Applications in Plant Sciences最新文献

{"title":"A low-cost protocol for the optical method of vulnerability curves to calculate P50","authors":"Georgina González-Rebeles,&nbsp;Miguel Ángel Alonso-Arevalo,&nbsp;Eulogio López,&nbsp;Rodrigo Méndez-Alonzo","doi":"10.1002/aps3.70004","DOIUrl":"https://doi.org/10.1002/aps3.70004","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The quantification of plant drought resistance, particularly embolism formation, within and across species, is critical for ecosystem management and agriculture. We developed a cost-effective protocol to measure the water potential at which 50% of hydraulic conductivity (<i>P</i>₅₀) is lost in stems, using affordable and accessible materials in comparison to the traditional optical method.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Our protocol uses inexpensive USB microscopes, which are secured along with the plants to a pegboard base to avoid movement. A Python program automatized the image acquisition. This method was applied to quantify <i>P</i>₅₀ in an exotic species (<i>Nicotiana glauca</i>) and native species (<i>Rhus integrifolia</i>) of the Mediterranean vegetation in Baja California, Mexico.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The intra- and interspecific patterns of variation in stem <i>P</i>₅₀ of <i>N. glauca</i> and <i>R. integrifolia</i> were obtained using the low-cost optical method with widely available and affordable materials that can be easily replicated for other species.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884020","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":"The PteridoPortal: A publicly accessible collection of over three million records of extant and extinct pteridophytes","authors":"Carl J. Rothfels,&nbsp;Jaemin Lee,&nbsp;Michael A. Sundue,&nbsp;Alan R. Smith,&nbsp;Amy Kasameyer,&nbsp;Joyce Gross,&nbsp;Garth Holman,&nbsp;Shusheng Hu,&nbsp;Matt von Konrat,&nbsp;Emily B. Sessa,&nbsp;Kimberly Watson,&nbsp;Alan Weakley,&nbsp;Libing Zhang,&nbsp;Patricia Gensel,&nbsp;Michael Hassler,&nbsp;Katelin D. Pearson,&nbsp;Ed Gilbert,&nbsp;Robyn J. Burnham,&nbsp;Richard K. Rabeler,&nbsp;Patrick Sweeney,&nbsp;Alejandra Vasco,&nbsp;Weston Testo,&nbsp;David E. Giblin,&nbsp;Stefanie M. Ickert-Bond,&nbsp;Margaret Landis,&nbsp;Melanie Link-Perez,&nbsp;Tatyana Livshultz,&nbsp;Ian Miller,&nbsp;Christopher Neefus,&nbsp;Kathleen Pigg,&nbsp;Mitchell Power,&nbsp;Alan Prather,&nbsp;Tiana Rehman,&nbsp;Lena Struwe,&nbsp;Michael Vincent,&nbsp;George Weiblen,&nbsp;Timothy Whitfeld,&nbsp;Michael D. Windham,&nbsp;George Yatskievych,&nbsp;Aaron Liston,&nbsp;Elizabeth Makings,&nbsp;Kathleen M. Pryer,&nbsp;Caroline Strömberg,&nbsp;Eve Atri,&nbsp;Jason Best,&nbsp;Ian Glasspool,&nbsp;Layne Huiet,&nbsp;Elizabeth Johnson,&nbsp;Megan R. King,&nbsp;Az Klymiuk,&nbsp;Richard Lupia,&nbsp;Lucas C. Majure,&nbsp;Carol Ann McCormick,&nbsp;Richard McCourt,&nbsp;Shanna Oberreiter,&nbsp;Kent D. Perkins,&nbsp;Yarency Rodriguez,&nbsp;Chelsea Smith,&nbsp;James Solomon,&nbsp;Jordan Teisher,&nbsp;Donna Ford-Werntz,&nbsp;Petra Fuehrding-Potschkat,&nbsp;Holly Little,&nbsp;Tom A. Ranker,&nbsp;Eric Schuettpelz,&nbsp;Carrie M. Tribble,&nbsp;Diane M. Erwin,&nbsp;Cindy V. Looy","doi":"10.1002/aps3.70003","DOIUrl":"https://doi.org/10.1002/aps3.70003","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Pteridophytes—vascular land plants that disperse by spores—are a powerful system for studying plant evolution, particularly with respect to the impact of abiotic factors on evolutionary trajectories through deep time. However, our ability to use pteridophytes to investigate such questions—or to capitalize on the ecological and conservation-related applications of the group—has been impaired by the relative isolation of the neo- and paleobotanical research communities and by the absence of large-scale biodiversity data sources.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here we present the Pteridophyte Collections Consortium (PCC), an interdisciplinary community uniting neo- and paleobotanists, and the associated PteridoPortal, a publicly accessible online portal that serves over three million pteridophyte records, including herbarium specimens, paleontological museum specimens, and iNaturalist observations. We demonstrate the utility of the PteridoPortal through discussion of three example PteridoPortal-enabled research projects.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The data within the PteridoPortal are global in scope and are queryable in a flexible manner. The PteridoPortal contains a taxonomic thesaurus (a digital version of a Linnaean classification) that includes both extant and extinct pteridophytes in a common phylogenetic framework. The PteridoPortal allows applications such as greatly accelerated classic floristics, entirely new “next-generation” floristic approaches, and the study of environmentally mediated evolution of functional morphology across deep time.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The PCC and PteridoPortal provide a comprehensive resource enabling novel research into plant evolution, ecology, and conservation across deep time, facilitating rapid floristic analyses and other biodiversity-related investigations, and providing new opportunities for education and community engagement.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884192","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":"A comprehensive illustrated protocol for clearing, mounting, and imaging leaf venation networks","authors":"Isabella Niewiadomski,&nbsp;Monica Antonio,&nbsp;Luiza Maria T. Aparecido,&nbsp;Mickey Boakye,&nbsp;Sonoma Carlos,&nbsp;Andrea Echevarria,&nbsp;Adrian Fontao,&nbsp;Joseph Mann,&nbsp;Ilaíne Silveira Matos,&nbsp;Norma Salinas,&nbsp;Bradley Vu,&nbsp;Benjamin Wong Blonder","doi":"10.1002/aps3.70002","DOIUrl":"https://doi.org/10.1002/aps3.70002","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Leaf venation network architecture can provide insights into plant evolution, ecology, and physiology. Venation networks are typically assessed through histological methods, but existing protocols provide limited guidance on processing large or challenging leaves.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and results</h3>\u0000 \u0000 <p>We present an illustrated protocol for visualizing whole leaf venation networks, including sample preparation, clearing, staining, mounting, imaging, and archiving steps. The protocol also includes supply lists, troubleshooting procedures, safety considerations, and examples of successful and unsuccessful outcomes. The protocol is suitable for a wide range of leaf sizes and morphologies and has been used with all major plant groups.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusion</h3>\u0000 \u0000 <p>We provide a workflow for obtaining high-quality mounts and images of venation networks of a wide range of species, using readily available materials.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884061","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":"Enhancing plant morphological trait identification in herbarium collections through deep learning–based segmentation","authors":"Hanane Ariouat,&nbsp;Youcef Sklab,&nbsp;Edi Prifti,&nbsp;Jean-Daniel Zucker,&nbsp;Eric Chenin","doi":"10.1002/aps3.70000","DOIUrl":"https://doi.org/10.1002/aps3.70000","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Deep learning has become increasingly important in the analysis of digitized herbarium collections, which comprise millions of scans that provide valuable resources for studying plant evolution and biodiversity. However, leveraging deep learning algorithms to analyze these scans presents significant challenges, partly due to the heterogeneous nature of the non-plant material that forms the background of the scans. We hypothesize that removing such backgrounds can improve the performance of these algorithms.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We propose a novel method based on deep learning to segment and generate plant masks from herbarium scans and subsequently remove the non-plant backgrounds. The semi-automatic preprocessing stages involve the identification and removal of non-plant elements, substantially reducing the manual effort required to prepare the training dataset.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The results highlight the importance of effective image segmentation, which achieved an F1 score of up to 96.6%. Moreover, when used in classification models for plant morphological trait identification, the images resulting from segmentation improved classification accuracy by up to 3% and F1 score by up to 7% compared to non-segmented images.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our approach isolates plant elements in herbarium scans by removing background elements to improve classification tasks. We demonstrate that image segmentation significantly enhances the performance of plant morphological trait identification models.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70000","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883986","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":"Looking to the past to inform the future: What eDNA from herbarium specimens can tell us about plant–animal interactions","authors":"Christopher Waters,&nbsp;Carla Hurt,&nbsp;Shawn Krosnick","doi":"10.1002/aps3.11633","DOIUrl":"https://doi.org/10.1002/aps3.11633","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The importance of natural history collections in modern ecological and genetic research cannot be overstated. Herbarium specimens provide historical information that can be used to investigate community ecology, phenology, and population genetics. In this study, environmental DNA (eDNA) metabarcoding and next-generation sequencing were used to test the efficacy of detecting historical plant–animal interactions from herbarium specimen flowers.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>A modified eDNA isolation method and standard Illumina sequencing protocols were used. Animal eDNA was amplified using both cytochrome c oxidase subunit I (COI) and 16S primers to increase detection probability. The relationship between specimen age (0–69 years) and target taxa read depth was also investigated.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We generated and identified over 1.5 million sequences of animal taxa belonging to 29 clades (families or orders). These methods enabled the detection of taxa including birds, mammals, hymenopterans, lepidopterans, coleopterans, and taxa belonging to “intrafloral” communities. While herbarium specimens overall yielded less identifiable eDNA compared to fresh material, the age of the herbarium specimen negligibly affected the amount of target and/or non-target eDNA detected in flowers.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>With careful consideration of the types of data that may be obtained through sampling eDNA from herbarium specimens, these methods could prove valuable to future research on plant–animal interactions.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11633","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883790","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":"mvh: An R tool to assemble and organize virtual herbaria from openly available specimen images","authors":"Thais Vasconcelos,&nbsp;James D. Boyko","doi":"10.1002/aps3.11631","DOIUrl":"https://doi.org/10.1002/aps3.11631","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Recent advances in imaging herbarium specimens have enhanced their use in biodiversity studies. However, user-friendly tools that facilitate the assembly of customized sets of herbarium specimen images on personal devices are still lacking.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Here we present the R package mvh (“my virtual herbarium”), which includes functions designed to search and download metadata and openly available images associated with herbarium specimens based on taxon or geography. We tested the functionalities of mvh by searching metadata associated with five sets of 10 vascular plant species and five sets of 10 terrestrial coordinates. The download function had a success rate of 99%, downloading 291 out of the 293 images found in the search. Possible reasons for download failure are discussed.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>As long as an internet connection is available, mvh simplifies the assembly and organization of virtual herbaria, thereby facilitating the investigation of novel empirical questions as well as trends in digitization efforts.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11631","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883941","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":"Acknowledgment of Reviewers","authors":"","doi":"10.1002/aps3.11630","DOIUrl":"https://doi.org/10.1002/aps3.11630","url":null,"abstract":"&lt;p&gt;The editors gratefully acknowledge our reviewers, who have generously given their time and expertise to review manuscripts submitted to &lt;i&gt;Applications in Plant Sciences&lt;/i&gt;. The list includes those who reviewed manuscripts from December 31, 2023, to December 31, 2024. Thank you for helping &lt;i&gt;APPS&lt;/i&gt; maintain a prompt and fair peer-review process.&lt;/p&gt;&lt;p&gt;Abrahams, R. Shawn&lt;/p&gt;&lt;p&gt;Adit, Arjun&lt;/p&gt;&lt;p&gt;Ajay, B. C.&lt;/p&gt;&lt;p&gt;Ameen, Safinatu (Safeenah)&lt;/p&gt;&lt;p&gt;Angeles, Guillermo&lt;/p&gt;&lt;p&gt;Arias, Tatiana&lt;/p&gt;&lt;p&gt;Armbruster, Scott&lt;/p&gt;&lt;p&gt;Arstingstall, Katherine&lt;/p&gt;&lt;p&gt;Attigala, Lakshmi&lt;/p&gt;&lt;p&gt;Avila-Lovera, Eleinis&lt;/p&gt;&lt;p&gt;Awana, Monika&lt;/p&gt;&lt;p&gt;Baker, Robert&lt;/p&gt;&lt;p&gt;Banerjee, Pritam&lt;/p&gt;&lt;p&gt;Barclay, Richard S.&lt;/p&gt;&lt;p&gt;Bird, Kevin&lt;/p&gt;&lt;p&gt;Blischak, Paul&lt;/p&gt;&lt;p&gt;Borokini, Israel&lt;/p&gt;&lt;p&gt;Borràs, Joshua&lt;/p&gt;&lt;p&gt;Boyko, James&lt;/p&gt;&lt;p&gt;Brown, Herrick&lt;/p&gt;&lt;p&gt;Brown, Matilda&lt;/p&gt;&lt;p&gt;Brun, Guillaume&lt;/p&gt;&lt;p&gt;Chauhan, Chetan&lt;/p&gt;&lt;p&gt;Clare, Shaun&lt;/p&gt;&lt;p&gt;Cobo-Simón, Irene&lt;/p&gt;&lt;p&gt;Colli-Silva, Matheus&lt;/p&gt;&lt;p&gt;Cort, John&lt;/p&gt;&lt;p&gt;Crawford, Daniel&lt;/p&gt;&lt;p&gt;Cruz, Rafael&lt;/p&gt;&lt;p&gt;Davis, Mark&lt;/p&gt;&lt;p&gt;Diaz Tapia, Pilar&lt;/p&gt;&lt;p&gt;Dikow, Rebecca&lt;/p&gt;&lt;p&gt;Emelianova, Katherine&lt;/p&gt;&lt;p&gt;Ezquer, Ignacio&lt;/p&gt;&lt;p&gt;Fernie, Alisdair&lt;/p&gt;&lt;p&gt;Giongo, Adriana&lt;/p&gt;&lt;p&gt;Gladish, Daniel&lt;/p&gt;&lt;p&gt;Godbout, Julie&lt;/p&gt;&lt;p&gt;Goldberg, Jay K.&lt;/p&gt;&lt;p&gt;Hanschen, Erik&lt;/p&gt;&lt;p&gt;Hendrickson, Brandon&lt;/p&gt;&lt;p&gt;Hernández-Castellano, Carlos&lt;/p&gt;&lt;p&gt;Heyduk, Karolina&lt;/p&gt;&lt;p&gt;Hodel, Richard&lt;/p&gt;&lt;p&gt;Hossain, Kabir&lt;/p&gt;&lt;p&gt;Hu, Guanjing&lt;/p&gt;&lt;p&gt;Iniesto, Miguel&lt;/p&gt;&lt;p&gt;Jangid, Vinod&lt;/p&gt;&lt;p&gt;Katabuchi, Masatoshi&lt;/p&gt;&lt;p&gt;Kattenborn, Teja&lt;/p&gt;&lt;p&gt;Kobrlová, Lucie&lt;/p&gt;&lt;p&gt;Kolter, Andreas&lt;/p&gt;&lt;p&gt;Krieg, Christopher&lt;/p&gt;&lt;p&gt;LaFountain, Amy&lt;/p&gt;&lt;p&gt;Le Guillarme, Nicolas&lt;/p&gt;&lt;p&gt;Leroy, Thibault&lt;/p&gt;&lt;p&gt;Long, Evan&lt;/p&gt;&lt;p&gt;Ma, Chuang&lt;/p&gt;&lt;p&gt;Mabry, Makenzie&lt;/p&gt;&lt;p&gt;Malik, Afsheen&lt;/p&gt;&lt;p&gt;Mannochio Russo, Helena&lt;/p&gt;&lt;p&gt;Mason, Chase&lt;/p&gt;&lt;p&gt;McAdam, Scott&lt;/p&gt;&lt;p&gt;Milleville, Kenzo&lt;/p&gt;&lt;p&gt;Mohn, Rebekah&lt;/p&gt;&lt;p&gt;Monroe, Grey&lt;/p&gt;&lt;p&gt;Moore, Abigail&lt;/p&gt;&lt;p&gt;Muangmai, Narongrit&lt;/p&gt;&lt;p&gt;Murch, Susan&lt;/p&gt;&lt;p&gt;Noman, Muhammad&lt;/p&gt;&lt;p&gt;Ochoa-Fernandez, Rocio&lt;/p&gt;&lt;p&gt;Odufuwa, Phebian&lt;/p&gt;&lt;p&gt;Opedal, Øystein&lt;/p&gt;&lt;p&gt;Osorio Zambrano, Mayra Andreina&lt;/p&gt;&lt;p&gt;Paredes Burneo, Diego F.&lt;/p&gt;&lt;p&gt;Petruzzellis, Francesco&lt;/p&gt;&lt;p&gt;Pluskal, Tomas&lt;/p&gt;&lt;p&gt;Pramanik, Dewi&lt;/p&gt;&lt;p&gt;Puppo, Pamela&lt;/p&gt;&lt;p&gt;Rey, Elodie&lt;/p&gt;&lt;p&gt;Rodríguez López, Carlos&lt;/p&gt;&lt;p&gt;Salzman, Shayla&lt;/p&gt;&lt;p&gt;Sanchez, Jose Maria&lt;/p&gt;&lt;p&gt;Santos, Wagner Luiz dos&lt;/p&gt;&lt;p&gt;Sarkar, Shagor&lt;/p&gt;&lt;p&gt;Saroja, Seethapathy G.&lt;/p&gt;&lt;p&gt;Schmidt-Lebuhn,Alexander&lt;/p&gt;&lt;p&gt;Schmitt, Sylvain&lt;/p&gt;&lt;p&gt;Seglias, Alexandra&lt;/p&gt;&lt;p&gt;Senthil-Kumar,Muthappa&lt;/p&gt;&lt;p&gt;Serra Marin, Pau Enric&lt;/p&gt;&lt;p&gt;Session, Adam&lt;/p&gt;&lt;p&gt;Sigel, Erin&lt;/p&gt;&lt;p&gt;Smith, Alison&lt;/p&gt;&lt;p&gt;Smith, Stephen&lt;/p&gt;&lt;p&gt;Soltis, Pamela&lt;/p&gt;&lt;p&gt;Sorojsrisom, Elissa&lt;/p&gt;&lt;p&gt;Steinecke, Christina&lt;/p&gt;&lt;p&gt;Storchova, Helena&lt;/p&gt;&lt;p&gt;Storey, Gary&lt;/p&gt;&lt;p&gt;Suissa, Jacob&lt;/p&gt;&lt;p&gt;Sutherland, Brittany&lt;/p&gt;&lt;p&gt;Svolacchia, Noemi&lt;/p&gt;&lt;p&gt;Takano, Atsuko&lt;/p&gt;&lt;p&gt;Talavera, Alicia&lt;/p&gt;&lt;p&gt;Tavares, Rachel&lt;/p&gt;&lt;p&gt;Thomas, Shawn&lt;/p&gt;&lt;p&gt;Trindade, Weverton&lt;/p&gt;&lt;p&gt;Urbina-Casanova, Rafael&lt;/p&gt;&lt;p&gt;Van Steenderen, Clarke&lt;/p&gt;&lt;p&gt;Vivek, A. T.&lt;/p&gt;&lt;p&gt;Vlcek, Jakub&lt;/p&gt;&lt;p&gt;Walker, Joseph&lt;/p&gt;&lt;p&gt;Wallace, Lisa&lt;/p&gt;&lt;p&gt;We","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11630","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143117288","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":"The sensitivity of reconstructed carbon dioxide concentrations to stomatal preparation methods using a leaf gas exchange model","authors":"Michael D. Machesky,&nbsp;Nathan D. Sheldon,&nbsp;Michael T. Hren,&nbsp;Selena Y. Smith","doi":"10.1002/aps3.11629","DOIUrl":"https://doi.org/10.1002/aps3.11629","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Mechanistic models using stomatal traits and leaf carbon isotope ratios to reconstruct atmospheric carbon dioxide (CO₂) concentrations (<i>c</i>_<i>a</i>) are important to understand the Phanerozoic paleoclimate. However, methods for preparing leaf cuticles to measure stomatal traits have not been standardized.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Three people measured the stomatal density and index, guard cell length, guard cell pair width, and pore length of leaves from the same <i>Ginkgo biloba</i>, <i>Quercus alba</i>, and <i>Zingiber mioga</i> leaves growing at known CO₂ levels using four preparation methods: fluorescence on cleared leaves, nail polish, dental putty on fresh leaves, and dental putty on dried leaves.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>There are significant differences between trait measurements from each method. Modeled <i>c</i>_<i>a</i> calculations are less sensitive to method than individual traits; however, the choice of assumed carbon isotope fractionation also impacted the accuracy of the results.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We show that there is not a significant difference between <i>c</i>_<i>a</i> estimates made using any of the four methods. Further study is needed on the fractionation due to carboxylation of ribulose bisphosphate (RuBP) in individual plant species before use as a paleo-CO₂ barometer and to refine estimates based upon widely applied taxa (e.g., <i>Ginkgo</i>). Finally, we recommend that morphological measurements be made by multiple observers to reduce the effect of individual observational biases.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11629","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143117163","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":"Microbial methods matter: Identifying discrepancies between microbiome denoising pipelines using a leaf biofilm taphonomic dataset","authors":"Brianne Palmer,&nbsp;Sabina Karačić,&nbsp;Gabriele Bierbaum,&nbsp;Carole T. Gee","doi":"10.1002/aps3.11628","DOIUrl":"https://doi.org/10.1002/aps3.11628","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The occurrence of different microorganisms on aquatic macrophyte fossils suggests that biofilm microbes may facilitate leaf preservation. Understanding the impact of microorganisms on leaf preservation requires studies on living plants coupled with microbial amplicon sequencing. Choosing the most suitable bioinformatic pipeline is pivotal to accurate data interpretation, as it can lead to considerably different estimations of microbial community composition.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We analyze biofilms from floating and submerged leaves of <i>Nymphaea alba</i> and <i>Nuphar lutea</i> and mock communities using primers for the 16S ribosomal RNA (rRNA), 18S rRNA, and ITS amplicon regions and compare the microbial community compositions derived from three bioinformatic pipelines: DADA2, Deblur, and UNOISE.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The choice of denoiser alters the total number of sequences identified and differs in the identified taxa. Results from all three denoising pipelines show that the leaf microbial communities differed between depths and that the effect of the environment varied depending on the amplicon region.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Considering the performance of denoising algorithms and the identification of amplicon sequence variants (ASVs), we recommend DADA2 for analyzing 16S rRNA and 18S rRNA. For the ITS region, the choice is more nuanced, as Deblur identified the most ASVs and was compositionally similar to DADA2.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 2","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11628","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143884069","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":"Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species","authors":"Irene T. Liao,&nbsp;Karen E. Sears,&nbsp;Lena C. Hileman,&nbsp;Lachezar A. Nikolov","doi":"10.1002/aps3.11627","DOIUrl":"https://doi.org/10.1002/aps3.11627","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Orthology inference is crucial for comparative genomics, and multiple algorithms have been developed to identify putative orthologs for downstream analyses. Despite the abundance of proposed solutions, including publicly available benchmarks, it is difficult to assess which tool is most suitable for plant species, which commonly have complex genomic histories.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We explored the performance of four orthology inference algorithms—OrthoFinder, SonicParanoid, Broccoli, and OrthNet—on eight Brassicaceae genomes in two groups: one group comprising only diploids and another set comprising the diploids, two mesopolyploids, and one recent hexaploid genome.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The composition of the orthogroups reflected the species' ploidy and genomic histories, with the diploid set having a higher proportion of identical orthogroups. While the diploid + higher ploidy set had a lower proportion of orthogroups with identical compositions, the average degree of similarity between the orthogroups was not different from the diploid set.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Three algorithms—OrthoFinder, SonicParanoid, and Broccoli—are helpful for initial orthology predictions. Results produced using OrthNet were generally outliers but could still provide detailed information about gene colinearity. With our Brassicaceae dataset, slight discrepancies were found across the orthology inference algorithms, necessitating additional analyses such as tree inference to fine-tune results.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11627","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143119411","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}