanidin reductases (LAR) are crucial for the biosynthesis of epicatechin and prodelphinidin C2 during salt stress. Taken together, it is one of the future breeding goals to cultivate salt-resistant blueberry varieties by increasing the expression of flavonoid biosynthetic genes, especially 4CL, F3′5′H, and LAR genes, to promote flavonoid content in blueberry leaves. Full article

The basic helix–loop–helix (bHLH) gene family is a crucial regulator in plants, orchestrating various developmental processes, particularly flower formation, and mediating responses to hormonal signals. The molecular mechanism of bamboo flowering regulation remains unresolved, limiting bamboo breeding efforts. In this study, we identified 309 bHLH genes and divided them into 23 subfamilies. Structural analysis revealed that proteins in specific DlbHLH subfamilies are highly conserved. Collinearity analysis indicates that the amplification of the DlbHLH gene family primarily occurs through segmental duplications. The structural diversity of these duplicated genes may account for their functional variability. Many DlbHLHs are expressed during flower development, indicating the bHLH gene’s significant role in this process. In the promoter region of DlbHLHs, different homeopathic elements involved in light response and hormone response co-exist, indicating that DlbHLHs are related to the regulation of the flower development of D. latiflorus. Full article

The color of coffee fruits is influenced by several factors, including cultivar, ripening stage, and metabolite composition. However, the metabolic accumulation of pigments and the molecular mechanisms underlying peel coloration during the ripening process of Coffea arabica L. remain relatively understudied. In this study, UPLC-MS/MS-based metabolomics and RNA sequencing (RNA-seq)-based transcriptomics were integrated to investigate the accumulation of anthocyanins and carotenoids in the peel of Coffea arabica at different ripening stages: green peel (GP), green-yellow peel (GYRP), red peel (RP), and red-purple peel (RPP). This integration aimed at elucidating the molecular mechanisms associated with these changes. A total of ten anthocyanins, six carotenoids, and thirty-five xanthophylls were identified throughout the ripening process. The results demonstrated a gradual decrease in the total carotenoid content in the peel with fruit maturation, while anthocyanin content increased significantly. Notably, the accumulation of specific anthocyanins was closely associated with the transition of peel colors from green to red. Integrated metabolomics and transcriptomics analyses identified the GYRP stage as critical for this color transition. A weighted gene co-expression network analysis (WGCNA) revealed that enzyme-coding genes such as 3AT, BZ1, and lcyE, along with transcription factors including MYB, NAC, and bHLH, which interact with PHD and SET TR, may regulate the biosynthesis of anthocyanins and carotenoids, thereby influencing peel pigmentation. These findings provide valuable insights into the molecular mechanisms underlying the accumulation of anthocyanins and carotenoids in Coffea arabica peel during fruit maturation. Full article

Self-incompatibility (SI) poses a significant reproductive barrier, severely impacting the yield, quality, and economic value of Camellia oleifera. In this study, methyl jasmonate (MeJA) was employed as an exogenous stimulus to alleviate SI in C. oleifera. The research findings revealed that an exogenous dose of 1000 μmol·L⁻¹ MeJA enhanced the germination and tube growth of C. oleifera self-pollen and greatly improved ovule penetration (18.75%) and fertilization (15.81%), ultimately increasing fruit setting (18.67%). It was discovered by transcriptome analysis that the key genes (CAD, C4H) involved in the lignin production process exhibited elevated expression levels in self-pistils treated with MeJA. Further analysis showed that the lignin concentration in the MeJA-treated pistils was 31.70% higher compared with the control group. As verified by pollen germination assays in vitro, lignin in the appropriate concentration range could promote pollen tube growth. Gene expression network analysis indicated that transcription factor bHLH may be pivotal in regulating lignin biosynthesis in response to MeJA, which in turn affects pollen tubes. Further transient knockdown of bHLH (Co_33962) confirmed its important role in C. oleifera pollen tube growth. In summary, the application of MeJA resulted in the stimulation of self-pollen tube elongation and enhanced fruit setting in C. oleifera, which could be associated with the differential change in genes related to lignin synthesis and the increased lignin content. Full article

Paulownia species not only have significant economic benefits but also show great potential in ecological conservation. However, they are highly susceptible to phytoplasma infections, causing Paulownia witches’ broom (PaWB), which severely restricts the development of the Paulownia industry. Salicylic acid (SA) plays a crucial role in plant disease resistance. However, there have been no reports on the effect of SA on PaWB. Due to the properties of SA, it may have potential in controlling PaWB. Based on the above speculation, the prevention and therapeutic effect of SA on PaWB and its effect on the PaWB-infected Paulownia transcriptome and proteome were studied in this work. The results indicated that 0.1 mmol/L was the optimal SA concentration for inhibiting the germination of Paulownia axillary buds. In terms of resistance physiological indicators, SA treatment significantly affected both Paulownia tomentosa infected (PTI) seedlings and Paulownia fortunei infected (PFI) seedlings, where the activities of peroxidase (POD) and superoxide dismutase (SOD) were enhanced. Malondialdehyde (MDA), O₂⁻, and H₂O₂, however, were significantly reduced. Specifically, after SA treatment, SOD activity increased by 28% in PFI and 25% in PTI, and POD activity significantly increased by 61% in PFI and 58% in PTI. Moreover, the MDA content decreased by 30% in PFI and 23% in PTI, the H₂O₂ content decreased by 26% in PFI and 19% in PTI, and the O₂⁻ content decreased by 21% in PFI and 19% in PTI. Transcriptomic analysis showed that there were significant upregulations of MYB, NAC, and bHLH and other transcription factors after SA treatment. Moreover, genes involved in PaWB-related defense responses such as RAX2 also showed significant differences. Furthermore, proteomic analysis indicated that after SA treatment, proteins involved in signal transduction, protein synthesis modification, and disease defense were differentially expressed. This work provides a research foundation for the prevention and treatment of PaWB and offers references for exploring anti-PaWB methods. Full article

Drought stress, as one of the most common environmental factors, seriously affects seed- ling establishment as well as plant growth and productivity. The growth of Toona ciliata is constrained by soil moisture deficit, and drought stress can reduce its productivity and limit its suitable growing environment. To explore the molecular mechanism of Toona ciliata responding to drought stress, leaves of two-year-old Toona ciliata seedlings were used as experimental materials for transcriptome sequencing and physiological index measurements. Under drought stress, the contents of Chl, MDA, POD, SP, SS, and RWC all change differently. We performed transcriptome sequencing, obtaining 4830 differential genes. The enrichment analysis indicates that the primary effects on the leaves of Toona ciliata under drought stress are related to photosynthesis and responses to plant hormone signal transduction. Transcription factor families associated with drought resistance include the NAC, WRKY, bZIP, bHLH, AP2-EREBP, C3H, GRAS, and FRAI transcription factor families. A weighted gene co-expression network analysis (WGCNA) analysis successfully identified 10 hub genes in response to drought stress in Toona ciliata leaves. Real-time quantitative PCR (RT-qPCR) validated the reliability of the transcriptomic data, and the analysis of its results showed a close correlation with the data obtained from RNA-seq. This study clarifies the transcriptional response of Toona ciliata to drought stress, contributing to the revelation of the molecular mechanisms of drought adaptation. Full article

Background: The bHLH genes play a crucial role in plant growth, development, and stress responses. However, there is currently limited research on bHLH genes in the important horticultural plant Rhododendron delavayi Franch. Methods: In this study, we conducted a comprehensive genome-wide identification and in-depth analysis of the bHLH gene family in R. delavayi using bioinformatics approaches. Results: A total of 145 bHLH family members were identified, encoding proteins ranging from 98 to 3300 amino acids in length, with molecular weights ranging from 11.44 to 370.51 kDa and isoelectric points ranging from 4.22 to 10.80. These 145 bHLH genes were unevenly distributed across 13 chromosomes, with three bHLH genes located on contig 52. Chromosome 8 contained the highest number of bHLH family members with 19 genes, while chromosomes 9 and 13 had the lowest, with 7 genes each. Phylogenetic analysis revealed a close evolutionary relationship between bHLH genes in R. delavayi and Arabidopsis thaliana. Subcellular localization analysis indicated that most bHLH genes were located in the nucleus. Promoter analysis of R. delavayi bHLH genes revealed the presence of various cis-regulatory elements associated with light responses, methyl jasmonate responses, low-temperature responses, and coenzyme responses, suggesting that bHLH genes are involved in multiple biological processes in R. delavayi. Through transcriptome analysis, we identified three key functional genes—Rhdel02G0041700, Rhdel03G0013600, and Rhdel03G0341200—that may regulate flower color in R. delavayi. Conclusions: In conclusion, our study comprehensively identified and analyzed the bHLH gene family in R. delavayi and identified three bHLH genes related to flower color, providing a foundation for molecular biology research and breeding in R. delavayi. Full article

Alfalfa species Medicago sativa L. (MS) and Medicago falcata L. (MF), globally prominent perennial leguminous forages, hold substantial economic value. However, our comprehension of the molecular mechanisms governing their resistance to cold stress remains limited. To address this knowledge gap, we scrutinized and compared MS and MF cold-stress responses at the molecular level following 24 h and 120 h low-temperature exposure (4 °C). Our study revealed that MF had superior physiological resilience to cold stress compared with MS, and its morphology was healthier under cold stress, and its malondialdehyde content and superoxide dismutase activity increased, first, and then decreased, while the soluble sugar content continued to accumulate. Transcriptome analysis showed that after 120 h of exposure, there were different gene-expression patterns between MS and MF, including 1274 and 2983 genes that were continuously up-regulated, respectively, and a total of 923 genes were included, including star cold-resistant genes such as ICE1 and SIP1. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed numerous inter-species differences in sustained cold-stress responses. Notably, MS-exclusive genes included a single transcription factor (TF) gene and several genes associated with a single DNA repair-related pathway, whereas MF-exclusive genes comprised nine TF genes and genes associated with 14 pathways. Both species exhibited high-level expression of genes encoding TFs belonging to AP2-EREBP, ARR-B, and bHLH TF families, indicating their potential roles in sustaining cold resistance in alfalfa-related species. These findings provide insights into the molecular mechanisms governing cold-stress responses in MS and MF, which could inform breeding programs aimed at enhancing cold-stress resistance in alfalfa cultivars. Full article