BMC Plant Biology最新文献

{"title":"Population structure, genetic diversity and genome-wide association analysis of the seed morphology traits in Handroanthus chrysanthus (Jacq.) s.o.grose.","authors":"Xiuhua Shang, Zhihua Wu, Guowu Zhang, Youshuang Wang, Xiaoming Li, Peijian Zhang","doi":"10.1186/s12870-025-07285-0","DOIUrl":"10.1186/s12870-025-07285-0","url":null,"abstract":"","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1249"},"PeriodicalIF":4.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12486526/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198318","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":"Study on the differences in sugar-acid metabolism of Sweet Orange 'Newhall' with different rootstocks.","authors":"Qingqing Ma, Taimei Deng, Bei Yang, Wenjia Wu, Linlv Han, Chenming Wang, Hongzhen Chen, Lalapei Ji, Ling Liao, Guochao Sun, Mingfei Zhang, Xun Wang, Siya He, Zhihui Wang, Bo Xiong","doi":"10.1186/s12870-025-07286-z","DOIUrl":"10.1186/s12870-025-07286-z","url":null,"abstract":"<p><strong>Background: </strong>Citrus rootstock selection plays a critical role in modulating sugar-acid metabolism, thereby influencing fruit flavor quality. This study systematically investigated the dynamic changes in sugar and acid components, key enzyme activities, and related gene expression in 'Newhall' navel orange (Citrus sinensis) grafted onto Citrus reticulata (Rt), Citrus junos (Cj), and Poncirus trifoliata (Pt) rootstocks during fruit development (150-240 days after flowering, DAF).</p><p><strong>Results: </strong>Pt significantly enhanced late-stage sucrose accumulation (48.86 ± 2.63 mg·g⁻¹), surpassing the means of Rt and Cj by 26.78% and 60.72% at 240 DAF, respectively. This was associated with elevated sucrose synthase (SS) activity and upregulated CsSS2 expression. In contrast, Rt rootstock promoted malic and quinic acid retention and exhibited the highest citrate synthase (CS), isocitrate dehydrogenase (IDH), and isocitrate lyase (ICL) activities, supported by significantly increased upregulation of acid metabolism genes (CsCS1, CsNADP-IDH1/2/3). Comprehensive evaluation using the TOPSIS model, weighted by entropy analysis (with tartaric acid, fructose, and glucose identified as primary determinants), ranked fruit quality as Pt > Rt > Cj at maturity.</p><p><strong>Conclusions: </strong>These findings establish a mechanistic framework linking rootstock-specific regulation of enzymatic activities and gene expression with dynamic sugar-acid profiles, providing valuable insights for optimizing rootstock-scion combinations to enhance citrus flavor quality.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1250"},"PeriodicalIF":4.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12486767/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198334","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":"Physiological and antioxidant responses of marjoram (Origanum Majorana L.) under drought stress mediated by Salicylic acid and mycorrhizal symbiosis.","authors":"Babak Modara, Mohammad Mehdi Rahimi, Moslem Abdipour, Mehdi Hosseinifarahi","doi":"10.1186/s12870-025-07225-y","DOIUrl":"10.1186/s12870-025-07225-y","url":null,"abstract":"<p><p>Drought stress, exacerbated by climate change, is a major limiting factor for herbs cultivation. This study aimed to evaluate the combined effects of salicylic acid (SA) and mycorrhizal fungi (MF) on marjoram under drought stress conditions. The experiment was conducted over two years (2022-2023) using a split factorial design within a randomized complete block with three replications. The study's primary factor was drought stress at three levels: 90% (D0), 70% (D1), and 35% (D2) of field capacity (FC). The secondary factor included two sub-factors: SA concentrations (0, 100, and 300 mg L^-1) and MF inoculation (non-inoculated (M0) and inoculated with Glomus hoi (M1)). Results demonstrated that drought stress decreased relative water content (RWC) (46.8%), chlorophyll content (35%), carotenoids (25.7%), and dry weight (49.3%), while increasing proline (38.6%), soluble sugars (29.4%), electrolyte leakage (44.8%), superoxide dismutase (35.2%), peroxidase (43.1%), and catalase activities (29.3%). Additionally, the combined treatment of SA and MF enhanced water status by 44%, proline content by 12%, and soluble sugar content by 6% under severe drought conditions. Antioxidant enzyme activities (Catalase) were also significantly increased by up to 91% with the combined treatments, supporting the hypothesis that the synergy of SA and MF can effectively mitigate the adverse effects of drought stress on marjoram. Overall, this study demonstrated that the combined application of SA and MF could be a promising strategy for enhancing drought tolerance in marjoram, especially in drought-prone areas. TRIAL REGISTRATION: This study does not involve clinical trials or human participants and, as such, does not require clinical trial registration.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1248"},"PeriodicalIF":4.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12486875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198237","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":"EDDet: efficient deep-fusion and dynamic optimization for small target detection in eggplant diseases.","authors":"Ye Li, Xiaofang Li, Rui Fu, Zhenqi Cheng, Jianchun Yu, Xuewei Wang, Hao Sun","doi":"10.1186/s12870-025-07268-1","DOIUrl":"10.1186/s12870-025-07268-1","url":null,"abstract":"<p><p>With the development of smart agriculture and the growth of the global population, vegetable production is facing the dual challenges of diversified planting environments and increased concealment of diseases. Eggplant, as an important economic crop, has its disease detection accuracy directly affecting yield and quality. However, traditional detection methods fail to effectively capture small diseased areas. To address this issue, this paper proposes an improved deep learning small target detection model-the Efficient Deep-fusion Detection Model (EDDet), which is specifically optimized for the recognition of small diseased spots in eggplant disease detection. In the detection network, we innovatively designed the Pinwheel Fusion Feature Extractor (PFFE) framework, replacing the standard convolutions of the first two layers with Pinwheel Convolutions (PConv). By using asymmetric padding and parallel convolution kernel design, the receptive field is effectively expanded, the ability to capture underlying features is enhanced, and the detection of small diseased areas in eggplants is more precise. In the feature fusion stage, this paper designs a Cross-layer Attention Module (CAM), including Cross-layer Channel Attention (CCA) and Cross-layer Spatial Attention (CSA), which can efficiently interact and fuse features of different scales without additional sampling, alleviating the information loss caused by semantic gaps. In addition, to solve the instability caused by IoU fluctuations in the bounding box regression process, the model introduces Scale-based Dynamic Loss (SD Loss), which dynamically adjusts the loss weight based on the size of the target. By adaptively adjusting the proportion of IoU-based loss and location constraint loss, more precise localization and stable regression of small diseased areas in eggplants are achieved. Experimental results demonstrate that EDDet achieves a notable improvement in mAP50 (85.4%), outperforming the baseline by 2.8%.Importantly, EDDet also Maintains excellent efficiency with only 2.75 M parameters, 9.1 GFLOPs, and a high inference speed of 288.3 FPS, which is 37.5 FPS higher than the baseline.These results highlight the model's strong potential for real-time deployment in complex agricultural scenarios where both precision and speed are critical.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1261"},"PeriodicalIF":4.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487401/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198462","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":"Floral anatomy and ultrastructure of Lepanthes calodictyon, L. saltatrix and L. tentaculata (Orchidaceae).","authors":"Rykaczewski Max, Kapusta Małgorzata, Narajczyk Magdalena, Łuszczek Dorota, Brzezicka Emilia, Dariusz L Szlachetko","doi":"10.1186/s12870-025-07141-1","DOIUrl":"10.1186/s12870-025-07141-1","url":null,"abstract":"<p><strong>Background: </strong>Previous studies have shown that the ultrastructure and histochemistry of flowers give insight into the pollination mechanisms of orchid species. The microscopic features of species within the Pleurothallidine subtribe are poorly understood. In this study, we investigated three Lepanthes species: L. calodictyon, L. saltatrix and L. tentaculata. These species have a similar flower morphology that is distinct from that of the other representative of the genus.</p><p><strong>Results: </strong>Our analyses revealed the presence of features usually associated with myophily. The papillae of lips and petals of the L. calodictyon group were rich in lipids and proteins, which were correlated with high metabolic activity. Furthermore, the ultrastructural and morphological features were similar to those observed in other fragrance-emitting orchid species.</p><p><strong>Conclusions: </strong>Histochemical, ultrastructural and morphological features of the papillae on the surface of the lips and petals of examined taxa indicate that the papillae are osmophores.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1252"},"PeriodicalIF":4.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145197837","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":"Integrated of metabolome and transcriptome analysis reveals the effect of artificial light at night on Platanus orientalis L.","authors":"Zhiyuan Lv, Yue Hu, Hanyu Zhou, Chong Hu, Rong Liang, Lijiao Ai, Lichao Tian","doi":"10.1186/s12870-025-07179-1","DOIUrl":"10.1186/s12870-025-07179-1","url":null,"abstract":"<p><strong>Background: </strong>Artificial light at night (ALAN) and its associated biological impacts have regularly been characterized as predominantly urban issues. ALAN delays the senescence of plane tree leaves in cities, resulting in the longer retention of green leaves. Some studies have described the effects of ALAN on plane trees at the physiological and biochemical levels. However, there is a lack of research at the molecular level.</p><p><strong>Results: </strong>In this study, we performed metabolic and transcriptomic analyses on plane green leaves with and without streetlight, as well as natural yellowing leaves away from the streetlight. In green leaves exposed to streetlights, numerous genes associated with auxin and cytokinins that inhibit leaf senescence were activated, while most genes associated with salicylic acid, jasmonic acid, ethylene and brassinolide that promote senescence were suppressed. Some candidate senescence-associated genes (SAGs) were identified, and brassinolide (6alpha-hydroxy-castasterone and castasterone), jasmonic acid ((-)-jasmonic acid and methyl jasmonate) and most flavonoids were significantly enriched in yellowing leaves. Combined analyses of transcriptome and metabolome data revealed that compared with the two green leaf groups, biosynthesis of amino acid, phenylpropanoid biosynthesis, tryptophan metabolism and flavonoid biosynthesis were the most significantly enriched metabolic pathway in yellowing leaves. Especially for phenylpropanoid biosynthesis and flavonoid biosynthesis related to leaf yellowing pigment accumulation, most of DEGs and DAMs are upregulated in yellowing leaves, but downregulated in green leaves under streetlight.</p><p><strong>Conclusion: </strong>Our results indicate that ALAN retarded plant leaf senescence mainly by altering plant hormone levels and inhibiting metabolic pathways such as flavonoid biosynthesis, betalain biosynthesis, caffeine metabolism and phenylpropanoid biosynthesis. This study provides insights into how streetlights affect plane trees.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1236"},"PeriodicalIF":4.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198206","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":"Indigenous plant growth-promoting rhizobacteria for cocoa growth enhancement and Phytophthora pod rot management in coastal Andhra Pradesh, India.","authors":"B Neeraja, V Prasanna Kumari, K Gopal, G S Madhu, K Vijay Kumar, T Madhumathi, N B V Chalapathi Rao, B R Sayiprathap","doi":"10.1186/s12870-025-07166-6","DOIUrl":"10.1186/s12870-025-07166-6","url":null,"abstract":"<p><p>Plant growth-promoting rhizobacteria (PGPR) are beneficial microbes that support plant development through mechanisms such as nutrient solubilization, phytohormone production, and antagonism against phytopathogens. This study focused on isolating and characterizing PGPR strains native to the cocoa rhizosphere in the coastal region of Andhra Pradesh and assessing their efficacy against Phytophthora palmivora, the causal agent of cocoa pod rot. A total of 50 bacterial isolates were initially screened based on hydrolytic enzyme production, siderophore activity, phosphate solubilization, and antagonistic potential. Six promising isolates NEG27, NWG12, NSK3, NEG14, NEG16, and NEG3-showed strong antifungal activity and were identified through 16 S rRNA sequencing as Pseudomonas fluorescens (NEG27, NEG3), Stutzerimonas stutzeri (NWG12), and Pseudomonas otitidis (NEG14, NEG16, NSK3). In vitro antagonism assays demonstrated that NEG27 inhibited P. palmivora mycelial growth by 82.26%, followed by NWG12 (77.41%) and NEG14 (76.30%), with microscopy revealing severe hyphal disintegration and malformed zoospores. PGPR seed treatment significantly enhanced cocoa germination rates (35.71% increase over control), seedling vigour index (by 441.84%), and root-shoot biomass (p < 0.05). Field trials conducted over two cropping seasons (2022-23 and 2023-24) revealed that combined foliar application of NEG27, NWG12, and NSK3 at 1.5% significantly (p < 0.05) reduced pod rot disease severity compared to untreated controls, while also improving yield-related traits and the benefit-to-cost (B: C) ratio. These results highlight the potential of indigenous PGPR strains as sustainable biocontrol agents and viable alternatives to chemical fungicides.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1258"},"PeriodicalIF":4.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198224","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":"Bacillus tequilensis S40 inoculation alleviates salt stress by modifying bacterial community structure and regulating elemental cycling rhizosphere of Reaumuria soongorica.","authors":"Xin-Guang Bao, Pei-Fang Chong, Cai He, Xue-Ying Wang, Feng Zhang, Bing-Bing Tan, Kai-Xin Lou","doi":"10.1186/s12870-025-07122-4","DOIUrl":"10.1186/s12870-025-07122-4","url":null,"abstract":"<p><p>Plant growth‒promoting rhizobacteria (PGPRs) are pivotal in forest cultivation and saline‒alkaline soil improvement by altering the structure of rhizosphere bacterial communities and improving soil nutrient utilization efficiency. However, there are few reports on the exploration of PGPR bacterial resources and the mechanism by which PGPR enhance the salt tolerance of Reaumuria soongorica (R. soongorica) in desert shrubs. This study focused on Bacillus tequilensis (B. tequilensis) S40, which is a PGPR isolated from the rhizosphere of R. soongorica by our research group. We investigated the effects of the S40 strain on the rhizosphere microbial community and functional genes of R. soongorica through pot experiments. The results demonstrated that inoculation with the S40 strain could alleviate the negative effects of NaCl stress on the plant height, total root length, and rhizome leaf biomass. Proteobacteria, Bacteroidetes, and Planctomycetota were the dominant phyla. Notably, inoculation with S40 strain significantly increased the absolute abundances of functional genes involved in carbon (C), nitrogen (N), and phosphorus (P) cycling (p < 0.05). Furthermore, the genes related to C, N, and P cycling were significantly correlated with soil properties (available phosphorus, urease activity, sucrase activity), and the biomass of R. soongorica leaves, stems, and roots (p < 0.05). In conclusion, the PGPR strain S40 mediates the reorganization of bacterial community, drives the element cycle, and enhances soil nutrient availability, thus promoting plant growth and enhancing salt tolerance of plants and providing a method and scientific basis for cultivating shrub seedlings and alleviating the degree of soil salinization.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1251"},"PeriodicalIF":4.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198373","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":"Comparative chloroplast genome of six species in Hypoxidaceae from China: insights into phylogenetic relationships and molecular marker development.","authors":"Dong Ma, Qin Tian, Yunqiang Wang, Hanning Duan, Yuan Zhang, Yan Luo, Lu Li","doi":"10.1186/s12870-025-07191-5","DOIUrl":"10.1186/s12870-025-07191-5","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;The family Hypoxidaceae (order Asparagales) is a predominantly Southern Hemisphere lineage comprising approximately 11 genera and 200 species, many of which possess significant medicinal and ornamental value. Despite their economic importance, Hypoxidaceae has received limited research attention, leading to problematic identification of species and misuse of wild resources in traditional medicine markets. Taxonomically, the phylogenetic position of Hypoxidaceae and the intergeneric relationships within this family remain controversial and unresolved, particularly concerning the delimitation of Curculigo and Molineria. Previous studies based on morphological traits and molecular markers have yielded inconsistent results, highlighting the need for more robust genomic evidence. In angiosperms, complete chloroplast genomes have proven highly effective in resolving systematic uncertainties considering their conserved structure and high informational content. However, such genomic data remain scarce for Hypoxidaceae, limiting phylogenetic clarity. In this research, the complete chloroplast genomes of six species representing three key genera (Curculigo, Molineria, and Hypoxis) were sequenced and characterized for a comparative and phylogenetic analysis.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;The chloroplast genomes of six species exhibited conserved quadripartite structures, measured 157,472 bp to 158,550 bp in length. The overall GC content of these genomes ranged between 37.3 and 37.5%. Gene annotations identified 132 genes, 19 duplicated in the inverted repeat regions, and had complete ndh gene. Comparative analysis of six complete chloroplast genomes revealed highly similarity, but they were varied in repeats sequence, codon usage bias, contractions and expansions in the IR region. Five molecular markers showed the highest degree of variability between the six cp genomes. Phylgenetic analysis based on cp genomic data confirmed that Hypoxidaceae was a monophyly, being a sister to Asteliaceae with higher supports than the previous research. Three main clades were recognized in Hypoxidaceae, including Curculigo clade, Hypoxis clade, and Pauridia-Empodium clade. And what's more, Curculigo clade could be divided into three subclades, containing Molineria subclade, Curculigo subclade, and Seychellean subclade, indicating significantly phylogenetic insights.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;The complete cp genomes of six species of three representative genera from Hypoxidaceae were sequenced and analyzed in detail, including the general data on the genome length, repeat sequence, codon usage, IR expansion and contraction, structural comparison and divergence hotspot identification analyses, and phylogenetic analysis. A comparative analysis revealed that the cp genome was highly consistent of four Molineria species, but varied greatly at the generic level between Hypoxis, Curculigo, and Molineria, which could be used for generic","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1232"},"PeriodicalIF":4.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198416","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":"Chloroplast genome, an effective strategy for identifying hybrid species, using Dendrobium 'Black Gold' as an example.","authors":"Chaohai Li, Yujiao Zhang, Yaping Wang, Changwei Wu, Mingyue Shang, Rong Liu, Kanglin Bai, Nengbo Li, Weihong Liu, Xinping Li, Baozhong Duan","doi":"10.1186/s12870-025-07189-z","DOIUrl":"10.1186/s12870-025-07189-z","url":null,"abstract":"<p><strong>Background: </strong>Misusing Dendrobium hybrid varieties in herbal products poses a substantial challenge to authenticity and safety concerns. D. 'Black Gold', a hybrid of D. nobile and D. officinale, closely mimics D. officinale in appearance. However, the accurate identification of genetic traits has been impeded by the scarcity of genetic data. Molecular markers derived from chloroplast genomes (cp genomes) have emerged as practical tools for authenticating cultivars.</p><p><strong>Results: </strong>In this study, three Dendrobium species (D. 'Black Gold', D. nobile, and D. officinale) cp genomes were de novo sequenced, assembled, And characterized. The Analysis revealed high conservation in gene organization and structure across the three genomes. The genome sizes ranged from 150,114 bp to 150,602 bp, with the large single-copy (LSC) regions spanning 84,781 bp to 85,089 bp, the small single-copy (SSC) regions ranging from 13,799 bp to 14,503 bp, and the inverted repeat (IRa and IRb) regions varying from 26,011 bp to 26,309 bp. A total of 73 to 86 protein-coding genes (PCGs), 38 to 39 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes were identified in the three species. Phylogenetic analysis revealed that D. officinale is the maternal parent of D. 'Black Gold'. The crown group divergence of Dendrobium species was estimated to have occurred approximately 29.22 million years ago (Mya). Additionally, eight highly variable regions were identified, with the accD-psaI and matK-rps16 region confirmed as effective molecular markers for distinguishing D. 'Black Gold' from related species.</p><p><strong>Conclusions: </strong>These findings provide valuable insights into the genetic characteristics of D. 'Black Gold' and offer a reliable strategy for distinguishing hybridized counterparts. This research not only aids in precisely identifying Dendrobium hybrids but also supports future studies on their conservation and utilization.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"1257"},"PeriodicalIF":4.8,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12487424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145198447","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}