Planta最新文献

{"title":"Population transcriptome reveals genetic divergence and expression diversity of medicinally effective ingredients-related genes for Rheum palmatum complex derived from the top-geoherb area.","authors":"Yadi Tang, Lipan Zhou, Tianyi Zhang, Fan Jiang, Yang Pu, Zhengyuan Wang, Jie Liu, Li Feng, Tao Zhou, Xumei Wang","doi":"10.1007/s00425-025-04643-y","DOIUrl":"10.1007/s00425-025-04643-y","url":null,"abstract":"<p><strong>Main conclusion: </strong>The study revealed genetic diversity and moderate differentiation among the R. palmatum complex within the top-geoherb area. RNA-seq-derived SNP datasets hold the potential to trace geographic origins of the core germplasm. The Rheum palmatum complex, the source plant of rhubarb, has been widely used for centuries due to its diverse functions in clinical treatments. However, the wild resources of rhubarb are currently declining and even facing depletion. Therefore, revealing the genetic background of the R. palmatum complex within the top-geoherb area is important for the efficient utilization and conservation of its wild resources. In this study, population transcriptomic analyses were conducted to assess the genetic diversity and gene expression diversity of different populations in the R. palmatum complex within the top-geoherb area. Candidate single nucleotide polymorphisms (SNPs) were identified as specific molecular markers for tracing the origin of the R. palmatum complex from various top-geoherb areas. Based on the reference genome, a total of 30,480 transcripts and 100,966 SNPs were generated across 82 individuals from 17 populations of the R. palmatum complex. Moderate genetic differentiation was detected for the two genetic lineages of the R. palmatum complex derived from the top-geoherb area. Fourteen genes encoding key enzymes were differentially expressed between two genetic lineages. Besides, 26 specific SNPs located on the genes involved in the biosynthesis of the active components were screened out, and these SNPs were highly differentiated between 2 genetic lineages. A large-scale reference-based assembly transcriptome of the R. palmatum complex from the top-geoherb area provided insights into the genetic divergence and expression differentiation of genetic lineages. The results not only help to understand the genetic background of the R. palmatum complex in the top-geoherb area but also contribute to future genetic conservation and directive breeding of rhubarb.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"261 4","pages":"90"},"PeriodicalIF":3.6,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Remedying SARS-CoV-2 through nature: a review highlighting the potentiality of herbs, trees, mushrooms, and endophytic microorganisms in controlling Coronavirus.","authors":"Babita Patni, Malini Bhattacharyya, Anshika Pokhriyal, Devendra Pandey","doi":"10.1007/s00425-025-04647-8","DOIUrl":"10.1007/s00425-025-04647-8","url":null,"abstract":"<p><strong>Main conclusion: </strong>Medicinal plants, mushrooms, and endophytes offer a rich source of secondary metabolites (SMs), including flavonoids, alkaloids, tannins, and terpenoids, with proven antiviral properties against SARS-CoV-2. Plant-associated microorganisms that colonize in living tissues of different parts of a plant possess the ability to produce SMs of immense therapeutic value and this biological interaction between plants and microbes can be exploited to develop antiviral drugs against SARS-CoV-2. The unprecedented lethality of the SARS-CoV-2 virus during the recent global pandemic has prompted extensive research into new treatment options and preventive strategies for COVID-19. Phytochemicals, particularly those derived from medicinal plants, microbes, and mushrooms, show promising results in combating the virus when combined with synthetic components. These natural compounds include terpenes, phenolics, flavonoids, and alkaloids that possess antiviral properties. Medicinal plants and their endophytic microbes, and mushrooms, offer a rich source of secondary metabolites (SMs) with potential antiviral effects against SARS-CoV-2. Given the urgency of addressing the swift spread of the new coronavirus strain, exploring and understanding these SMs could lead to the development of innovative and potent antiviral drugs. This review provides a comprehensive overview of plant-, microbial- and mushroom-derived SMs, their classification, and their applications in treating diseases caused by the coronavirus family, offering insights into the potential future production of natural medicines.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"261 4","pages":"89"},"PeriodicalIF":3.6,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The biotechnological and economic potential of macroalgae in the Baltic Sea.","authors":"Ilona Złoch, Aleksandra Zgrundo, Julia Bryłka","doi":"10.1007/s00425-025-04661-w","DOIUrl":"10.1007/s00425-025-04661-w","url":null,"abstract":"<p><strong>Main conclusion: </strong>Baltic Sea macroalgae exhibit unique bioactive compounds and diverse applications, supporting sustainable industries in food, cosmetics, and medicine while promoting environmental restoration. Common in the Baltic Sea, macroalgae hold great biotechnological and commercial promise in various industries, such as food, cosmetics, and medicines. The present study investigates the various uses of the Baltic macroalgae, emphasizing their nutritional worth, which encompasses vital amino acids, vitamins, and minerals, as well as their suitability as natural gelling agents, food additives, and dietary supplements. Additionally, these macroalgae's bioactive chemicals show promise as therapeutic agents due to their antiviral and anticancer capabilities, making them essential assets for the pharmaceutical and medical sectors. A lot of research has been done on macroalgae, but not much on Baltic species. With an emphasis on their unique qualities and possible benefits to environmental preservation and sustainability, this paper attempts to present a thorough review of the uses of the Baltic macroalgae.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"261 4","pages":"88"},"PeriodicalIF":3.6,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143616767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retraction Note: Transgenic rice expressing Allium sativum leaf lectin with enhanced resistance against sap-sucking insect pests.","authors":"Prasenjit Saha, Pralay Majumder, Indrajit Dutta, Tui Ray, S C Roy, Sampa Das","doi":"10.1007/s00425-025-04668-3","DOIUrl":"10.1007/s00425-025-04668-3","url":null,"abstract":"","PeriodicalId":20177,"journal":{"name":"Planta","volume":"261 4","pages":"86"},"PeriodicalIF":3.6,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miRNA-seq analysis revealed a potential strategy underlying poplar root responses to low nitrogen stress.","authors":"Chun Wang, Tiantian Fu, Zeqi Wang, Siyu Hou, Kaijing Rong, Jing Wang, Yiyi Yin, Xiaoqian Yang, Ruen Yu, Dandan Xiao, Yanwei Wang","doi":"10.1007/s00425-025-04663-8","DOIUrl":"10.1007/s00425-025-04663-8","url":null,"abstract":"<p><strong>Main conclusion: </strong>87 miRNAs responding to low nitrogen stress in poplar roots were identified by miRNA-seq, and their target genes were predicted. Additionally, several key miRNA-mRNA modules were summarized.</p><p><strong>Asbtract: </strong>Nitrogen (N) is an essential nutrient for plants, and low nitrogen (LN) availability can constrain plant growth and development. MicroRNAs (miRNAs) play an important role in plant response to nutrient stress as a regulatory factor. However, studies on the function of poplar miRNAs under LN stress are limited. In this study, we investigated the potential role of miRNA in poplar roots under LN stress using miRNA-seq. 305 conserved miRNAs belonging to 48 miRNA families were identified, and 15 novel miRNAs were predicted. Among these, 83 known miRNAs from 21 families and 4 novel miRNAs were confirmed as differential expressed miRNAs (DEMs) following LN stress treatment at 6, 9, 24, 72, 240, and 504 h compared to 0 h. Functional annotation analysis indicated that an array of miRNAs, including miR160, miR172, and miR166, should be involved in LN stress. TargetFinder and psRobot predicted that 52 of these miRNAs target 248 genes, resulting in 319 miRNA targeting pairs. Degradome sequencing further revealed that these 52 miRNAs targeted 457 genes, with 358 miRNA-target pairs. Gene annotation of target genes indicated that AP2, ARF, HD-ZIP, and other genes might respond to LN stress by regulating root growth and development. These findings provide valuable insights into miRNA functions and establish a framework for further investigating miRNA-mediated N signal transduction networks under LN stress. This research may offer new perspectives for genetic engineering to enhance nitrogen use efficiency in forest trees.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"261 4","pages":"87"},"PeriodicalIF":3.6,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Implication of ribosomal protein in abiotic and biotic stress.","authors":"Zainab Fakih, Hugo Germain","doi":"10.1007/s00425-025-04665-6","DOIUrl":"10.1007/s00425-025-04665-6","url":null,"abstract":"<p><strong>Main conclusion: </strong>This review article explores the intricate role, and regulation of ribosomal protein in response to stress, particularly emphasizing their pivotal role to ameliorate abiotic and biotic stress conditions in crop plants. Plants must coordinate ribosomes production to balance cellular protein synthesis in response to environmental variations and pathogens invasion. Over the past decade, research has revealed ribosome subgroups respond to adverse conditions, suggesting that this tight coordination may be grounded in the induction of ribosome variants resulting in differential translation outcomes. Furthermore, an increasing snumber of studies on plant ribosomes have made it possible to explore the stress-regulated expression pattern of ribosomal protein large subunit (RPL) and ribosomal protein small subunit (RPS) genes. In this perspective, we reviewed the literature linking ribosome heterogeneity to plants' abiotic and biotic stress responses to offer an overview on the expression and biological function of ribosomal components including specialized translation of individual transcripts and its implications for the regulation and expression of important gene regulatory networks, along with phenotypic analysis in ribosomal gene mutations in physiologic and pathologic processes. We also highlight recent advances in understanding the molecular mechanisms behind the transcriptional regulation of ribosomal genes linked to stress events. This review may serve as the foundation of novel strategies to customize cultivars tolerant to challenging environments without the yield penalty.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"261 4","pages":"85"},"PeriodicalIF":3.6,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143605497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trends in plant tissue culture, production, and secondary metabolites enhancement of medicinal plants: a case study of thyme.","authors":"Aicha Nordine","doi":"10.1007/s00425-025-04655-8","DOIUrl":"10.1007/s00425-025-04655-8","url":null,"abstract":"<p><strong>Main conclusion: </strong>Thymus plants are greatly threatened by overharvesting and climate change. Plant cell and tissue culture techniques provide effective alternatives for the production and the enhancement of both biomass and bioactive compounds. Medicinal and aromatic plants are rich sources of various bioactive compounds known as secondary metabolites, which are used across a range of fields, including medicinal, cosmetics, pharmaceuticals, perfumes, agrochemicals and agrofood industries. Thyme is considered one of the most popular herbs globally, valued for its significant medicinal, pharmaceutical, and nutritional benefits. However, its natural habitats are rapidly diminishing due to excessive harvesting and climate change. Consequently, several approaches have been developed to find alternatives to harvesting wild thyme. Plant cell and tissue culture techniques offer a superior alternative to traditional propagation methods, such as seeds, cuttings, or tuft division. These techniques enable the production of large quantities of uniform, disease-free plantlets for commercial cultivation and facilitate the development of new genotypes. Additionally, they support the production and enhancement of bioactive compounds from thyme plants. This review explores the application of plant cell, tissue, and organ culture biotechnology in thyme plants, focusing on enhancing production and improving secondary metabolite yields and biomass production.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"261 4","pages":"84"},"PeriodicalIF":3.6,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586647","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptional reprogramming and microbiome dynamics in garden pea exposed to high pH stress during vegetative stage.","authors":"Asha Thapa, Md Rokibul Hasan, Ahmad H Kabir","doi":"10.1007/s00425-025-04656-7","DOIUrl":"10.1007/s00425-025-04656-7","url":null,"abstract":"<p><strong>Main conclusion: </strong>High soil pH induces the upregulation of genes involved in oxidative stress and nutrient transport, while the enrichment of beneficial microbes (Variovorax, Chaetomium, and Pseudomonas) highlights their potential role in promoting stress adaptation. High soil pH severely impacts plant growth and productivity, yet the transcriptomic changes and microbial dynamics underlying stress adaptation in garden pea (Pisum sativum ssp. hortense) remain unclear. This study demonstrates that high soil pH leads to stunted growth, reduced biomass, impaired photosynthesis, and nutrient status in garden pea. Further, disruption in key nitrogen-fixing bacteria (Rhizobium indicum, R. leguminosarum, and R. redzepovicii), along with the downregulation of NifA and NifD genes and upregulation of NifH in nodules highlights the critical role of micronutrient balance in legume-microbe symbiosis and a compensatory response to maintain nitrogen status. RNA seq analysis revealed extensive transcriptional reprogramming in roots, characterized by the upregulation of oxidative stress response genes (e.g., oxidoreductase and glutathione transferase activities, metal ion transporters) and the downregulation of genes related to ammonia-lyase activity and ion binding, reflecting broader disruptions in nutrient homeostasis. KEGG pathway analysis identified enrichment of MAPK signaling pathway, likely interacting with other pathways associated with stress tolerance, metabolic adjustment, and structural reorganization as part of adaptive responses to high pH. Root microbiome analysis showed significant enrichment of Variovorax, Shinella, and Chaetomium, suggesting host-driven recruitment under high pH stress. Stable genera, such as Pseudomonas, Novosphingobium, Mycobacterium, Herbaspirillum, and Paecilomyces, displayed resilience to stress conditions, potentially forming core microbiome components for adaptation to high pH. In a targeted study, inoculation of plants with an enriched microbiome, particularly C. globosum, under high pH conditions improved growth parameters and increased the abundance of Stenotrophomonas and Pseudomonas in the roots. It suggests that these bacterial genera may act as helper microbes to C. globosum, collectively promoting stress resilience in pea plants suffering from high pH. These findings provide a foundation for microbiome-aided breeding programs and the development of microbial consortia to enhance the adaptation of pea plants to high pH conditions.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"261 4","pages":"83"},"PeriodicalIF":3.6,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multidisciplinary and integrative review of the structural genome and epigenome of Capsicum L. species.","authors":"Breno Machado de Almeida, Wellington Ronildo Clarindo","doi":"10.1007/s00425-025-04653-w","DOIUrl":"10.1007/s00425-025-04653-w","url":null,"abstract":"<p><strong>Main conclusion: </strong>We revised and integrated the genomic and epigenomic data into a comparative Capsicum ideogram, evidencing the advances and future perspectives. Capsicum L. (Solanaceae) genome has been characterized concerning karyotype, nuclear and chromosomal genome size, genome sequencing and physical mapping. In addition, the epigenome has been investigated, showing chromosomal distribution of epimarks in histone amino acids. Genetic and epigenetic discoveries have given light to understanding the structure and organization of the Capsicum \"omics\". In addition, interspecific and intraspecific similarities and diversities have been identified, characterized and compared in taxonomic and evolutive scenarios. The journey through Capsicum studies allows us to know the 2n = 2x = 24 and 2n = 2x = 26 chromosome numbers, as well as the relatively homomorphic karyotype, and the 1C chromosomal DNA content. In addition, Capsicum \"omics\" diversity has mainly been evidenced from the nuclear 1C value, as well as from repeatome composition and mapping. Like this, Capsicum provides several opportunities for \"omics\", ecological, agronomic and conservation approaches, as well as subjects that can be used at different levels of education. In this context, we revisit and integrate Capsicum data about the genome size, karyotype, sequencing and cytogenomics, pointing out the progress and impact of this knowledge in taxonomic, evolutive and agronomic contexts. We also noticed gaps, which can be a focus of further studies. From this multidisciplinary and integrative review, we intend to show the beauty and intrigue of the Capsicum genome and epigenome, as well as the outcomes of these similarities and differences.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"261 4","pages":"82"},"PeriodicalIF":3.6,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586595","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of copy number variation in diverse black pepper accessions.","authors":"Parinita Das, T E Sheeja, Bibek Saha, A Fayad, Tilak Chandra, U B Angadi, M S Shivakumar, T P Muhammed Azharudheen, Sarika Jaiswal, Mir Asif Iquebal, Dinesh Kumar","doi":"10.1007/s00425-025-04658-5","DOIUrl":"10.1007/s00425-025-04658-5","url":null,"abstract":"<p><strong>Main conclusion: </strong>A genome-wide resequencing analysis reveals the involvement of copy-number variation in black pepper accessions influencing advantageous agronomic traits and the evolution of elite genotypes with specific attributes. Black pepper (Piper nigrum L.) is renowned as a versatile seasoning, offers numerous health benefits, and possesses historical significance in the global spice trade. Variations in advantageous agronomic traits among diverse black pepper genotypes underscore the potential value of understanding their underlying genetic regulation. One emerging genetic component of interest is copy number variation (CNV), which represents a significant source of intra-varietal genetic diversity by altering the dosage of DNA segments, thereby influencing phenotypic characteristics. In this study, we conducted genome-wide resequencing of thirty-nine black pepper germplasm accessions to identify high-confidence CNVs and explore their functional impact on agronomic traits. Our analysis identified a total of 159,390 CNVs and delineated 11,360 CNV regions (CNVRs) with an average length of 87,106 base pairs. Among these, we observed 82,027 deletion and 77,363 duplication events across the 26 chromosomes of black pepper. Notably, deletions were more frequent than duplications. Enrichment analysis of genes harbored within CNVRs revealed their involvement primarily in piperine biosynthesis and immune response pathways. Principal component analysis demonstrated varietal differentiation and highlighted intra-varietal evolutionary linkage among tested genotypes, suggesting that CNVRs play a significant role in shaping the evolution of elite black pepper genotypes. For instance, genotype IISR-Malabar Excel exhibited the highest number of deletions, whereas genotype Acc:7211 showed the most duplications. Chromosome 1 exhibited the highest frequency of deletions, while chromosome 3 showed the highest frequency of duplications. While the overall number of CNVRs did not significantly differ among genotypes, 33 CNVRs contained genes crucial for phenylpropanoid biosynthesis, with 14 genes undergoing deletions and 19 genes showing duplications. Additionally, we developed a web resource BPCNVDb, which could be retrieved ( https://bpcnvdb.daasbioinfromaticsteam.in/index.php ) to facilitate access to genotype-specific CNVs and CNVRs, aiming to enhance breeding efforts in black pepper.</p>","PeriodicalId":20177,"journal":{"name":"Planta","volume":"261 4","pages":"81"},"PeriodicalIF":3.6,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}