Applications in Plant Sciences最新文献

{"title":"Astragalean819: An Astragalean clade-specific bait set to resolve phylogenetic relationships in Astragalus","authors":"Daniele Buono,&nbsp;Gudrun Kadereit,&nbsp;Diego F. Morales-Briones","doi":"10.1002/aps3.70024","DOIUrl":"10.1002/aps3.70024","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p><i>Astragalus</i> (Fabaceae) is the largest genus of flowering plants, with about 3100 species. Most phylogenies of the genus are based on a few nuclear or plastid loci (with one exception that uses ~100 loci) and usually provide poorly resolved trees and even conflicting subgeneric classifications. Target enrichment can greatly improve phylogenetic resolution, even at recently diverged taxonomic units, by generating sequences for hundreds of phylogenetically informative, putative single-copy loci. However, a specific bait set for the Astragalean clade is still lacking.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>In this study, we use transcriptome data from 17 species in the Astragalean clade (of which eight are <i>Astragalus</i>) to identify putative single-copy nuclear loci to build a bait set for target enrichment. This resulted in 819 exons from 686 genes across the Astragalean clade. The bait set was validated with a phylogenetic study based on 20 taxa selected across major clades in <i>Astragalus</i> plus three Astragalean species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We recovered, on average, 739.3 loci covering at least 75% of the corresponding target reference length. The average number of paralog warnings was 76.2, ranging from 12 to 373. Our phylogenetic inference produced full support for all nodes, largely in agreement with the current subgeneric classifications of <i>Astragalus</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our bait set, Astragalean819, effectively retrieved highly informative loci to build a robust phylogeny that will help to clarify the complex relationships among members of the Astragalean clade and the subgeneric relationships in <i>Astragalus</i>. This study provides a foundation for advancing the understanding of the systematics and evolution of the largest flowering plant genus.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70024","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145341360","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148024384","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148089903","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":"catalogoUCsBR: A new R package and application for creating comprehensive plant species lists for Brazilian Protected Areas","authors":"Thuane Bochorny,&nbsp;Pablo H. A. de Melo,&nbsp;Rafaela C. Forzza","doi":"10.1002/aps3.70016","DOIUrl":"10.1002/aps3.70016","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The increased online publication of data associated with Brazilian botanical collections and biodiversity information systems has significantly improved access to information on plant species occurring in Brazil. However, information about Brazilian flora within Protected Areas is fragmented.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>The catalogoUCsBR package—developed in R and as a Shiny application—performs several data refinement processes to facilitate creating comprehensive plant checklists of Brazilian Protected Areas. Functions include combining herbarium records into a desired format and removing duplicates from different databases, extracting information on accepted species names, facilitating taxonomic revision through digitized images and labels from herbarium collections, and publishing the plant species list in the Catálogo de Plantas das Unidades de Conservação do Brasil.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The catalogoUCsBR package is an open platform designed for creating taxonomically verified plant species lists that enhances the effectiveness of Brazilian conservation efforts, ensuring that they are based on accurate and up-to-date biodiversity information.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145341451","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":"Just add water: A simple floral bud injection method for stable Agrobacterium-mediated transformation in two ecotypes of Mimulus guttatus","authors":"Lauren E. Stanley,&nbsp;David B. Lowry","doi":"10.1002/aps3.70025","DOIUrl":"10.1002/aps3.70025","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Stable transformation is the biggest barrier to studying gene function in plants. In most species, transformation requires tissue culture and regeneration methods that may be arduous and cause undesirable genetic changes. Floral dip methods bypass these challenges by directly transforming ovules of developing flowers, but these methods have limited success outside of the Brassicaceae.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We demonstrate that floral dip methods are effective for some genotypes of the yellow monkeyflower, <i>Mimulus guttatus</i>, an ecological and evolutionary model system. In genotypes where floral dip failed, we developed an effective floral bud injection method that allows plants to be infiltrated multiple times and reduces floral abscission and male sterility.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Through a combination of floral dip and injection methods, we transformed both coastal perennial and inland annual genotypes of <i>M. guttatus</i>, setting the stage for understanding the molecular genetic underpinnings of local adaptation to the divergent habitats occupied by these distinctive ecotypes.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145341484","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":"From WGS to gels: Development and testing of PCR primers targeting toxic Digitalis in support of food safety","authors":"Elizabeth Sage Hunter,&nbsp;Sydnee Fo,&nbsp;Robert Literman,&nbsp;Richard H. Uva,&nbsp;Jennifer L. Wolny,&nbsp;Sara M. Handy","doi":"10.1002/aps3.70013","DOIUrl":"10.1002/aps3.70013","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>This study capitalized on a library of single-nucleotide polymorphisms created via whole genome sequencing (WGS) to develop and test a PCR assay for detecting toxic <i>Digitalis</i> species in food products. Complex foods can be difficult to analyze, but safeguarding consumer well-being and public health necessitates that products regulated by the U.S. Food and Drug Administration are contaminant free.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Ten pairs of PCR primers were designed, optimized, and tested against a subset of vouchered specimens. Two primer sets were screened using 55 vouchered Plantaginaceae species, complex food matrices, five different plant tissues, a dilution series, and spiked food products with 0.5%, 1%, and 5% biomass of <i>D. purpurea</i> and <i>D. lanata</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>At optimized annealing temperatures, these primers amplified only <i>Digitalis</i> spp. (5). Both primer sets could detect spikes of <i>D. purpurea</i> and <i>D. lanata</i> down to 0.5% biomass and across three orders of magnitude, as well as five tissue types of <i>D</i>. <i>purpurea</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>This study provides an enhanced DNA-based method for detecting <i>Digitalis</i> in complex food products. This novel method of primer development from WGS data lays the groundwork for a larger, more comprehensive panel for the rapid identification of botanical contaminants that may pose risks to consumers.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145341506","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":"Effectiveness of interval photography cameras for a survey of pollinator communities: Comparison with direct observation","authors":"Tomohiro Watazu,&nbsp;Masayoshi K. Hiraiwa,&nbsp;Masahito Inoue,&nbsp;Hideo Mishima,&nbsp;Atushi Ushimaru,&nbsp;Tetsuro Hosaka","doi":"10.1002/aps3.70023","DOIUrl":"10.1002/aps3.70023","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Pollinator communities have been surveyed through direct observation, which is labor intensive and difficult for monitoring nocturnal pollinators. Interval photography surveys are increasingly used, although the resulting data from pollinator community surveys have rarely been validated.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We surveyed a pollinator community using both interval photography and direct observation and compared the two methods for differences in identification accuracy, pollinator composition, and number of pollinator visits detected.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Compared to direct observation, the species-level identification rate of pollinators using interval photography was significantly lower, although the order-level identification remained comparable. The number of pollinator observations was highly correlated between interval photography and direct observation, regardless of flower shape or pollinator groups. A longer observation period using interval photography (10 h), despite fewer observable flowers per camera, could yield a comparable or even greater number of pollinator observations than a much shorter period of direct observation (15 min).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Although interval photography has limitations for species-level identification, it could be a powerful tool for surveying pollinator communities at higher taxonomic levels (e.g., order), including nocturnal pollinators, with reduced labor requirements and without human presence censuses.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70023","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145341782","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":"Raspberry Pi–powered temperature monitoring of growth chamber microclimates","authors":"Joseph Ballenger,&nbsp;Samuel Kenney,&nbsp;Jared Gordon,&nbsp;Leonardo Chavez,&nbsp;Joseph G. Duenwald,&nbsp;Katherine M. Murphy,&nbsp;Leonardo W. Lima,&nbsp;Cesar Lizarraga,&nbsp;Malia A. Gehan","doi":"10.1002/aps3.70022","DOIUrl":"10.1002/aps3.70022","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>While controlled environments are desirable for growing and measuring plants, growth chambers and greenhouses typically have microclimates that impact plant growth, development, and stress responses. Furthermore, opening and closing the doors of a controlled environment introduces variation in the environment, especially at temperature extremes, affecting both the measurements and the organisms within. Using multiple temperature data loggers to normalize results can be cost-prohibitive and rarely offers real-time feedback on temperature status.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We used low-cost single-board computers, cameras, and temperature sensors to manage and capture growth chamber temperatures while acquiring plant image data. Detailed here are methods to document microclimates within a growth chamber so that data can be normalized to measured temperature information.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This protocol describes a low-cost method for automated temperature monitoring, which enables both high-throughput measurements of temperature along with plant growth and stress responses via plant imaging.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145341860","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":"Improving plant DNA metabarcoding accuracy with ecological filters and Angiosperms353: Field and pollen microscopy validation","authors":"Reed Clark Benkendorf,&nbsp;Emily J. Woodworth,&nbsp;Paul J. CaraDonna,&nbsp;Jane E. Ogilvie,&nbsp;Sophie Taddeo,&nbsp;Jeremie B. Fant","doi":"10.1002/aps3.70026","DOIUrl":"10.1002/aps3.70026","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Metabarcoding has become a successful tool for the identification of species in ecological assemblages. However, the usefulness of metabarcoding for identifying plant species has been hampered due to a lack of universal gene regions that work across all taxa, limiting the applications of metabarcoding in ecology.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here, we outline a spatiotemporal approach that combines Angiosperms353 baits with species distribution models and phenological analyses to generate a list of candidate species to increase metabarcoding accuracy. To evaluate the ecological realism of our framework, we compared the results of DNA metabarcoding pollen loads of wild bumble bees to long-term field observations of bee–plant interactions and visual pollen identification.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We show that metabarcoding bumble bee pollen loads was most accurate when combined with a candidate taxa list of plants flowering when the bumble bees were foraging, which improved the accuracy and taxonomic precision of 77.5% of samples relative to non-filtered matches.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>With the proliferation of species occurrence and phenology data and advances in computing and software, spatiotemporal filtering provides an improved approach for interpreting metabarcoding results. Additionally, we demonstrate that Angiosperms353 offers significant promise for metabarcoding projects to reveal species interactions.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70026","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145341796","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 4","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148021898","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}