Botanical Studies最新文献

{"title":"Sample preparation of some plant tissues for transmission electron microscopy using high pressure freezing and freeze substitution.","authors":"Chia-Mei Hsu, Yi-Chia Chou, Hsiao-Jung Yen, Wann-Neng Jane","doi":"10.1186/s40529-026-00499-x","DOIUrl":"10.1186/s40529-026-00499-x","url":null,"abstract":"<p><p>For sample preparation of biological block sectioning, high pressure freezing and freeze substitution (HPF-FS) is a better choice than chemical fixation. Freezing fixation can retain the original structures and preserve the soluble materials, and avoid the disadvantage of chemical fixation. Using high-pressure freezing, plant tissues are more difficult to freeze successfully than animal tissues and microbes because they have cell walls and varying degrees of vacuolation. For plant tissues, including the roots of Arabidopsis thaliana, 1-hexadecene is an ideal cryoprotectant/filler. The ability of highly vacuolated plant tissues (such as mature leaves and petals) to effectively remove intercellular air is crucial for successful high pressure freezing. Using the anthers of Arabidopsis thaliana, the leaves of Brachypodium distachyon, Axonopus compressus and Plantago asiatica, and the petals of Phalaenopsis bellina as examples, we found an effective method to remove air from the intercellular spaces: plant tissue in 1-hexadecene is placed in a vacuum desiccator, and then the air is removed using a vacuum pump, resulting in the release of numerous air bubbles. Plant tissue samples taken at different degassing times are then subjected to high pressure freezing and the subsequent required procedures of sample preparation. Based on the presentation of fine structures, the optimal time for different plant tissues can be determined and shows a positive correction with sample thickness. Good HPF-FS results show that the lipid bilayer within each organelle of the plant cells is clearly visible.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13672732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149191435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reproductive system and agronomic performance of the wild husk tomatillo Physalis gracilis.","authors":"Omar Enríquez-Antonio, María Del Pilar Zamora-Tavares, Lislie Solís-Montero, Fabián A Rodríguez-Zaragoza, Carla Vanessa Sánchez-Hernández, Gabriela Alcalá-Gómez, José Alberto Sánchez-Nuño, Ofelia Vargas-Ponce","doi":"10.1186/s40529-026-00500-7","DOIUrl":"10.1186/s40529-026-00500-7","url":null,"abstract":"<p><p>Physalis gracilis is a wild perennial herb with sweet, orange-colored fruits harvested for household consumption in Mexico. For species with potential for cultivation and nutritional value, a basic information is known their reproductive system. This study aimed to evaluate the reproductive system of P. gracilis and its agronomic performance. Floral longevity and development stages were determined in 30 flower buds until floral senescence, using individuals grown under greenhouse and open-field conditions. Six artificial cross treatments were conducted to characterize the reproductive system, and self-incompatibility and pollen limitation indices were calculated. Stigma receptivity was assessed using hydrogen peroxide. To assess agronomic performance, an open-field crop was established within three accessions, each with 48 individuals (in total 144 plants); six descriptors were evaluated from five fruits per plant per descriptor. Artificial crossing showed that the three accessions exhibited a completely self-incompatible reproductive system; however, it was not pollen limitated. P. gracilis responded positively to agricultural management (93.8% plant survival) and showed a potential average yield of 8.178 t·ha^- 1. Equatorial diameter of the fruit ranged from 11 to 22 mm. The average sweetness was 11.29° Brix, and the pH was 4.18. This study demonstrates that P. gracilis could be a candidate as a new open-field crop with desirable fruit traits, such as weight, size, and sweetness.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13669291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149179593","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Carex ensiformis (C. subg. Siderosticta), a new species from southern China based on morphological and molecular evidence.","authors":"Zhaocen Lu, Yifei Lu, Xiaofeng Jin","doi":"10.1186/s40529-026-00498-y","DOIUrl":"10.1186/s40529-026-00498-y","url":null,"abstract":"<p><strong>Background: </strong>Carex subg. Siderosticta is one of the six subgenera recognized in the recently revised infrageneric classification of Carex based on phylogenetic studies. It represents the earliest-diverging lineage within Carex and it is sister to all remaining species in the genus. This morphologically diverse subgenus is distributed across East and Southeast Asia. Historically, the approximately 30 species of this subgenus were assigned to four morphology-based sections, namely Siderostictae, Hemiscaposae, Surculosae, and Hypolytroides.</p><p><strong>Results: </strong>Phylogenetic analyses based on three plastid (matK, ndhF, and rps16) and two nuclear (ETS and ITS) DNA markers recovered the four individuals of Carex ensiformis as a strongly supported monophyletic lineage. Micromorphological observations revealed that C. ensiformis differs from the morphologically similar species C. damiaoshanensis in the slightly undulate anticlinal cell walls of the nutlet epidermis and a markedly shorter beak at the nutlet apex. Morphologically, the new species can be distinguished from C. damiaoshanensis by its more numerous inflorescence branches and spikes, as well as smaller utricles, nutlets, and shorter glumes.</p><p><strong>Conclusions: </strong>Both morphological and molecular evidence reveal that Carex ensiformis is a new species belonging to subg. Siderosticta from southern China. The discovery of this species enriches our understanding of species diversity and taxonomic complexity within the subgenus, and emphasizes the importance of continued taxonomic studies in this part of Asia.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13650099/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149135010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biocontrol potential of Burkholderia spp. against Fusarium oxysporum f. sp. lycopersici infecting tomato.","authors":"Sunil Khayamali, Tao-Ho Chang, Kusum Mushyakhwo, Jenn-Wen Huang, Pi-Fang Linda Chang","doi":"10.1186/s40529-026-00497-z","DOIUrl":"10.1186/s40529-026-00497-z","url":null,"abstract":"<p><strong>Background: </strong>Fusarium wilt of tomato caused by Fusarium oxysporum f. sp. lycopersici (FOL) is a serious disease. Host resistance and soil fumigation may reduce the impact of FOL, but the effectiveness may decrease over time due to the diversity and evolution of pathogens. Silicon is the second most abundant element in the Earth's crust, but has been overlooked in crop protection due to its poor availability to plants. Silicate-solubilizing bacteria (SSB) are reported to enhance soil nutrition, plant growth, and stress tolerance by transforming inorganic silicon into a plant-available form. Hence, SSB with antimicrobial properties can act as green alternatives to fungicides. Therefore, this study aims to isolate rhizospheric SSB and uncover their benefits in crop protection.</p><p><strong>Results: </strong>Among thirteen potentially beneficial strains identified through 16S rDNA sequencing, Burkholderia contaminans NRBC (NRBC) and Burkholderia sp. NRBA (NRBA) were chosen for greenhouse experiments to evaluate their effectiveness in promoting plant growth and suppressing FOL (race 2). Under normal greenhouse conditions, the co-application of NRBC and silicon significantly increased shoot dry weight. Under FOL stress, all bacteria-treated groups were taller than the control groups. Bacterial treatments significantly reduced disease incidence and suppressed disease progression with no significant effect of the silicon supplement. The expression profiling of some defense-related genes revealed that soil-inoculation with NRBA and NRBC induced transcriptional patterns consistent with the involvement of salicylic acid (SA) and jasmonic acid/ethylene (JA/ET)-related defense responses.</p><p><strong>Conclusions: </strong>SSB isolates, NRBA and NRBC, are effective standalone biocontrol agents for managing Fusarium wilt in tomato. Silicon supplementation did not show the anticipated plant growth promotion of tomato plants and FOL suppression.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13525146/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148849681","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomic revision and phylogenetic analysis of Xylaria in French Guiana, including 38 new species and one new combination.","authors":"Yu-Ming Ju, Jacques Fournier, Huei-Mei Hsieh, Christian Lechat","doi":"10.1186/s40529-026-00496-0","DOIUrl":"10.1186/s40529-026-00496-0","url":null,"abstract":"<p><strong>Background: </strong>French Guiana is one of the earliest regions in the Neotropics where Xylaria species were extensively explored, notably by François Mathias René Leprieur during the 1830s, with many taxa subsequently described as new by Jean Pierre François Camille Montagne. Despite this long history and its clear biogeographical importance, the Xylaria diversity of French Guiana has remained insufficiently documented. Numerous species have been poorly defined, misidentified, or lack molecular data, and no modern, integrative synthesis combining morphology, typification, and phylogenetics has been available for the region.</p><p><strong>Results: </strong>Based on extensive recent field collections by two of us (JF and CL) and a re-examination of historical material, a total of 98 taxa of Xylaria are documented from French Guiana, with X. cantareirensis and X. guadalupensis additionally treated from Brazil and the French West Indies, respectively. Among these, 39 taxa are considered novel to science, including 38 newly described species and one newly recombined name. Multilocus phylogenetic analyses based on protein-coding loci support the separation of the analyzed taxa and clarify relationships among morphologically similar taxa. Of the newly described species, 37 were included in the phylogenetic analyses and are further confirmed as distinct. Several species closely related to X. scruposa are shown to constitute a species complex. Numerous historical names originally reported from French Guiana are re-evaluated through type studies, epitypifications, and critical morphological reassessments. These results highlight the remarkable Xylaria species richness of the region.</p><p><strong>Conclusion: </strong>This study demonstrates that French Guiana harbors a remarkably rich and complex Xylaria diversity that remains only partially resolved. The integration of detailed morphology and molecular phylogenetics reveals a much higher level of diversity than previously recognized and exposes significant taxonomic uncertainty in several species complexes. These findings underscore the need for continued sampling, especially of fresh material suitable for culturing, sequencing, and emphasize the importance of French Guiana as a key region for understanding the taxonomy, evolution, and biogeography of Xylaria in the Neotropics.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13462050/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148705473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Anatomical drivers of organ size and trait coordinated association between pseudobulbs and roots in Dendrobium.","authors":"Feng-Ping Zhang, Dong-Qin Lǚ, Han-Run Li, Shi-Bao Zhang","doi":"10.1186/s40529-026-00495-1","DOIUrl":"10.1186/s40529-026-00495-1","url":null,"abstract":"<p><strong>Background: </strong>Organ size is a key phenotypic trait linking plant structure, physiological function, and ecological adaptation. The epiphytic orchid genus Dendrobium comprises highly diversified species adapted to heterogeneous canopy microhabitats, where water and nutrients are scarce and unpredictable. It has evolved two specialized organs, water-storing pseudobulbs and absorptive succulent roots that are critical for epiphytic survival. However, their central role in drought adaptation, interspecific anatomical variation and the drivers of organ size remain poorly understood. Here, we quantified 7 pseudobulb and 13 root traits across 37 Dendrobium species, using phylogenetic independent contrasts to explore the relationships among traits.</p><p><strong>Results: </strong>All traits exhibited considerable interspecific variation, with pseudobulbs showing greater trait lability than roots, reflecting diversified water-use strategies under epiphytic pressure. Weak phylogenetic signals across traits indicate environmental selection dominates anatomical diversification. Pseudobulb radius correlated strongly with parenchyma area and vascular bundle traits, regardless of phylogenetic correction, but not with epidermis thickness after phylogenetic correction. Root radius was associated closely with cortex, velamen, and vascular bundle traits across analyses, but not with exodermis thickness after phylogenetic correction. Functionally analogous traits (pseudobulb radius vs. root radius; pseudobulb vascular bundle area vs. root vascular bundle area and root exodermis area; pseudobulb parenchyma area vs. root cortex thickness, velamen area, and velamen cell area) between pseudobulbs and roots were consistently and positively correlated, revealing coordinated water-use strategies across organs.</p><p><strong>Conclusion: </strong>Dendrobium organ size is determined by tissue-level adaptive architecture. Pseudobulb size depends primarily on water-storage parenchyma, while root size is tightly linked to absorptive velamen. The species-level variation, driven mainly by environmental selection, underscores diversified hydraulic strategies in epiphytic orchids. Coordinated trait association between pseudobulb and root traits reflects adaptive integration of storage and absorption organs, a key evolutionary strategy for epiphytic survival. These findings highlight the fundamental role of cell and tissue dimensions in shaping orchid organ morphology.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13294433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148307015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Colonization of three Sphagneticola species by Funneliformis mosseae under cadmium stress is beneficial to phosphatase activity and nutrient uptake in rhizosphere soil.","authors":"ZhengChao Yu, RuiRui Lu, QiLei Zhang, YuanXiao Jing, ChangLian Peng","doi":"10.1186/s40529-026-00494-2","DOIUrl":"10.1186/s40529-026-00494-2","url":null,"abstract":"<p><strong>Background: </strong>Soil cadmium (Cd) contamination poses threats to ecosystems and human health, and the plant arbuscular mycorrhizal fungi (AMF) symbiotic system represents a promising green remediation strategy. However, the underlying mechanisms are complex and context-dependent, and systematic comparative studies remain scarce regarding differential regulation of Cd tolerance enhancement in plants of the same genus but different ecotypes. This study used a native species (Sphagneticola calendulacea), invasive species (Sphagneticola trilobata), and their hybrid as materials. It conducted an integrated analysis of the synergistic effects of inoculating Funneliformis mosseae (FM) on the rhizosphere microenvironment and mineral element uptake of three plants under a Cd stress gradient. The objective was to elucidate the interactive mechanisms by which FM enhances plant Cd tolerance and to evaluate its remediation potential.</p><p><strong>Results: </strong>Results indicate that FM regulation of rhizosphere pH exhibits species specificity but generally alleviates Cd induced acidification. FM significantly enhances acid phosphatase activity in rhizosphere soil and substantially promotes plant phosphorus (P) uptake. FM comprehensively altered plant mineral element uptake, including promoting root accumulation of sodium (Na), magnesium (Mg), and calcium (Ca), shoot potassium (K) allocation, and copper (Cu) and zinc (Zn) absorption.</p><p><strong>Conclusions: </strong>This study elucidates how FM enhances P uptake and systematically optimizes elemental absorption homeostasis by regulating rhizosphere pH and phosphatase activity. These synergistic effects improve Cd tolerance in Sphagneticola species and highlight the broad potential of AMF-plant symbioses for Cd remediation. It provides crucial theoretical foundations and germplasm selection references for targeted soil restoration using ecologically distinct Sphagneticola ecotypes and their optimal FM partners.</p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13161417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147866930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Both semi-dwarf and photoperiod-insensitive traits in rice were important for the Green Revolution.","authors":"Cheng-Chieh Wu, Yi-Tzu Tseng, Lin-Tzu Huang, Chun-Kai Liu, Kai-Cheng Hsu, Hao-Ching Wang, Yue-Ie Caroline Hsing, Wan-Yi Chiou","doi":"10.1186/s40529-026-00493-3","DOIUrl":"10.1186/s40529-026-00493-3","url":null,"abstract":"<p><p>BACKGROUND: The semi-dwarf high-yielding rice (Oryza sativa) variety IR8 was the major modern line that gave rise to the “Green Revolution” in Asia approximately 60 years ago. Although the sd1 mutation in IR8 responsible for semi-dwarfism is well known, the sequence variation, evolutionary origins, and functional impacts of SD1 haplotypes remain incompletely characterized. RESULTS: By analyzing whole-genome sequences from the 3K Rice Genomes Project, Taiwanese landraces, and Asian wild rice, we classified SD1 into 12 haplotypes, including two newly identified loss-of-function alleles: a 1,279-bp deletion and an E100/R340 variant. Phylogenetic and nucleotide analyses traced the origins of several haplotypes, including the widely used 383-bp deletion (DGWG type), to the wild accession W1718 in southern China, from which they were later introgressed into landraces and subsequently brought to Taiwan. Protein structural modeling further revealed that distinct amino acid substitutions affect GA20ox-2 activity by altering the catalytic pocket or local protein stability. Screening of SD1 and Hd1 genotypes showed that most modern indica varieties carry loss-of-function alleles of both sd1 and hd1, reflecting strong post–Green Revolution selection for semi-dwarfism and early maturity. CONCLUSION: Our results clarify the evolutionary history and functional consequences of SD1 variation and highlight that the combined loss-of-function sd1–hd1 genotype was central to the development of high-yielding, lodging-resistant, and photoperiod-insensitive rice varieties. These findings provide a comprehensive framework for understanding key Green Revolution genes and offer guidance for future rice improvement and genome-editing strategies. </p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13022152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147520168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Drivers of floristic discovery in a temperate flora: insights from three decades of vascular plant records in Ukraine.","authors":"Mykyta Peregrym, Ihor Olshanskyi, Svitlana Zhygalova","doi":"10.1186/s40529-026-00492-4","DOIUrl":"10.1186/s40529-026-00492-4","url":null,"abstract":"<p><p>BACKGROUND: Floristic discoveries continue to occur even in regions with a long history of botanical exploration. Ukraine, one of the largest countries in Europe, has been the subject of intensive botanical study for more than two centuries, yet new species, subspecies, and national records are still regularly documented. Understanding the ecological and methodological factors that drive these discoveries is important for improving biodiversity assessment, guiding field surveys, and updating national floras. This study provides a comprehensive synthesis of all vascular plant taxa newly described for science or newly recorded from Ukraine during the period from 1997 to 2024 and identifies the principal drivers of floristic discovery in a temperate flora. RESULTS: A total of 331 species and subspecies of vascular plant were discovered or newly recorded during the study period, including 57 taxa described as new to science. These findings span lycopods, ferns, gymnosperms, and flowering plants, with flowering plants contributing the largest share. Synanthropic habitats, particularly those associated with human disturbance and escaped cultivated plants, yielded the highest number of discoveries. Grasslands, woodlands, stone outcrops, and coastal habitats also contributed substantially, while mountainous areas were notable centres for both newly described taxa and hybridogenic diversity. The majority of discoveries were based on material collected during spring and summer, although historical herbarium specimens, some over a century old, were essential for many taxonomic descriptions and for confirming previously overlooked taxa. Citizen science platforms supported several recent national records by enabling rapid detection and preliminary verification of unusual occurrences, although they have not yet contributed directly to the description of new taxa. CONCLUSIONS: Our findings highlight the continued incompleteness of floristic knowledge, even in well-studied temperate regions, and underscore the need for targeted survey strategies that integrate historical collections, underexplored habitats, and public participation. While Ukraine provides the case study, these patterns and methodological approaches are broadly applicable to biodiversity assessment and conservation planning in similar biogeographic contexts worldwide. </p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":"67 1","pages":""},"PeriodicalIF":3.3,"publicationDate":"2026-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12965962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147364265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Birth and death evolution of polyphenol oxidase (PPO) gene family in Oryza species.","authors":"Yuan-Ching Tsai, Yi-Jing Chen, Sou-Yu Cheng, Charng-Pei Li, Ming-Der Huang","doi":"10.1186/s40529-026-00491-5","DOIUrl":"10.1186/s40529-026-00491-5","url":null,"abstract":"<p><p>BACKGROUND: Polyphenol oxidases (PPOs) are copper-containing enzymes that catalyze the oxidation of phenolic substrates to quinones. In cereal crops, PPOs contribute to both grain browning and defense responses. During domestication, multiple independent PPO mutations have been selected, creating a trade-off between grain quality and plant fitness. In rice, most PPO-related studies have focused on the reference genome of Oryza sativa ssp. japonica cv. Nipponbare, yet a comprehensive understanding of PPO gene diversity, copy number variation, and evolutionary history across the Oryza genus remains lacking. RESULTS: We systematically identified PPO genes in 21 fully sequenced wild and cultivated Oryza species, along with three close relatives. PPOs were classified into three types (PPO1–3), with PPO1 further divided into two subtypes (PPO1-1 and PPO1-2) and PPO3 is reported here for the first time. Both PPO1 and PPO3 possess thylakoid transfer domains and Tat-specific motifs, whereas PPO2 lacks these features. PPO1 and PPO2 expanded through tandem duplications, forming two major clusters: the PPO1 cluster and the PPO2/PPO3 cluster. Truncated PPO variants were found to be widespread across Oryza, present in roughly half of the surveyed species and often outnumbering intact PPO counterparts. Most truncated PPOs contain multiple indels: those in PPO1-1 and PPO3 arose independently, whereas the truncations in PPO1-2 and PPO2 are conserved. Furthermore, PPO mutations in Nipponbare (PPO1 and PPO3) and O. glaberrima (PPO1-1) are associated with domestication, with PPO1-2.1 in Nipponbare disrupted by transposable-element insertions and O. glaberrima harboring a novel truncated PPO1-1 allele. CONCLUSIONS: This study provides the first comprehensive analysis of the PPO gene family across Oryza, revealing three major PPO types. The expansion of PPOs through tandem duplications, coupled with frequent loss-of-function mutations due to frameshift-indel truncations, is consistent with a birth-and-death model of gene family evolution. Our findings highlight the combined contributions of domestication and natural selection in shaping PPO diversity in Oryza. </p>","PeriodicalId":9185,"journal":{"name":"Botanical Studies","volume":"67 1","pages":"4"},"PeriodicalIF":3.3,"publicationDate":"2026-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12876524/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146123853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}