BMC Plant Biology最新文献

{"title":"Prediction of Sorghum bicolor (L.) distribution ranges provides insights on potential sorghum cultivation across tropical ecoregions of Indonesia.","authors":"Suyud Warno Utomo, Fatma Lestari, Andrio Adiwibowo, Micah R Fisher","doi":"10.1186/s12870-025-06454-5","DOIUrl":"10.1186/s12870-025-06454-5","url":null,"abstract":"<p><p>Sorghum bicolor (L.) is a plant species that has staple and medicinal potential and is common in tropical regions, including Southeast Asia regions. Despite sorghum being used widely, the information about potential distributions of sorghum in various ecoregions in Indonesia is still limited. Indonesia is a vast country with distinct ecoregions, with wet ecoregions in western parts of Indonesia and arid environments in eastern parts. The information on sorghum potential distribution in various ecoregions is important, and in this situation, this study aimed to model the sorghum potential distribution in various ecoregions using MaxEnt based machine learning. The total area of Indonesia that is suitable for sorghum is estimated to be 68,527,000 ha, or 28.17% of Indonesia's areas. Among all ecoregions in Indonesia, Sulawesi and Lesser Sunda, representing dry ecoregions, are having the largest suitable areas. The Lesser Sunda and Sulawesi ecoregions have the highest suitable percentages of 44.76% for Lesser Sunda and 21.53% for Sulawesi ecoregions. The lowest percentages were observed in the Sumatra, Kalimantan, and Papua ecoregions, representing wet ecoregions. This confirms that sorghum prefers the dry ecoregions, as high percentages of suitable areas are observed in these kinds of ecoregions.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"401"},"PeriodicalIF":4.3,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956226/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751207","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":"Synergetic effects of potassium and biochar on morphological, physiological, and biochemical attributes of maize crop grown under different levels of drought stress.","authors":"Shafeeq Ur Rahman, Jing-Cheng Han, Ghulam Yasin, Muhammad Talha Imtiaz, Xu Zhao, Sulaiman Ali Alharbi, Saleh Alfarraj, Abdullah A Alarfaj","doi":"10.1186/s12870-025-06391-3","DOIUrl":"10.1186/s12870-025-06391-3","url":null,"abstract":"<p><p>Global climate change accelerates the challenges of agricultural drought spells, which are alarming for food security and can trigger food scarcity. Therefore, improving soil-water retention capability and crop drought resilience is becoming more important for sustainable agriculture. This study investigates the individual and combined effects of biochar and potassium on soil water retention, crop drought resilience, and related physio-biochemical mechanisms over a 50-day growth period in potted plants. Pine needle biochar (350 g/10 Kg of soil) was used during the soil preparation stage while potassium sulfate (100 mg/L) was applied as a foliar spray at the development (10 days) and vegetative stages (45 days) under three drought stress conditions: control (100% FC), mild (75% FC) and severe (40% FC). The results revealed that the combined application of biochar and potassium significantly increased morphological, physiological, and biochemical attributes of maize plants under drought stress, improving shoot fresh weight by 11%, 6%, and 5%, root fresh weight by 19%, 19%, and 23%, shoot length by 17%, 16%, and 19%, and root length by 21%, 30%, and 29% under control, mild, and severe drought stress conditions, respectively. Similarly, relative water contents (RWC) increased by 12%, 16%, and 20%, water potential (Ψ) increased by 26%, 22%, and 24%, osmotic potential (Ψs) increased by 100%, 59%, and 30%, and turgor potential (Ψp) increased by 28%, 35%, and 51% under combined treatment compared to control, mild, and severe drought stress. Additionally, biochar application with potassium foliar spray also improved membrane stability and integrity, cell wall loosening, membrane lipid peroxidation, and protein denaturing by decreasing electrolytic leakage by 35%, 28%, and 43%, proline by 30%, 27%, and 22%, hydrogen peroxidase by 47%, 45%, and 41%, and malondialdehyde contents by 24%, 20%, and 28% through activation of enzymatic (CAT, POD, SOD) and non-enzymatic (TSS, AsA, GSH) antioxidants. Furthermore, nutrient uptake was enhanced, with N increasing by 47%, 19%, and 45%, P by 64%, 82%, and 52%, and K by 24%, 42%, and 35% in shoots compared to normal, mild, and severe drought stress. These improvements mitigated cell dehydration, reduced transpiration inefficiency and delayed senescence, and ultimately supporting plant growth under drought stress. In conclusion, integrating biochar with potassium application effectively improves soil-water retention, alleviates oxidative stress and enhances drought tolerance in maize plants. This strategy can play a crucial role in sustainable agriculture by mitigating the adverse effects of drought stress and improving food security in drought-prone regions.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"402"},"PeriodicalIF":4.3,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956366/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751215","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":"Glycolysis and signal transduction participate in Lycium barbarum in response to NaCl stress through protein phosphorylation.","authors":"Wangli Liang, Zheng Zhang, Ning Yao, Bo Wang, Wenjing Yu, Qiang Zhu, Shujuan Yang, Jijuan Zeng, Lingxia Wang, Wenyu Liang","doi":"10.1186/s12870-025-06402-3","DOIUrl":"10.1186/s12870-025-06402-3","url":null,"abstract":"<p><strong>Background: </strong>Lycium barbarum L. possesses great salt tolerance and medicinal values, studying its salt tolerance contribute to variety improvement, as well as the increase in yield and quality.</p><p><strong>Results: </strong>The study integrated the tandem mass tags (TMT) phosphoproteomics and physiological indexes of L. barbarum exposed to different concentrations of NaCl, with the aim of characterizing salt adaptation characteristics of L. barbarum. The findings indicated that a total of 2189 differentially phosphorylated peptides were identified, functional analysis revealed their involvement in glycolysis, plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signal transduction and other pathways, and that the enzyme activities and substances related to glycolysis and signal transduction underwent significant changes under salt stress.</p><p><strong>Conclusion: </strong>Salt stress enhanced the glycolysis pathway through protein phosphorylation, and the changes in related enzymes activity accelerated the conversion of intermediate metabolites and energy supply. Salt stress led to the accumulation of abscisic acid (ABA), jasmonic acid (JA), and salicylic acid (SA) levels, triggering signal transduction events regulated by phosphorylated proteins to improve salt tolerance for L. barbarum in saline environments. The phosphorylation of MAPK signaling pathway-related proteins is triggered by reactive oxygen species (ROS) and ABA as signal molecules to induce the expression of downstream salt stress response factors. This study provides a foundation for further analysis of the molecular regulatory mechanism of protein phosphorylation in L. barbarum for salt stress.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"405"},"PeriodicalIF":4.3,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956257/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751186","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 metabolomics and transcriptomics reveal differences in terpenoids and the molecular basis among the roots of three Bupleurum species.","authors":"Dong Wen, Hongliang Ji, Mei Rong, Yang Liu, Jiemei Jiang, Xinwei Guo, Zhihui Gao, Yanhong Xu, Jianhe Wei","doi":"10.1186/s12870-025-06441-w","DOIUrl":"10.1186/s12870-025-06441-w","url":null,"abstract":"<p><strong>Background: </strong>Radix Bupleuri is a popular traditional Chinese medicinal plant. Its root contains saikosaponin and volatile oil compounds with antipyretic, anti-inflammatory, and hepatoprotective pharmacological effects. However, there are differences in the content and type of main chemical components in the roots of three Bupleurum species: Bupleurum chinense DC. (Bchi), Bupleurum scorzonerifolium Willd. (Bsco), and Bupleurum marginatum var. stenophyllum (Wolff) Shan et Y.Li (Bmar). The molecular mechanism behind these differences is still unclear. The present study used integrated metabolome and transcriptome analyses to uncover the differences in metabolites and expressed genes among the three Bupleurum species.</p><p><strong>Results: </strong>Metabolomics results revealed that Bmar contained more saikosaponins than Bchi and Bsco. Conversely, Bsco had the highest content of volatile oil monoterpenes but a lower sesquiterpene content than Bchi and Bmar. Transcriptome analysis showed that several genes were highly expressed in Bchi, Bsco, or Bmar, demonstrating the molecular mechanism responsible for the differences in their metabolic components. We combined the metabolomics and transcriptomics data to investigate the relationship between metabolites and genes. The results showed a high correlation between CYP450, UGT, and β-AS genes and 6''-acetyl-saikosaponins A, saikosaponins B1, C, and D. The subcellular localization of the two P450 genes (Bc087391 and Bc036879) in the endoplasmic reticulum suggests that they may be involved in saikosaponin biosynthesis.</p><p><strong>Conclusion: </strong>We performed an integrated transcriptome and metabolome analysis to investigate the diversity of the terpenoid biosynthetic pathway in three Bupleurum species. The study provides new insights into the molecular basis of the metabolic differences between the three Bupleurum species. It also serves as a theoretical basis for the clinical application and breeding of Bupleurum resources.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"403"},"PeriodicalIF":4.3,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956408/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751201","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":"QTL mapping and candidate gene identification for fodder quality traits in Pearl millet.","authors":"Harmanpreet Singh Daduwal, Ruchika Bhardwaj, Jaspal Singh Lamba, Yogesh Vikal, Rakesh K Srivastava","doi":"10.1186/s12870-025-06381-5","DOIUrl":"10.1186/s12870-025-06381-5","url":null,"abstract":"<p><strong>Background: </strong>Pearl millet is an excellent forage crop with significant potential for forage production. Its fodder is rich in protein, calcium, phosphorus and other essential minerals while being low in undesirable components such as hydrocyanic acid and oxalic acid. Globally, the shortage of high-quality fodder poses challenges for maintaining animal health and productivity, ultimately impacting dairy farmers. Therefore, improving pearl millet for fodder traits should be a priority to meet the global demand for nutritious livestock feed.</p><p><strong>Results: </strong>Significant variability was observed for all forage quality related traits at both locations. A linkage map was constructed using 755 single-nucleotide polymorphisms (SNPs) markers, spanning a total length of 3080.44 cM. A total 8, 6 and 10 QTLs were identified for Ludhiana, Abohar and across the locations, respectively, for fodder quality. A common genomic interval with flanking markers S6_234379851- S6_64109715 was associated with IVOMD, CP and ME at all locations, with 10-34% phenotypic variance. Further, expression analysis identified BHLH 148, Resistance to phytophthora, Laccase 15, cytochrome P450, PLIM2c, GRF11, NEDD AXR1, NAC 92 and TF 089 as differentially expressed candidate genes in the leaf tissues of parental lines. A phylogenetic tree constructed using these genes revealed two clades identified with six paralogous events. Additionally, a phylogenetic tree of eight cereal species showed that the majority of shared similarity with the Pgl genes, suggestinga recent speciation event among them. Common genes, including cytochrome P450, PLIM2c, NEDD AXR1 and NAC domains were identified between QTL regions and expression analysis.</p><p><strong>Conclusion: </strong>The differentially expressed genes incorporating the regulatory elements governing the lignin pathway have direct or indirect effects on fodder digestibility and quality. Exploiting these factors can contribute to the direct improvement of fodder quality. The identified QTLs and candidate genes from this study could facilitate the development of gene based markers for fodder improvement.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"404"},"PeriodicalIF":4.3,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751209","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":"Genetic dissection of leaf rust resistance in a diversity panel of tetraploid wheat (Triticum turgidum).","authors":"Jitendra Kumar Yadav, Shruti Sinha, Hariom Shukla, Ankur Singh, Tanmaya Kumar Sahu, Shailendra Kumar Jha, Jyoti Kumari, Manjusha Verma, Sundeep Kumar, Rakesh Singh, Gyanendra Pratap Singh, Amit Kumar Singh","doi":"10.1186/s12870-025-06330-2","DOIUrl":"10.1186/s12870-025-06330-2","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Leaf rust, caused by Puccinia triticina Eriks (Pt) is a major threat to wheat cultivation worldwide. The rapid evolution of this pathogen has led to the emergence of new virulent strains that can overcome the resistance of commonly cultivated wheat varieties. To address this threat, continuous monitoring of leaf rust pathotypes is conducted in wheat-growing regions across the world. This approach helps prioritize the development and deployment of resistant cultivars, as well as the implementation of other effective control measures against the prevailing races. The key wheat leaf rust pathotypes in India include 77-5 (121R63-1), 77-6 (121R55-1), 77-9 (121R60-1), 12-5 (29R45), and 104 (17R23). Among these pathotypes, 77-5 (121R63-1) and 77-9 (121R60-1) are the most prevalent since 2016. As virulent pathotypes continue to evolve and adapt, there is an urgent need to continually explore the vast germplasm repositories of wheat and its related species to identify novel genetic resources and genes that confer resistance to these evolving leaf rust pathotypes. Therefore, the present study aims to identify genes and genomic regions responsible for leaf rust resistance against prevalent pathotypes in India, focusing on a subset of the Global Durum Wheat Panel, which includes genotypes from various tetraploid wheat species.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;This study revealed wide variation in seedling-stage resistance among 189 tetraploid wheat accessions against five prevalent leaf rust pathotypes in India namely, 77-5 (121R63-1), 77-6 (121R55-1), 77-9 (121R60-1), 12-5 (29R45) and 104 (17R23). Approximately 45% of the population exhibited immune/highly resistant to moderately resistant responses to pathotypes 77-5, 77-6 and 104, while around 23-27% showed similar levels of resistance to pathotypes 77-9 and 12-5. A genome-wide association study using six multi-locus models identified 88 significantly associated quantitative trait nucleotides (QTNs) across the five leaf rust pathotypes. Among these, 22 QTNs were considered reliable, including four for pathotype 77-5, six for 12-5, three for 77-9, seven for 104, and two for 77-6. Among the 22 reliable QTNs, 10 coincided with the rust resistance regions reported in previous studies, whereas 12 appeared to be novel. Further investigations of the regions flanking all 88 QTNs revealed 300 genes, including 62 associated with disease resistance or defense responses. In silico expression analysis of these defense-related genes revealed two nucleotide-binding site-leucine-rich repeat genes: one on chromosome 6B (TRITD6Bv1G224600) near QTN RAC875_c35430_373, and another on chromosome 6A (TRITD6Av1G225060) in the vicinity of QTN Excalibur_c77841_224 with significantly higher levels of expression in the leaf-resistant genotype during the early hours of Pt infection. Therefore, these two genes could be potential candidates for resistance to leaf rust in tetraploid wheat germplasm.&lt;/p&gt;&lt;p&gt;","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"406"},"PeriodicalIF":4.3,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751184","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 factors influencing climate-smart agriculture: Daylength-mediated interaction between tillering and flowering in rice.","authors":"Hyeon-Seok Lee, Ju-Hee Kim, So-Hye Jo, Seo-Yeong Yang, Jae-Kyeong Baek, Yeong-Seo Song, Jung-Il Cho, Jiyoung Shon","doi":"10.1186/s12870-025-06430-z","DOIUrl":"10.1186/s12870-025-06430-z","url":null,"abstract":"<p><strong>Background: </strong>Controlling rice tillering and flowering is essential for reducing greenhouse gas emissions from paddy fields, a key objective in climate-smart agriculture. However, the interaction between tillering and flowering remains controversial and poorly understood. In this study, we subjected plants of the rice cultivars 'Saenuri' and 'Odae' to short- and long-day conditions and compared their growth and flowering responses after tiller removal.</p><p><strong>Results: </strong>The effects of tiller removal differed depending on daylength conditions. Under short days, plants in the tiller-removal group flowered earlier than the controls, whereas the opposite trend was observed under long days. This response was associated with changes in florigen gene expression. Under short days, the expression of Hd3a, which promotes flowering, increased in the tiller-removal group compared with that in the controls. In contrast, under long days, the expression of OsMFT1, a gene that delays flowering and promotes spikelet formation, was significantly upregulated, leading to an increased spikelet number. Notably, spikelets per panicle in the tiller-removal groups increased approximately 3.4-fold in 'Saenuri' and 2.2-fold in 'Odae' under long-day conditions compared with those in their respective controls.</p><p><strong>Conclusions: </strong>These findings highlight the daylength-dependent variability in tillering and flowering interactions, providing new insights into their regulatory mechanisms. This study offers a foundation for optimizing rice growth strategies under varying photoperiod conditions, contributing to climate-smart agricultural practices and improved breeding programs.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"400"},"PeriodicalIF":4.3,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11956260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751205","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":"Unveiling transfer RNA modifications of oil palm and their dynamic changes during fruit ripening.","authors":"Dehai Deng, Yichao Qin, Xiuying Lin, Meng Chu, Daizhu Lv, Huan Lin","doi":"10.1186/s12870-025-06426-9","DOIUrl":"https://doi.org/10.1186/s12870-025-06426-9","url":null,"abstract":"<p><strong>Background: </strong>The oil palm (Elaeis guineensis) is a crucial agricultural commodity, yielding the highest oil output among oil-bearing crops. Despite its significance, productivity challenges persist due to genetic and environmental factors. This study breaks new ground by mapping tRNA modifications in oil palm, exploring their roles during fruit ripening, an area not extensively studied in non-model crops.</p><p><strong>Results: </strong>Utilizing advanced RNA mass spectrometry techniques, we identified 48 distinct tRNA modifications across 88 sites, alongside 164 genes associated with tRNA modifying enzymes. This comprehensive mapping reveals the decreasing nature of most tRNA modifications during fruit development, except for adenosine 2'-O methylation (Am). It hints at a gradual weakening of protein translation quality control and highlights a unique role for Am during fruit ripening. Additionally, lipidomic analysis tracked 674 lipids in oil palm fruits, indicating a correlation between tRNA modifications and the accumulation of specific lipids.</p><p><strong>Conclusions: </strong>This study mapped tRNA modifications in oil palm for the first time and showed the diversity of dynamic changes in tRNA modifications as the fruits develop.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"398"},"PeriodicalIF":4.3,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742350","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 genomes of Incarvillea species (Bignoniaceae) unveiled genomic diversity and shed light on phylogenetic relationships.","authors":"Yunhui Jiang, Hong Li, Mei Wu, Xuemei Zhang, Shukherdorj Baasanmukh, Hongzhe Li, Hang Sun, Shaotian Chen","doi":"10.1186/s12870-025-06380-6","DOIUrl":"https://doi.org/10.1186/s12870-025-06380-6","url":null,"abstract":"<p><strong>Background incarvillea: </strong>Juss. is a small herbaceous genus within the Bignoniaceae family. It comprises 16 species, which are subdivided into five subgenera. The species are distributed mainly in the Himalaya-Hengduan Mountains, although there are exceptions, including I. sinensis, I. algae, I. semiretschenskia, and I. potaninii. Phylogenetic analyses based on trnL-F and nr ITS sequences provided support for the monophyly of the genus and its subgenera. However, the interspecific relationships among subgenera remain unresolved, and further investigation is necessary to elucidate these relationships. In this study, we sequenced and assembled 34 chloroplast genomes from 12 Incarvillea species, representing all five subgenera, and explored the phylogeny of the genus based on the cp. genome data.</p><p><strong>Results: </strong>The results demonstrated that 34 newly assembled chloroplast genomes exhibited lengths between 159,132 and 169,244 bp, and encoded a total of 129-141 genes. These included 84-95 protein-coding genes, 37 or 38 tRNA genes, and eight rRNA genes. A comparative analysis of the chloroplast genomes revealed the structural rearrangements and the expansions/contractions of the IR regions among the Incarvillea species. A total of 12 mutation hotspot regions were identified in the cp. genomes of the genus Incarvillea, encompassing six genes (atpI, psaI, rps18, trnQ-UUG, infA and ycf1) and six intergenic spacer regions (psbT-psbf1, rps11-rpl36, infA-rps8, trnN-GUU-ycf1, ndhE-ndhG and ndhI-ndhA). The Pi values of all highly variable regions exceeded 0.06. The phylogenetic analysis corroborated the monophyly of the genus and elucidated the relationships between five subgenere, namely ((Niedzwedzkia, Incarvillea), ((Amphicome, Olgaea),Pteroscleris)).</p><p><strong>Conclusion: </strong>A comprehensive comparison of cp. genomic sequences revealed the diversity of the genus Incarvillea in terms of size, gene content and gene order of cp. genomes. Based on the cp. genome data, a robust phylogenetic tree of the genus Incarvillea was generated through phylogenetic analysis, with interspecific relationships well resolved. The results of this study enhance the understanding of the evolutionary history of the genus, and will facilitate further studies on the diversity and resource protection of the genus.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"399"},"PeriodicalIF":4.3,"publicationDate":"2025-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742346","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":"Low genetic diversity and weak population structure of Albizia odoratissima on Hainan Island.","authors":"Zhiting Li, Qiaomiao Ji, Yong Yang, Meng Xu, Yali Guan","doi":"10.1186/s12870-025-06373-5","DOIUrl":"10.1186/s12870-025-06373-5","url":null,"abstract":"<p><strong>Background: </strong>The increasing demand for wood owing to societal development has highlighted the potential of Albizia odoratissima, a valuable timber species, to address significant timber shortages in China. However, the lack of effective genetic and genomic resources has limited the development and utilization of this species.</p><p><strong>Results: </strong>In this study, we utilised 95.3 Gb of HiFi reads to assemble a draft genome of A. odoratissima, resulting in a genome size of 788 Mb, comprising 511 contigs. We conducted whole-genome resequencing on 106 individuals from 7 populations on Hainan Island to explore these resources. Our analysis identified 498,308 high-quality single nucleotide polymorphisms, which were used to assess the genetic diversity, structure, and demographic history of A. odoratissima on Hainan Island. The results indicated that the genetic diversity of A. odoratissima on Hainan Island is relatively low (observed heterozygosity = 0.189, expected heterozygosity = 0.189, genetic diversity = 1.319 × 10^-4) with minimal genetic differentiation (Fst = 0.0151) among the seven populations. Furthermore, molecular variance, principal coordinate analysis, neighbour-joining tree analysis, and genetic structure analysis revealed a shallow population structure. The linkage disequilibrium (LD) decay ranged from 11.4 kb for Jianfengling (JFL) to 39.2 kb for Wuzhishan (WZS). LD decay, demographic history, and Tajima's D analyses indicated that the WZS population has experienced a bottleneck effect.</p><p><strong>Conclusions: </strong>This study offers new insights into the genetic diversity and population structure of A. odoratissima on Hainan Island, providing a foundation for future resource utilization and genetic improvement strategies for this species.</p>","PeriodicalId":9198,"journal":{"name":"BMC Plant Biology","volume":"25 1","pages":"395"},"PeriodicalIF":4.3,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143728651","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}