Applications in Plant Sciences最新文献

{"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}

{"title":"An optimized CTAB method for genomic DNA extraction from green seaweeds (Ulvophyceae)","authors":"Riyad Hossen,&nbsp;Myles Courtney,&nbsp;Alasdair Sim,&nbsp;Md Abdullah Al Kamran Khan,&nbsp;Heroen Verbruggen,&nbsp;Trevor Bringloe","doi":"10.1002/aps3.11625","DOIUrl":"https://doi.org/10.1002/aps3.11625","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Seaweeds are gaining substantial research interest, particularly for genomic applications, where high-quality DNA is a prerequisite. Extracting DNA from these organisms presents challenges due to high levels of biomacromolecules resulting from their diverse cell structures. Existing protocols often lack versatility, leading to inconsistent outcomes across various materials and taxa, which highlights the need for a universal method for use with a variety of green seaweed samples.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We optimized the conventional cetyltrimethylammonium bromide (CTAB) protocol for green seaweed DNA extraction. Our method, involving an initial sample treatment, lysis buffer adjustment, and enzyme incubation alterations, outperformed the conventional CTAB and commercial kits in terms of DNA yield and purity. Notably, the protocol's effectiveness was demonstrated across various green algal materials and preservation methods, and was tested with downstream applications with satisfactory results.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our optimized CTAB protocol offers a reliable solution for high-quality genomic DNA extraction from a wide variety of green seaweed samples.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11625","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143120545","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 phylogenomics to breeding: Can universal target capture probes be used in the development of SNP markers for kinship analysis?","authors":"Kedra M. Ousmael,&nbsp;Ole K. Hansen","doi":"10.1002/aps3.11624","DOIUrl":"https://doi.org/10.1002/aps3.11624","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Leveraging DNA markers, particularly single-nucleotide polymorphisms (SNPs), in parentage analysis, sib-ship reconstruction, and genomic relatedness analysis can enhance plant breeding efficiency. However, the limited availability of genomic information, confined to the most commonly used species, hinders the broader application of SNPs in species of lower economic interest (e.g., most tree species). We explored the possibility of using universal target capture probes, namely Angiosperms353, to identify SNPs and assess their effectiveness in genomic relatedness analysis.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We tested the approach in 11 tree species, six of which had a half-sib family structure. Variants were called within species, and genomic relatedness analysis was conducted in species with two or more families. Scalability via amplicon sequencing was tested by designing primers and testing them in silico.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Adequate SNPs for relatedness analysis were identified in all species. Relatedness values from Angiosperms353-based SNPs highly correlated with those from thousands of genome-wide DArTseq SNPs in <i>Cordia africana</i>, one of the species with a family structure. The in silico performance of designed primers demonstrated the potential for scaling up via amplicon sequencing.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Utilizing universal target capture probes for SNP identification can help overcome the limitations of genomic information availability, thereby enhancing the application of genomic markers in breeding plant species with lower economic interest.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11624","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143114422","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":"Ensemble automated approaches for producing high-quality herbarium digital records","authors":"Robert P. Guralnick,&nbsp;Raphael LaFrance,&nbsp;Julie M. Allen,&nbsp;Michael W. Denslow","doi":"10.1002/aps3.11623","DOIUrl":"https://doi.org/10.1002/aps3.11623","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>One of the slowest steps in digitizing natural history collections is converting labels associated with specimens into a digital data record usable for collections management and research. Here, we address how herbarium specimen labels can be converted into digital data records via extraction into standardized Darwin Core fields.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We first showcase the development of a rule-based approach and compare outcomes with a large language model–based approach, in particular ChatGPT4. We next quantified omission and commission error rates across target fields for a set of labels transcribed using optical character recognition (OCR) for both approaches. For example, we find that ChatGPT4 often creates field names that are not Darwin Core compliant while rule-based approaches often have high commission error rates.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our results suggest that these approaches each have different strengths and limitations. We therefore developed an ensemble approach that leverages the strengths of each individual method and documented that ensembling strongly reduced overall information extraction errors.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>This work shows that an ensemble approach has particular value for creating high-quality digital data records, even for complicated label content. While human validation is still needed to ensure the best possible quality, automated approaches can speed digitization of herbarium specimen labels and are likely to be broadly usable for all natural history collection types.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11623","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143112425","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}