The PP2C (protein phosphates 2C) are key regulators of abscisic acid (ABA) signaling that play a crucial role in plant stress responses. In this study, we performed a comprehensive genome-wide analysis and identified 71 DlPP2C genes in Dimocarpus longan which is an economically important fruit crop. The evolutionary analysis revealed that DlPP2C genes were classified into distinct subgroups based on phylogenetic relationships with Arabidopsis thaliana and Oryza sativa. Structural analysis demonstrated conserved motif composition and gene organization within subgroups, whereas chromosomal distribution and synteny analysis revealed that segmental duplication events contributed to gene family expansion. Promoter analysis findings identified numerous cis-acting elements related to hormone and stress responsiveness especially abscisic acid-responsive elements (ABREs), suggesting their potential involvement in ABA signaling pathways. Under exogenous ABA treatments, expression profiling of the DlPP2C genes exhibited dynamic, dose and time dependent response with several genes showing peak expression at 10 μM ABA after 16 h, especially the DlPP2C1 displayed a strong transcriptional response, indicating its potential role as a key regulator. Overexpression and GUS staining assays revealed enhanced activity under ABA treatment, further supporting its involvement in ABA-responsive regulation. Moreover, RNA sequencing analysis revealed a total of 1799 differentially expressed genes, with prevalence of downregulated genes, showing extensive transcriptional reprograming. Functional enrichment analysis demonstrated that these genes were largely associated with plant hormone signaling, stress response and metabolic pathways. Together, these findings propose that DlPP2C genes, especially DlPP2C1, play a key role in ABA-mediated regulatory networks and provide valuable insights intro stress adaption mechanisms during early somatic embryogenesis in longan.

Banana productivity is severely limited by drought, yet the molecular basis of drought adaptation and endophyte-mediated stress alleviation remains poorly understood. Here, we performed a genome-wide analysis of the SQUAMOSA promoter-binding protein-like (SPL) transcription factor family in Musa acuminata and examined their transcriptional responses to drought stress and Serendipita indica inoculation. We identified 38 MaSPL genes, all encoding proteins with the conserved SBP domain and predicted nuclear localization. Phylogenetic, motif, gene structure, and collinearity analyses indicated that MaSPL genes are evolutionarily conserved, unevenly distributed across chromosomes, and expanded primarily through segmental duplication under purifying selection. Promoter analysis showed several cis-acting elements and transcription factor binding sites related to light, phytohormone, and stress signaling. Ten MaSPL genes were predicted as putative targets of miR156. qRT-PCR analysis showed that drought stress markedly downregulated the tested MaSPL genes, whereas miR156a expression increased, supporting an inverse regulatory relationship. Under drought, S. indica inoculation enhanced expression of most tested MaSPLs, restoring transcript accumulation while reducing miR156a to near-basal levels. Notable responses were observed in members of the MaSPL2, MaSPL9, and MaSPL13, respectively. S. indica improves drought tolerance by enhancing antioxidant defenses, reducing oxidative stress, and preserving photosynthetic and osmotic stability. Taken together, our results demonstrate that S. indica confers drought resilience in banana by counteracting drought-induced repression of MaSPL genes via the miR156-SPL module and by strengthening key physiological defense mechanisms.

Waterlily (Nymphaea L.), a globally renowned aquatic ornamental plant, is prized for its aesthetic flowers and intense floral fragrance. However, the molecular mechanisms underlying floral scent biosynthesis in waterlily remain poorly characterized, and integrated analyses of dynamic volatile emission patterns and their associated biosynthetic pathways are lacking. In this study, we combined headspace solid-phase microextraction/gas chromatography-mass spectrometry (HS-SPME/GC-MS) with transcriptome sequencing (RNA-seq) to investigate the composition, emission dynamics, and biosynthesis of volatile organic compounds (VOCs) in the stamens of Nymphaea 'Paul Stetson' across three developmental stages. A total of 671 VOCs, classified into 14 categories, were identified. Transcriptome analysis revealed 47,951 differentially expressed genes (DEGs). Integrative omics analysis demonstrated correlated DEGs and differentially accumulated volatiles were significantly enriched in pathways related to phenylpropanoid biosynthesis, terpenoid backbone biosynthesis, diterpenoid biosynthesis, and ubiquinone/other terpenoid-quinone biosynthesis. Five candidate functional genes exhibiting strong positive correlations with VOC accumulation levels were identified, three of which are implicated in terpenoid biosynthesis. These findings provide a theoretical foundation for elucidating aroma composition and biosynthesis in waterlily and offer novel avenues for the genetic improvement of fragrance traits for ornamental, beverage, and cosmetic applications.

PP2C (protein phosphatases 2C) are key regulators of abscisic acid (ABA) signaling that play a crucial role in plant stress responses. Our analysis identified 71 DlPP2C genes in Dimocarpus longan, which were classified into distinct subgroups based on phylogenetic relationships with Arabidopsis thaliana and Oryza sativa. Structural analysis demonstrated conserved motif composition and gene organization within subgroups, while chromosomal distribution and synteny analysis revealed that segmental duplication events contributed to the expansion of this gene family. Promoter analysis uncovered several cis-acting elements related to hormone and stress responsiveness, especially abscisic acid-responsive elements (ABREs), suggesting that DlPP2C genes may play a role in ABA signaling pathways. Furthermore, we examined the ABA-responsive expression profiles of DlPP2C genes under exogenous ABA treatments. The expression patterns were dynamic and dose- and time-dependent, with several genes showing peak expression at 10 μM ABA after 16 h. The DlPP2C1 in particular displayed a strong transcriptional response, indicating its potential role in ABA regulation. While overexpression and GUS staining assays revealed enhanced activity under ABA treatment, further supporting the involvement of PP2C in ABA-responsive regulation, further mechanistic studies are needed for a full characterization. Finally, RNA sequencing analysis revealed a total of 1799 differentially expressed genes in response to ABA, with a prevalence of downregulated genes, showing extensive transcriptional reprogramming. Functional enrichment analysis demonstrated that these genes were largely associated with plant hormone signaling, stress response, and metabolic pathways. Weighted gene co-expression network analysis revealed a total of 32 key gene modules associated with ABA signaling. Collectively, our findings propose that DlPP2C genes, especially DlPP2C1, play a key role in ABA-mediated regulatory networks and provide valuable insights into stress adaptation mechanisms, especially during early somatic embryogenesis in longan.

Background : Drug resistance is a major challenge in colorectal cancer (CRC) treatment. Overcoming drug resistance and improving therapeutic outcomes are crucial issues for patients with drug-resistant CRC. Crassocephalum rabens (Benth.) S. Moore (CR) is an edible plant and a folk medicine. Its galactolipids have anti-inflammatory and antitumor potential. Purpose : This study explored the pharmacological mechanism and therapeutic efficacy of galactolipids isolated from CR (designated CRA) for treating drug-resistant CRC in vitro and in vivo. Methods : The antitumor activity and molecular mechanisms of CRA were investigated using cytotoxicity, reactive oxygen species (ROS) production, RNA sequencing, quantitative PCR (qPCR), Western blotting, and LPA concentration assays. Virtual molecular docking was conducted to identify CRA’s action site on the target protein. The therapeutic effectiveness of CRA was evaluated using HT-29 xenograft mice. Results : CRA induced ROS-mediated cytotoxicity by inhibiting the expression of interferon-α-induced protein 6 (IFI6). IFI6 suppression by CRA led to ROS accumulation and oxidative DNA damage, ultimately resulting in cell death. CRA antagonistically targeted lysophosphatidic acid receptors (LPAR), specifically LPAR2, and blocked their downstream signaling pathways, including PI3K/AKT/mTOR, Ras/Raf/p38, PLC/PKC, Rho/PKA, and NF-κB, which inhibited cell survival. Furthermore, CRA also inhibited the intracellular synthesis of LPA. In HT-29 tumor-bearing mice, CRA significantly reduced tumor growth. The antitumor activity of CRA, through inhibiting LPAR2 expression and inducing IFI6-mediated oxidative stress, was also observed in tumors. Conclusion : CR galactolipids directly targeted LPAR2, inhibited the LPAR2 signaling pathways, and induced IFI6-mediated ROS accumulation to combat drug-resistant CRC.

Background Medulloblastoma (MB) is the most common malignant pediatric brain cancer. Patients diagnosed with Sonic Hedgehog (SHH) MB typically exhibit highly metastatic tumors and have an unfavorable prognosis. 7,7"-Dimethoxyagastisflavone (DMGF), a biflavonoid compound, isolated from needles of Taxus x media cv. Hicksii.The purpose of this study is to explore the potential targets of SHH MB and the therapeutic effects of DMGF in SHH MB. Methods RNA sequencing was used to analyze malignancy-related genes in SHH MB patient tumors. Experiments on cytotoxicity, apoptosis, cell cycle, migration, F-actin assembly, EMT, metabolite changes, and macrophage polarization demonstrated that DMGF induced cell death by inhibiting MYCN and MYBL2.The therapeutic effect of DMGF was studied in MB orthotopic xenograft mice. Three-dimensional images exhibited the brain-wide distribution of MB tumors. Patient-derived MB cells were utilized to demonstrate the potential of DMGF as a future therapy. Results Taiwanese SHH MB patients with high MYCN and MYBL2 expression had lower 5-year overall survival, suggesting that MYCN and MYBL2 are related to the malignancy. DMGF decreased MYCN and MYBL2 expression, which arrests the cell cycle, induces apoptosis, impedes cell migration, and inhibits the EMT response. DMGF disrupted redox balance and inhibited energy-related metabolism in SHH MB cells. DMGF-induced macrophage polarization that built an antitumor microenvironment. The inhibitory effects of DMGF on MYCN/MYBL2 were also confirmed in patient-derived MB cells. Conclusion Inhibiting MYCN and MYBL2 is the key to DMGF's anti-tumor effects. These findings suggest the potential of DMGF as a future chemotherapeutic agent for MB treatment.

Banana (Musa spp.) is susceptible to low-temperature stress and other environmental stresses, which can hinder the growth and development. Succinic semialdehyde dehydrogenase (SSADH) is critical for GABA biosynthesis and plays a crucial role in plants. However, the SSADH genes of bananas have not been studied. This study found 19 MaSSADHs, 18 MbSSADHs, and 18 MiSSADHs from the banana genome. According to the phylogenetic tree, these genes can be categorized into five branches. This study cloned the MaSSADH1-14 from banana. The subcellular localization assays of MaSSADH1-14 in tobacco leaves confirmed that the presence of SSADH was not only localized mitochondrion but also localized chloroplast. The cis-elements of the SSADH gene family are related to the potential regulation of the banana SSADH gene family; their involvement in diverse stress responses. Transcriptomic data was utilized to examine the effect of MaSSADH genes under cold stress in bananas. The results of RT-qPCR were consistent with transcriptome data. These results showed that most MaSSADHs are passively responsive to low-temperature treatment. In addition, transient overexpression of MaSSADH1-14 in Nicotiana benthamiana leaves resulted in the content of GABA increasing, indicating that MaSSADH1-14 may be involved in the accumulation of GABA of banana. Collectively, these results improve knowledge of the SSADH gene family in banana and establish a basis for comprehending its biological roles in response to low temperatures.

Metastasis of medulloblastomas (MBs) is difficult to treat and remains the primary cause of death in children with this brain tumor. Current treatment focuses on radiotherapy to limit metastatic recurrence and maintain survival, but this may cause long-term neurocognitive deficits. This challenge emphasizes the need for novel targeted therapies to combat metastatic MB. In this study, we report an RNA therapy model using targeted extracellular vesicles (EVs) to deliver therapeutic small-interfering (si)RNAs to MB. First, MB-targeted EVs (MB-tEVs) were generated via genetic modification of EV-producing cells to express E1-3, an MB-specific peptide. Next, isolated MB-tEVs were loaded with siRNAs that targeted LOXL1-AS1, a pro-metastatic long non-coding RNA in sonic-hedgehog MB (SHH-MB). Expression of the E1-3 peptide increased MB-tEV internalization into MB cells, where the delivered siRNAs effectively silenced LOXL1-AS1 and suppressed LOXL1-AS1-mediated metastatic traits of SHH-MB cells in vitro. Locoregional application of microbubble-enhanced focused ultrasound (FUS) improved the accumulation of systemically injected EVs in the mouse brain. Mice treated with siRNA-loaded MB-tEVs had decreased LOXL1-AS1 expression, reduced metastases, and improved survival in an SHH-MB orthotopic model. Our study provides the first and very promising evidence for the combined use of tumor-targeted EVs and microbubble-enhanced FUS to deliver therapeutic siRNAs to suppress metastatic MB, potentially supporting conventional treatments and improving clinical outcomes of this malignant pediatric tumor.

The basic-leucine zipper (bZIP) transcription factor (TF), which is abundant and highly conserved in eukaryotes, mainly participates in plant growth, development and adverse stress processes. However, the regulatory mechanisms of bZIP TFs under heat stress in Dimocarpus longan remain unclear. In this study, we reported a nuclear-localized bZIP TF, DlbZIP20, which was confirmed to be a positive regulator of thermotolerance in D. longan. It was identified as a strong interplay with hormone signalling pathways and oxidoreductase-related families. The transient overexpression DlbZIP20 could improve the thermotolerance of D. longan embryogenic callus (EC) and reduce the damage of cells under heat stress. Overexpression of DlbZIP20 in hairy roots significantly promoted roots elongation and photosystem II (PS II) responses in leaves, and significantly increased SOD and POD activities, promoted H2O2 scavenging, improved thermotolerance of D. longan by maintaining ROS homeostasis under heat stress. In addition, overexpression of DlbZIP20 increased endogenous MeJA content under heat stress. MeJA hormone synthesis genes DlMYC2 and DlCOI1 were up-regulated and DlJAZ3 was down-regulated in expression. This signalling pathway may play a role in the regulation of thermotolerance in D. longan. These results will provide a new insight into the molecular function of bZIP20 TF in response to heat stress in D. longan.

GRAS family plays a critical role in plant growth and stress responses. In this study, we identified 47 GRAS (DlGRAS) genes in the longan genome and conducted a comprehensive bioinformatics analysis of these genes. RNA-seq analysis revealed that the expression of these DlGRAS genes differed during early SE and across various longan tissues. The quantitative real-time PCR (qRT-PCR) results indicated that the DlGRAS genes exhibited differential expression during the early SE of longan, with most of them showing high expression at the globular embryo (GE) stage. Under GA3 treatment, the transcript levels of DlGRAS12/15 decreased significantly. In contrast, exogenous ABA promoted the expression of DlGRAS6/10/23, indicating that DlGRAS genes are responsive to hormones. Compared with CaMV35S-driven GUS expression, the promoters of DlGRAS10/22 increased GUS expression, GA3 and ABA treatments enhanced promoter activity. DlGRAS10/22 were located in the nucleus. Overexpression of DlGRAS10/22 in longan SE significantly promoted the transcription levels of SE-related genes, including DlGID1, DlGA20ox2, DlLEC1, DlFUS3, DlABI3 and DlLEC2. Therefore, DlGRAS may be involved in the early morphogenesis of longan SE through the hormone signaling pathway.

Polyamines, emerging as pivotal regulators, modulate a myriad of fundamental cellular processes and orchestrate key physiological and biochemical pathways, including putrescine, spermidine, spermine. This study explores the mechanisms by which exogenous polyamines regulate the growth and flavonoid accumulation in longan (Dimocarpus longan Lour.) embryogenic calli (EC). Here, we screened the effects of different types of polyamines and their inhibitor D-arginine in longan EC. Exogenous 10 mu mol/L spermine demonstrated superior efficacy, enhancing the fresh weight of longan EC by 12.65 % and increasing its flavonoids production rate by 26.11 % versus control. Exogenous spermine also up-regulated the expression of polyamines and flavonoids metabolism genes. Widely targeted metabolomics indicated flavonoids as predominant differential metabolites under spermine treatment, with vitexin-2 '-O-glucoside and quercetin-3-O-glucoside-7-O-rhamnoside showing the most pronounced differential accumulation. D-arginine acts mainly as inhibition. Intriguingly, exogenous 10 mu mol/L quercetin outperformed Spm and vitexin in promoting both longan EC growth (by 36.58 %) and flavonoids production rate (by 65.08 %), while concomitantly upregulating the expression of polyamines metabolism genes, suggesting a possible synergistic interaction between spermine and quercetin. Furthermore, exogenous quercetin and vitexin facilitated the development of longan EC into globular embryo. Cultivation of longan EC in a stirred bioreactor (5 L working volume) supplemented with 10 mu mol/L quercetin achieved 196.15 % higher flavonoid yield than that in solid medium, while reducing the culture duration from 30 to 9 days. This study establish a foundation for understanding the intrinsic mechanism by which polyamines regulate the growth and flavonoids accumulation in longan EC.

Dimocarpus longan Lour. is an evergreen tree of the genus Longan in the Sapindaceae family, native to tropical and subtropical regions. Longan embryonic development is closely related to fruit set and fruit quality. An in-depth study of the mechanism of longan embryonic development could therefore contribute to the development of the longan industry. DIMBOA is the principal compound representing benzoxazinoids (BXs), and is closely linked to auxin biosynthesis and signal transduction. Auxin is one of the crucial hormones for inducing somatic embryogenesis (SE) in plants. Previous research has shown that DIMBOA promotes morphogenesis in the early somatic embryogenesis of longan, but the specific regulatory mechanism has not yet been clarified. To elucidate the molecular mechanism by which DIMBOA affects early somatic embryogenesis in longan, we chose longan embryogenic cultures grown under 0 mg/L DIMBOA as the control group (the check, CK), and longan embryogenic cultures grown under 0.1 mg/L DIMBOA as the treatment group (D) to be analyzed by transcriptomic sequencing. A total of 478 differentially expressed genes (DEGs) are detected in check vs. D, of which 193 are upregulated and 285 are downregulated. These DEGs are significantly enriched in the biosynthetic and metabolic functions of various substances such as vitamin B6 (VB6) biosynthesis, phenylpropanoid pathways, and carbohydrate metabolism. DIMBOA affects SE processes in longan via TFs, including MYB, ZF, bHLH, LBD, NAC, WRKY, etc. After DIMBOA treatment, the expression of most of the key genes for IAA synthesis was significantly downregulated, VB6 content was significantly reduced, and H2O2 content was significantly increased. Therefore, it is suggested that DIMBOA directly or indirectly affects the H2O2 content through the VB6 metabolic pathway, thereby regulating the endogenous IAA level to modulate the early SE morphogenesis of longan.

The rhizome of Polygonatum cyrtonema Hua (P. cyrtonema) is a valuable medicinal and edible resource material. To explore functional metabolite spatial distribution and enhance utilization efficiency in P. cyrtonema, this study established a tissue culture system for rapid induction and proliferation of microrhizomes using mature seeds of P. cyrtonema, spatial metabolomics via MALDI-MSI analyzed metabolite distributions across wild rhizomes cross-sections, sprout/rhizome and microrhizomes longitudinal-sections. We mapped 93 metabolites (e.g., saccharides, organic/amino acid derivatives, alkaloids, esters, flavonoids). Saccharides accumulated primarily in rhizomes. Organic acid derivatives and alkaloids dominated sprouts and rhizomes. Amino acid derivatives localized mainly to sprouts and rhizome periderm. Small peptides were enriched in rhizome periderm and sprout surfaces, suggesting their potential role in rhizome growth and stress defense mechanisms of P. cyrtonema. Co-enrichment of amino acid derivatives and alkaloids in wild P. cyrtonema vascular bundles and shoot apex supports a putative long-distance transport function that may facilitate bud growth. Crucially, osmotic stress from high sucrose may contribute to elevated metabolite levels in microrhizomes, especially organic/amino acid derivatives and saccharides. These findings highlight the substantial application potential of microrhizomes for functional metabolite production. This study provides vital data for enhancing P. cyrtonema metabolite processing and industrial production.

As the main active ingredient in Anoectochilus roxburghii, kinsenoside has important health and medical effects including hepatoprotective, anti-oxidant, and bacteriostasis, among others. In recent years, with the limited application of high-throughput technology to A. roxburghii, there has been no research on the key regulatory genes involved in the synthesis of kinsenoside. Therefore, we examined three species of A. roxburghii that are widely planted in mainland China and Taiwan Province, A. roxburghii cultivar ‘Jian ye’, Anoectochilus formosanus, and Anoectochilus burmannicus, determining the content of kinsenoside, performing transcriptomic and metabolomic sequencing, identifying UDP glycosyltransferases, and screening for UDP glycosyltransferases that may be involved in kinsenoside synthesis. The results showed that among the three species of A. roxburghii, the content of kinsenoside in A. roxburghii cv. ‘Jian ye’ was the highest. Transcriptome and metabolome data showed that A. roxburghii cv. ‘Jian ye’ and the two other species of A. roxburghii have 3702 and 5369 differentially expressed genes and 69 and 120 differentially accumulated metabolites, respectively. Meanwhile, differentially expressed genes and differentially accumulated metabolites are enriched in the glucose metabolism and hormone pathways. We also treated the A. roxburghii samples with exogenous auxin and characterized the related genes. In A. roxburghii, we identified 73 members of the UDP glycosyltransferase family. Through phylogenetic tree, transcriptome data expression profile, and qPCR analyses, we screened for members that may be involved in the synthesis of kinsenoside. In summary, the results of this study provide insights for breeding high-kinsenoside-content and high-intron varieties of A. roxburghii.

Heat stress can seriously affect plant growth and development. Ethylene response factors (ERFs) play important roles in plant development and physiological responses. Here, we identified DlERF6, an ERF family transcription factor that promotes heat tolerance in Dimocarpus longan. DlERF6 was strongly induced by heat stress and IAA treatment in longan roots. Overexpression of DlERF6 generated abundant, fast-growing hairy roots and enhanced longan heat stress tolerance by promoting IAA biosynthesis and reactive oxygen species (ROS) scavenging. Additional assays indicated that DlERF6 directly binds to the DlGH3.5 promoter and represses its expression. Overexpressing DlGH3.5 reduced hairy root number, root length and heat tolerance, concomitant with a reduction in IAA content and ROS scavenging. Collectively, these results reveal the molecular mechanism through which the DlERF6–DlGH3.5 module regulates root growth and heat stress tolerance, providing a gene network that can be used for the genetic improvement of longan.

BES1 (BRI1 EMS SUPPRESSOR 1) is a critical transcription factor involved in plant growth, development, and stress responses. Although BES1 genes have been characterized in several species, their roles in longan (Dimocarpus longan Lour.) remain unclear. This study identified and analyzed eight BES1 genes in the longan genome. Phylogenetic analysis classified these genes into four subgroups (I-IV), with conserved motifs and intron-exon structures indicating potential functional similarities within subgroups. Cis-element analysis revealed that the promoters of DlBES1 genes contain numerous hormone-related elements, including ABRE, TGACG, and TCA motifs, suggesting their involvement in hormonal signaling and stress responses. Expression profiling showed differential expression patterns of DlBES1 genes across nine tissues, with notable up-regulation in roots and seeds. Additionally, DlBES1 genes exhibited distinct expression trends under varying temperatures and in response to IAA treatment, indicating potential roles in temperature stress adaptation and hormone signaling. These findings provide novel insights into the regulatory mechanisms of BES1 genes in longan and highlight their potential significance in stress tolerance and growth regulation.

Banana (Musa spp.) is a typical climacteric fruit. Xyloglucan endotransglucosylase/hydrolase (XTH) is a key factor regulating plant cell wall dynamic remodeling and participates in fruit ripening. To clarify the core physiological traits of banana ripening, four ripening stages of banana cultivar (Musa AAA ‘Minai No. 1’) fruits in the fully green stage (S1), green-yellow stage (S2), fully yellow stage (S3), and yellow with brown spots stage (S4) were used in this study’s experimental materials, to examine dynamic changes in key physiological–biochemical properties. The results showed that fruit firmness decreased continuously, starch content first increased then decreased, and soluble protein and total soluble solids (TSS) accumulated gradually during the ripening stages of banana fruits. Transcriptome analysis of the four stages found that there were 14,315 differentially expressed genes (DEGs) in S1 versus S4, the GO enrichment pathway is enriched in “protein dephosphorylation”, and the KEGG enrichment pathway is enriched in the “Protein processing in endoplasmic reticulum” and “Ubiquitin mediated proteolysis” pathways. The fruit ripening process involves the processing of numerous proteins. The heatmap revealed that MaXTH32.5 was significantly up-regulated during banana ripening and the result of RT-qPCR is consistent with the transcriptome data. A total of 989 XTH members across 16 Musa varieties of the XTH gene family were further identified. Among them, MaXTH32.5 localized at the chloroplast, and transient overexpression of MaXTH32.5 significantly reduced banana fruit firmness and may be involved in regulating ripening in banana fruits. This study indicated that the differential expression of XTH gene family members may regulate ripening-related processes in banana and MaXTH32.5 as a key candidate, providing insights into banana ripening mechanisms and a foundation for subsequent Musa XTH research.

In the life cycle of fruit, ripening is a crucial period for the formation of fruit quality. During this phase, a series of physiological and biochemical changes occur, leading to alterations in color and texture, softening, and the production of aroma volatiles. Relevant studies have demonstrated that ethylene-induced fruit ripening is a complex regulatory network involving numerous transcription factors, ethylene receptor protein families, signal transduction pathways, and downstream maturation-related genes. In this study, we conducted a genome-scale identification and characterization of long noncoding RNAs (lncRNAs) from the predominant AAA triploid banana cultivar, ‘Tianbaojiao’, using rich RNA-sequencing (RNA-seq) datasets from fruit tissues treated with ethylene and untreated controls. This represents one of the first comprehensive investigations into banana lncRNAs associated with ripening. A total of 11,268 banana fruit lncRNAs were identified and found to be distributed across all banana chromosomes; ∼76.1% of these lncRNAs were transcribed from intergenic regions. Banana fruit lncRNAs are relatively short, with 91.32% ranging from 100 to 1000 nucleotides in length. Most contain one or two exons, contrasting with protein-coding genes, which can have one to ≥10 exons. Compared with naturally ripened bananas, many lncRNAs exhibited significant differential expression in ethylene-treated banana fruits. Furthermore, downregulating the expression of lncRNA TCONS00507247 in the peel markedly inhibited the yellowing process. These findings suggest that lncRNAs play a vital role in regulating banana fruit ripening and offer new insights into fruit ripening research.

Polygonatum cyrtonema Hua (P. cyrtonema), a traditional medicinal herb, is renowned for its high metabolite content. Previous studies have found that APETALA2/Ethylene Responsive Factor (AP2/ERF) plays a vital role in the metabolisms of P. cyrtonema, while the regulatory mechanism of PcAP2/ERFs in the flavonoid accumulation remains unclear. A total of 53 PcAP2/ERFs were identified from the full-length transcriptome. The expression analysis of PcAP2/ERFs in different age section rhizomes and different tissue sections showed that PcERF114 was associated with flavonoid accumulation and located in the nucleus. The flavonoid content was significantly up-regulated with the transient overexpression of PcERF114, and significantly down-regulated with virus-induced gene silencing of PcERF114 in the P. cyrtonema leaves. Meanwhile, an integrative analysis of transcriptome and metabolome revealed that differentially expressed genes and differentially accumulated metabolites of transgenic leaves were closely related to the flavonoid biosynthesis pathway, and PcCHS1 was identified as a flavonoid biosynthesis-related key gene by WGCNA, qRT-PCR, and KEGG analysis. Overexpression of PcERF114 in the stable transgenic hairy roots and transiently transformed rhizomes increased the PcCHS1 expression, and the transient co-transformation of overexpressing PcERF114 and PcCHS1 promoted flavonoid accumulation, suggesting that PcERF114 may affect the expression of PcCHS1, thereby promoting the flavonoid accumulation of P. cyrtonema. The results provided a reference for further functional studies of secondary metabolism biosynthesis-related genes in medicinal plants.