BMC Plant Biology最新文献

{"title":"Seed coat transcriptomic profiling of 5-593, a genotype important for genetic studies of seed coat color and patterning in common bean (Phaseolus vulgaris L.).","authors":"Jayanta Roy, Avinash Sreedasyam, Caroline Osborne, Rian Lee, Phillip E McClean","doi":"10.1186/s12870-025-06282-7","DOIUrl":"10.1186/s12870-025-06282-7","url":null,"abstract":"<p><p>Common bean (Phaseolus vulgaris L.) market classes have distinct seed coat colors, which are directly related to the diverse flavonoids found in the mature seed coat. To understand and elucidate the molecular mechanisms underlying the regulation of seed coat color, RNA-Seq data was collected from the black bean 5-593 and used for a differential gene expression and enrichment analysis from four different seed coat color development stages. 5-593 carries dominant alleles for 10 of the 11 major genes that control seed coat color and expression and has historically been used to develop introgression lines used for seed coat genetic analysis. Pairwise comparison among the four stages identified 6,294 differentially expressed genes (DEGs) varying from 508 to 5,780 DEGs depending on the compared stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that phenylpropanoid biosynthesis, flavonoid biosynthesis, and plant hormone signal transduction comprised the principal pathways expressed during bean seed coat pigment development. Transcriptome analysis suggested that most structural genes for flavonoid biosynthesis and some potential regulatory genes were significantly differentially expressed. Further studies detected 29 DEGs as important candidate genes governing the key enzymatic flavonoid biosynthetic pathways for common bean seed coat color development. Additionally, four gene models, Pv5-593.02G016100, 593.02G078700, Pv5-593.02G090900, and Pv5-593.06G121300, encode MYB-like transcription factor family protein were identified as strong candidate regulatory genes in anthocyanin biosynthesis which could regulate the expression levels of some important structural genes in flavonoid biosynthesis pathway. These findings provide a framework to draw new insights into the molecular networks underlying common bean seed coat pigment development.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"284"},"PeriodicalIF":4.3,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of boron on Glycine max L. to mitigate salt stress by modulating the morpho-physiological and biochemical responses.","authors":"Maira Tanveer, Athar Mahmood, Hussam F Najeeb Alawadi, Atman Adiba, Muhammad Mansoor Javaid, Bilal Ahmad Khan, Abdul Wahid, Fnu Abdullah, Mahmoud F Seleiman","doi":"10.1186/s12870-024-06037-w","DOIUrl":"10.1186/s12870-024-06037-w","url":null,"abstract":"<p><strong>Background: </strong>Boron (B) is an essential micronutrient in higher plants, contributing to various physiological processes. However, its protective mechanism in mitigating salt stress remained less understood. This study investigates that exogenous boron (0, 1, 2 kg ha^- 1) can help alleviate salt stress (0, 60, 120 mM NaCl) in two soybean cultivars AARI-2021 (V1) and Ajmeri (V2). It examines B role in reactive oxygen species (ROS), secondary metabolites, and antioxidant defense systems in mitigating salt stress.</p><p><strong>Results: </strong>Salt stress negatively impacted morph-physiological and biochemical attributes. Boron supplementation (2 kg ha^- 1) reduced oxidative stress indicators, such as malondialdehyde (by 18% in V1 and by 21% in V2) and hydrogen peroxide (by 30% in V1 and by 38% in V2). Moreover, foliar application of boron (2 kg ha^- 1) increased the catalase (CAT) (58% in V1 and 57% in V2), superoxide dismutase (SOD) (7% in V1 and 10% in V2), and peroxidase (POD) (42% in V1 and 32% in V2) activities under salt stress. Salt stress also led to an increase in Na⁺ and a decrease in K⁺ and Ca²⁺. However, boron supplementation enhanced K⁺ and Ca²⁺ in salt-stressed plants. Furthermore, boron application (2 kg ha^- 1) increased the activity of secondary metabolites, total phenols content (TPC) (by 52% in V1 and by 59% in V2), total flavonoid content (TFC) (by 27% in V1 and by 21% in V2), and anthocyanins (ANTs) (by 33% in V1 and by 25% in V2) under salt stress.</p><p><strong>Conclusion: </strong>This study suggests that B can reduce salinity-induced oxidative damage in soybean plants by modifying antioxidant defense and secondary metabolites and preserving ion homeostasis.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"286"},"PeriodicalIF":4.3,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of the UGT genes family in Acer rubrum and role of ArUGT52 in anthocyanin biosynthesis under cold stress.","authors":"Khan Arif Kamal, Faheem Afzal Shah, Yue Zhao, Zhu Chen, Songling Fu, Zhiyong Zhu, Jie Ren, Hua Liu","doi":"10.1186/s12870-024-06043-y","DOIUrl":"10.1186/s12870-024-06043-y","url":null,"abstract":"<p><p>Acer rubrum is a widespread Acer species valued for its vibrant autumn foliage. The UGT (UDP-glycosyltransferase) gene family is integral to the biosynthesis of anthocyanins, the pigments responsible for leaf coloration. This study aimed to comprehensively identify and characterize the UGT gene family in the A. rubrum genome. The results of the phylogenetic analysis of 249 ArUGTs revealed 18 distinct subgroups. Conserved motif analysis demonstrated structural similarities within subgroups. Gene duplication analysis identified 21 tandem and 66 segmental duplication events across chromosomes. Transcriptomic data from autumn leaves of different colours and under low-temperature stress were analyzed for ArUGT expression patterns. Compared to controls, 44 UGTs were upregulated and 99 downregulated in yellow leaves, while 59 were upregulated and 84 downregulated in red leaves. Low-temperature treatments showed upregulation of 18 UGTs at 10 °C and 40 UGTs at 4 °C. Downregulation was observed in 7 UGTs at 10 °C and 33 UGTs at 4 °C. Among all UGT genes, ArUGT52 was common in highly expressed genes in both red leaf and low-temperature stress. Furthermore, the transient overexpression of ArUGT52 in tobacco plants demonstrated cytoplasmic localization and a marked increase in anthocyanin levels under cold stress. In vitro, biochemical assay results indicated that the ArUGT52 was involved in anthocyanin biosynthesis via the glucosylation of anthocyanidins. This study provides insights into the genetic mechanisms of leaf coloration and the potential of UGT manipulation for enhancing plant responses to low-temperature stress. These findings have applications in ornamental horticulture and agriculture.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"288"},"PeriodicalIF":4.3,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11881464/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143565795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolome and transcriptome analyses for explore heat stress responses and adaptation mechanisms in Rhododendron henanense subsp. lingbaoense.","authors":"Yonghui Li, Xufeng Li, Mengxin Lei, Junwang Han, Ziming Huang, Kai Zhang, Yifan Yang, Ning Yang, Xiangli Yu, Xiaojun Zhou","doi":"10.1186/s12870-025-06305-3","DOIUrl":"10.1186/s12870-025-06305-3","url":null,"abstract":"<p><p>In this study, we aimed to investigate the heat tolerance mechanism in Rhododendron henanense subsp. lingbaoense (Rhl). Rhl seedlings were treated at 40℃ (RLH), 32℃ (RLM), and 24℃ (RLC), and the changes in transcriptome and metabolome were compared. Overall, 78 differentially expressed metabolites were detected, and 8450 differentially expressed genes (DEGs) were identified. KEGG analysis revealed that the DEGs in RLH vs. RLC were mainly enriched in photosynthesis, secondary metabolic biosynthesis, and flavonoid biosynthesis. Most genes encoding glutathione-S-transferase were upregulated, whereas genes related to heat shock proteins were significantly downregulated. 31 genes related to photosynthesis were significantly upregulated (P-value < 0.001). It was speculated that these DEGs are related to the response of Rhl to high temperature stress (HTS). Overall, 9 TF families might be the key regulators of Heat stress response pathways in Rhl. Mining of DEGs revealed that the expression of some genes related to heat stress function increased highly significantly, e.g., the Rhe008987 related to Glutathione-S-transferase, Rhe016769 encoding peroxidase, and Rhe001827 encoding chalcone and stilbene synthases. Metabolome and transcriptome correlation analysis revealed that three comparison groups (RLH vs. RLC, RLH vs. RLM, and RLM vs. RLC) shared 12 metabolic pathways in which the DEMs were enriched. HTS inhibited or induced expression of genes in flavonoid biosynthesis pathway and led to decreace in kaempferol content and quercetin accumulation. HT induced expression of genes in ABC pathway, which may be one of the reasons for the significant accumulation of L-isoleucine, L-leucine, and L-proline. In this study, DEGs mining found that the expression of some genes related to heat stress function increased highly significantly. And two omics correlation analysis revealed that 12 metabolic pathways were enriched in three comparison groups. These results helped in elucidating the molecular mechanisms of response of Rhl to HTS.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"280"},"PeriodicalIF":4.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540142","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unraveling the response of secondary metabolites to cold tolerance in oil palm by integration of physiology and metabolomic analyses.","authors":"Yuqiao Song, Jerome Jeyakumar John Martin, Xiaoyu Liu, Xinyu Li, Mingming Hou, Ruimin Zhang, Wen Xu, Wenrao Li, Hongxing Cao","doi":"10.1186/s12870-025-06292-5","DOIUrl":"10.1186/s12870-025-06292-5","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Oil palm (Elaeis guineensis), a tropical crop, is highly sensitive to temperature fluctuations, with low temperatures significantly limiting its growth, development, and geographical distribution. Understanding the adaptive mechanisms of oil palm under low-temperature stress is essential for developing cold-tolerant varieties. This study focused on analyzing the physiological and metabolomic responses of annual thin-shell oil palm seedlings to low-temperature exposure (8 °C) for different time periods: 0 h (CK), 0.5 h (CD05), 1 h (CD1), 2 h (CD2), 4 h (CD4), and 8 h (CD8).&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Physiological analysis showed a significant increase in the activity of antioxidant enzymes, such as superoxide dismutase (SOD) and peroxidase (POD), highlighting the activation of oxidative stress defense mechanisms. Concurrently, elevated relative conductivity, indicated cell membrane damage, a common consequence of cold-induced oxidative stress. Metabolomic profiling using LC-MS/MS revealed significant changes in metabolite composition, with differential metabolites predominately enriched in key metabolic pathways such as arginine and proline metabolism, glycine, serine, and threonine metabolism, plant hormone biosynthesis, and flavonoid biosynthesis pathways. Notable metabolites such as citric acid, L-aspartic acid, L-tryptophan, and vitexin showed significant accumulation, indicating their roles in enhancing cold tolerance through improved antioxidant defenses, promoting osmoregulation, and stabilizing cellular structures. Correlation analysis further emphasized the importance of flavonoids and plant hormones in the cold stress response. In particular, vitexin, isovitexin, and apigenin 6-C-glucoside were significantly enriched, suggesting their contribution to antioxidant and stress signaling networks. Furthermore, metabolites involved in amino acid metabolism, including L-glutamic acid, sarcosine, and proline, were upregulated, supporting enhanced protein synthesis and cellular repair under stress. This metabolic reprogramming correlated with physiological improvements, as evidenced by increased relative conductivity and post cold exposure growth recovery.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;This study provides critical insights into the physiological and metabolic adaptations of oil palm to cold stress, emphasizing the significant role of secondary metabolites-such as flavonoids, amino acids, and plant hormones-in enhancing cold tolerance. Theses metabolites contribute to oxidative stress protection, osmotic regulation, and cell wall stabilization enabling the plant to better withstand with low temperature condition. The findings provide a strong foundation for molecular research and breeding initiatives aimed at developing cold tolerant oil palm varieties, a crop of siginificant economic value. By combining metabolomic profiling with physiological analyses, provides a holistic understanding of the adaptive m","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"279"},"PeriodicalIF":4.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877684/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of invertase genes in sweetpotato and its response to nitrogen and planting densities.","authors":"Zheng-Yu Hu, Pei-Xin He, Yu-Jie Li, Hong-Juan Liu, Rafiq Ahmad, Izhar Ali, Cheng-Cheng Si","doi":"10.1186/s12870-025-06295-2","DOIUrl":"10.1186/s12870-025-06295-2","url":null,"abstract":"<p><strong>Background: </strong>Invertases (INVs) included CWIN, CIN and VIN, are key enzymes in sucrose hydrolysis into glucose and fructose and essential for plant root development. Yet the effects of nitrogen and planting density on IbINVs expression remains unexplored in sweetpotato.</p><p><strong>Results: </strong>This study identified 22 invertase (IbINV) genes in the sweetpotato genome and conducted comprehensive analyses of their subcellular localization, gene structure, and conserved motifs and domains. Gene Ontology functional and protein interaction network analysis suggested that IbCWIN1/2/5/6 potentially interact with HKL1/3, HXK2/3/4, and other proteins, significantly influencing carbohydrate metabolic functions and biological processes in sweetpotato. Transcriptome data revealed that IbCIN2 and IbVIN3 were highly expressed in fibrous root (FR) and potential storage root (PSR), while IbVIN4 exhibited high expression levels in storage roots (SR), and IbCWIN2 was highly expressed in both FR and SR. Moreover, the field experiments demonstrated that, compared with EN (180 kg N ha^-1) combined with LD (50,000 plant ha^- 1), MN (120 kg N ha^- 1) combined with MD (62,500 plant ha^- 1) enhanced storage roots number and weight. Notably, compared with LDEN treatment, IbCIN2, IbCWIN2, IbVIN3 and IbVIN4 under MDMN treatment were significantly upregulated, extremely significant differences at 15DAP, of which IbCIN2 showed a maximum of 23.24-fold change, showing a positive correlation with increased INV enzyme activity, glucose (GLc), and fructose (FRc) content. Additionally, screening of homologous genes showed that IbCIN2 is homologous to AtA/N-INVI and AtA/N-INVG, IbCWIN2, IbVIN3 and IbVIN4 are homologous to VACUOLAR, INVERTASE1 and BFRUCT4, with similar functions, further supporting their involvement in storage root formation and development.</p><p><strong>Conclusion: </strong>These observations underscore the expansion of IbINVs in sweetpotato and provide a theoretical basis for optimizing the interaction between nitrogen application and planting density in sweetpotato, allowing for more efficient nitrogen use and improved growth.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"281"},"PeriodicalIF":4.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Delineation of genotype × environment interaction and identifying superior red sorghum [Sorghum bicolor L. Moench] genotypes via multi-trait-based stability selection methods.","authors":"Sureshkumar Rajesh-Kumar, Guruswamy Anand, Subramanian Lakshmi Narayanan, Elangovan Subramanian, Madhavan Lysal Mini","doi":"10.1186/s12870-025-06188-4","DOIUrl":"10.1186/s12870-025-06188-4","url":null,"abstract":"<p><p>Red sorghum, a versatile crop with high nutritional and biochemical value, was evaluated for agronomic and grain quality traits using 27 genotypes across diverse environmental zones of Tamil Nadu. The data collected were subjected to Additive Main Effects and Multiplicative Interaction (AMMI) and Genotype-by-Environment Interaction (GGE) biplot models to recommend a specific genotype for the particular locality. The analysis of variation of the pooled data revealed a significant interaction effect between genotype and environment for the majority of the examined traits. Correlation analysis revealed a significant positive association of panicle weight and a negative association of micronutrient content with grain yield. The G × E was smaller than the genetic variation of grain yield as it portrayed the maximum contribution of genotypic effects (50.2%). GGE biplot showed E2 as a highly discriminating environment for grain yield and also identified environment-specific genotypes viz., G11 for E1, E3 and G6 for E2 environments. The GGE biplots recommended G9 and G14 as high-yielding stable genotypes, outperforming the check variety PAIYUR 2 (G15) by 15.83% and 36.16% respectively, across all environments, particularly in E1 and E3. The genotypes G14, G18, G21 and G26 shown wide adaptation and excelled as biofortified genotypes with significant Fe and Zn contents. Multi-trait stability evaluation approaches such as multi trait stability index (MTSI), multitrait genotype‒ideotype distance index (MGIDI), multi-trait index based on factor analysis and genotype-ideotype distance (FAI-BLUP), multitrait mean performance and stability index (MTMPS) and Smith-Hazel index assuming 15% selection intensity were adopted. G14 consistently ranked as the top and steady performer in all evaluation methods. The identified genotype demonstrated exceptional reliability, high yield potential, and early maturity, making them suitable candidates for variety and hybrid development, as well as ideotype breeding programs aimed at ensuring food and nutritional security.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"283"},"PeriodicalIF":4.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877764/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sugarcane leaf disease classification using deep neural network approach.","authors":"Saravanan Srinivasan, S M Prabin, Sandeep Kumar Mathivanan, Hariharan Rajadurai, Suresh Kulandaivelu, Mohd Asif Shah","doi":"10.1186/s12870-025-06289-0","DOIUrl":"10.1186/s12870-025-06289-0","url":null,"abstract":"<p><strong>Objective: </strong>The objective is to develop a reliable deep learning (DL) based model that can accurately diagnose diseases. It seeks to address the challenges posed by the traditional approach of manually diagnosing diseases to enhance the control of disease and sugarcane production.</p><p><strong>Methods: </strong>In order to identify the diseases in sugarcane leaves, this study used EfficientNet architectures along with other well-known convolutional neural network (ConvNet) models such as DenseNet201, ResNetV2, InceptionV4, MobileNetV3 and RegNetX. The models were trained and tested on the Sugarcane Leaf Dataset (SLD) which consists of 6748 images of healthy and diseased leaves, across 11 disease classes. To provide a valid evaluation for the proposed models, the dataset was additionally split into subsets for training (70%), validation (15%) and testing (15%). The models provided were also assessed inclusively in terms of accuracy, further evaluation also took into account level of model's complexity and its depth.</p><p><strong>Results: </strong>EfficientNet-B7 and DenseNet201 achieved the highest classification accuracy rates of 99.79% and 99.50%, respectively, among 14 models tested. To ensure a robust evaluation and reduce potential biases, 5-fold cross-validation was used, further validating the consistency and reliability of the models across different dataset partitions. Analysis revealed no direct correlation between model complexity, depth, and accuracy for the 11-class sugarcane dataset, emphasizing that optimal performance is not solely dependent on the model's architecture or depth but also on its adaptability to the dataset.</p><p><strong>Discussion: </strong>The study demonstrates the effectiveness of DL models, particularly EfficientNet-B7 and DenseNet201, for fast, accurate, and automatic disease detection in sugarcane leaves. These systems offer a significant improvement over traditional manual methods, enabling farmers and agricultural managers to make timely and informed decisions, ultimately reducing crop loss and enhancing overall sugarcane yield. This work highlights the transformative potential of DL in agriculture.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"282"},"PeriodicalIF":4.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revisiting Phryma leptostachya L.: phylogenetic relationships and biogeographical patterns from complete plastome.","authors":"Yeseul Kim, Sumin Jeong, Inkyu Park, Hye-Kyoung Moon","doi":"10.1186/s12870-025-06272-9","DOIUrl":"10.1186/s12870-025-06272-9","url":null,"abstract":"<p><strong>Background: </strong>Phryma leptostachya L. is a notable example of a species with a disjunct distribution, found in both East Asia and Eastern North America. Despite the striking morphological similarities between these geographically isolated populations, molecular evidence suggests that they may have diverged sufficiently to be considered distinct taxa.</p><p><strong>Results: </strong>To clarify this, we analyzed the plastomes of P. leptostachya from Korea, Russia, and the USA. Their sizes ranged from 152,974 to 153,325 bp, each containing 113 genes. Differences were observed in the boundaries between large single copy (LSC)/IRa and IRb/LSC. In P. leptostachya_USA, the rps19 gene extended 30-31 bp into the IRa, and the rpl2 gene contracted 51-53 bp at the IRa/b compared to those of P. leptostachya_Korea and P. leptostachya_Russia, suggesting that expansion of the inverted repeat (IR) region occurred in P. leptostachya_USA. Regions such as psbZ-trnG, ccsA-ndhD, petA-psbJ, and psbC-trnS were identified as hotspots with sequence differences in the plastome, indicating differences among P. leptostachya variants. Phylogenetic analysis showed that P. leptostachya from Korea and Russia formed monophyletic groups, while the variety from the USA was paraphyletic. The divergence of P. leptostachya_USA occurred during the Pliocene, about 5.25 million years ago (MYA), whereas the split between P. leptostachya_Korea and P. leptostachya_Russia is estimated to have occurred approximately 0.87 MYA during the Pleistocene. The results also reveal that the family Phrymaceae underwent multiple dispersal and vicariance events from North America to East Asia, offering key insights into the phylogenetic relationships between P. leptostachya populations from Korea, Russia, and the USA. Based on the evidence, it is likely that P. leptostachya originated in North America and later migrated to East Asia via the Russian Far East and the Bering Land Bridge.</p><p><strong>Conclusions: </strong>In conclusion, our study demonstrates clear molecular differences among P. leptostachya populations from various geographic locations, suggesting that these populations should be recognized as distinct species rather than conspecifics.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"278"},"PeriodicalIF":4.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877724/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic signatures of SnRKs highlighted conserved evolution within orchids and stress responses through ABA signaling in the Cymbidium ensifolium.","authors":"Ruiyue Zheng, Kai Zhao, Jiemin Chen, Xuanyi Zhu, Yukun Peng, Mingli Shen, Zhong-Jian Liu, Donghui Peng, Yuzhen Zhou","doi":"10.1186/s12870-025-06280-9","DOIUrl":"10.1186/s12870-025-06280-9","url":null,"abstract":"<p><p>Sucrose non-fermenting 1-related protein kinases (SnRKs) are crucial for modulating plant responses to abiotic stresses, linking metabolism with stress signaling pathways. Investigating the roles and stress responses of SnRKs in plants paves the way for developing stress-tolerant strategies in orchid species. Here, 362 SnRK members were identified from nine current orchid genomes, highlighting the conservation of these genes in evolution. Among these, 33 CeSnRKs were found across 20 chromosomes of C. ensifolium genome. Multiple duplication events increased the complexity of CeSnRKs during independent evolution. Moreover, distinct functional domains beyond the kinase domain differentiated the subfamilies. These multi-copy members existed tissue specific expressions falling into 6 main trends, especially CeSnRK1, CeCIPK9, CeCIPK23 displayed a strict floral expression. ABA-related elements were enriched in the promoters of CeSnRKs, and stress-related miRNA binding sites were identified on partial CeSnRKs. Consequently, most CeSnRKs exhibited up-regulated expression during ABA treatment. Several genes, such as CeSnRK2.1 and CeCIPK28 involved growth and development at different times and various tissues. The up-regulation of SnRK2.1, along with high expression of SnRK1 and CIPK27 under drought stress, and the differential expression patterns of CeSnRKs under cold stress, underscore the involvement of CeSnRK genes in different stress responses. Additionally, the diverse interactions of CeSnRKs with proteins highlighted a multifaceted functional network.These findings offer valuable insights for the future functional characterization formation of CeSnRKs and the adaptive evolution of genes in orchids.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"277"},"PeriodicalIF":4.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11874761/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}