Applications in Plant Sciences最新文献

{"title":"An open-source LED lamp for use with the LI-6800 photosynthesis system","authors":"Aarón I. Vélez-Ramírez,&nbsp;Juan de Dios Moreno,&nbsp;Uriel G. Pérez-Guerrero,&nbsp;Antonio M. Juarez,&nbsp;Hector Castillo-Arriaga,&nbsp;Josefina Vázquez-Medrano,&nbsp;Ilane Hernández-Morales","doi":"10.1002/aps3.11622","DOIUrl":"https://doi.org/10.1002/aps3.11622","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Controlling light flux density during carbon dioxide assimilation measurements is essential in photosynthesis research. Commercial lamps are expensive and are based on monochromatic light-emitting diodes (LEDs), which deviate significantly in their spectral distribution compared to sunlight.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Using LED-emitted white light with a color temperature similar to sunlight, we developed a cost-effective lamp compatible with the LI-6800 Portable Photosynthesis System. When coupled with customized software, the lamp can be controlled via the LI-6800 console by a user or Python scripts. Testing and calibration show that the lamp meets the quality needed to estimate photosynthesis parameters.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The lamp can be built using a basic electronics lab and a 3D printer. Calibration instructions are supplied and only require equipment commonly available at plant science laboratories. The lamp is a cost-effective alternative to perform photosynthesis research coupled with the popular LI-6800 photosynthesis measuring system.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11622","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143119431","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":"Tailoring convolutional neural networks for custom botanical data","authors":"Jamie R. Sykes,&nbsp;Katherine J. Denby,&nbsp;Daniel W. Franks","doi":"10.1002/aps3.11620","DOIUrl":"https://doi.org/10.1002/aps3.11620","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Automated disease, weed, and crop classification with computer vision will be invaluable in the future of agriculture. However, existing model architectures like ResNet, EfficientNet, and ConvNeXt often underperform on smaller, specialised datasets typical of such projects.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We address this gap with informed data collection and the development of a new convolutional neural network architecture, PhytNet. Utilising a novel dataset of infrared cocoa tree images, we demonstrate PhytNet's development and compare its performance with existing architectures. Data collection was informed by spectroscopy data, which provided useful insights into the spectral characteristics of cocoa trees. Cocoa was chosen as a focal species due to the diverse pathology of its diseases, which pose significant challenges for detection.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>ResNet18 showed some signs of overfitting, while EfficientNet variants showed distinct signs of overfitting. By contrast, PhytNet displayed excellent attention to relevant features, almost no overfitting, and an exceptionally low computation cost of 1.19 GFLOPS.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>We show that PhytNet is a promising candidate for rapid disease or plant classification and for precise localisation of disease symptoms for autonomous systems. We also show that the most informative light spectra for detecting cocoa disease are outside the visible spectrum and that efforts to detect disease in cocoa should be focused on local symptoms, rather than the systemic effects of disease.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11620","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143117682","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":"Expression-based machine learning models for predicting plant tissue identity","authors":"Sourabh Palande,&nbsp;Jeremy Arsenault,&nbsp;Patricia Basurto-Lozada,&nbsp;Andrew Bleich,&nbsp;Brianna N. I. Brown,&nbsp;Sophia F. Buysse,&nbsp;Noelle A. Connors,&nbsp;Sikta Das Adhikari,&nbsp;Kara C. Dobson,&nbsp;Francisco Xavier Guerra-Castillo,&nbsp;Maria F. Guerrero-Carrillo,&nbsp;Sophia Harlow,&nbsp;Héctor Herrera-Orozco,&nbsp;Asia T. Hightower,&nbsp;Paulo Izquierdo,&nbsp;MacKenzie Jacobs,&nbsp;Nicholas A. Johnson,&nbsp;Wendy Leuenberger,&nbsp;Alessandro Lopez-Hernandez,&nbsp;Alicia Luckie-Duque,&nbsp;Camila Martínez-Avila,&nbsp;Eddy J. Mendoza-Galindo,&nbsp;David Cruz Plancarte,&nbsp;Jenny M. Schuster,&nbsp;Harry Shomer,&nbsp;Sidney C. Sitar,&nbsp;Anne K. Steensma,&nbsp;Joanne Elise Thomson,&nbsp;Damián Villaseñor-Amador,&nbsp;Robin Waterman,&nbsp;Brandon M. Webster,&nbsp;Madison Whyte,&nbsp;Sofía Zorilla-Azcué,&nbsp;Beronda L. Montgomery,&nbsp;Aman Y. Husbands,&nbsp;Arjun Krishnan,&nbsp;Sarah Percival,&nbsp;Elizabeth Munch,&nbsp;Robert VanBuren,&nbsp;Daniel H. Chitwood,&nbsp;Alejandra Rougon-Cardoso","doi":"10.1002/aps3.11621","DOIUrl":"https://doi.org/10.1002/aps3.11621","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The selection of <i>Arabidopsis</i> as a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural- or ecological-based model species were rejected, in favor of building knowledge in a species that would facilitate genome-enabled research.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here, we examine the ability of models based on <i>Arabidopsis</i> gene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested on <i>Arabidopsis</i> data achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained on <i>Arabidopsis</i> data, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance from <i>Arabidopsis</i>. <i>k</i>-nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our data-driven results highlight that the assertion that knowledge from <i>Arabidopsis</i> is translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis on <i>Arabidopsis</i> and prioritize plant diversity.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11621","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143116963","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":"FlowerMate: Multidimensional reciprocity and inaccuracy indices for style-polymorphic plant populations","authors":"Violeta Simón-Porcar,&nbsp;A. Jesús Muñoz-Pajares,&nbsp;Juan Arroyo,&nbsp;Steven D. Johnson","doi":"10.1002/aps3.11618","DOIUrl":"https://doi.org/10.1002/aps3.11618","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Heterostyly in plants promotes pollen transfer between floral morphs, because female and male sex organs are located at roughly reciprocal heights within the flowers of each morph. Reciprocity indices, which assess the one-dimensional variation in the height of sex organs, are used to define the phenotypic structure of heterostyly in plant populations and to make inferences about selection. Other reciprocal stylar polymorphisms (e.g., enantiostyly) may function in a similar manner to heterostyly. In-depth assessment of their potential fit with pollinators requires accounting for the multidimensional variation in the location of sex organs.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We have adapted the existing reciprocity indices used for heterostylous plant populations to incorporate multidimensional data. We illustrate the computation of the adapted and original indices in the freely available R package FlowerMate.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>FlowerMate provides fast computation of reliable indices to facilitate understanding of the evolution and function of the full diversity of reciprocal polymorphisms.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11618","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142758745","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":"Truly the best of both worlds: Merging lineage-specific and universal probe kits to maximize phylogenomic inference","authors":"Luiz Henrique M. Fonseca,&nbsp;Pieter Asselman,&nbsp;Katherine R. Goodrich,&nbsp;Francis J. Nge,&nbsp;Vincent Soulé,&nbsp;Kathryn Mercier,&nbsp;Thomas L. P. Couvreur,&nbsp;Lars W. Chatrou","doi":"10.1002/aps3.11615","DOIUrl":"https://doi.org/10.1002/aps3.11615","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Hybridization capture kits are now commonly used for reduced representation approaches in genomic sequencing, with both universal and clade-specific kits available. Here, we present a probe kit targeting 799 low-copy genes for the plant family Annonaceae.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>This new version of the kit combines the original 469 genes from the previous Annonaceae kit with 334 genes from the universal Angiosperms353 kit. We also compare the results obtained using the original Angiosperms353 kit with our custom approach using a subset of specimens. Parsimony-informative sites and the results of maximum likelihood phylogenetic inference were assessed for combined matrices using the genera <i>Asimina</i> and <i>Deeringothamnus</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The Annonaceae799 genes derived from the Angiosperms353 kit have extremely high recovery rates. Off-target reads were also detected. When evaluating size, the proportion of on- and off-target regions, and the number of parsimony-informative sites, the genes incorporated from the Angiosperms353 panel generally outperformed the genes from the original Annonaceae probe kit.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We demonstrated that the new sequences from the Angiosperms353 probe set are variable and relevant for future studies on species-level phylogenomics and within-species studies in the Annonaceae. The integration of kits also establishes a connection between projects and makes new genes available for phylogenetic and population studies.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11615","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142762825","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":"BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more","authors":"Nelson R. Salinas,&nbsp;Gil Eshel,&nbsp;Gloria M. Coruzzi,&nbsp;Rob DeSalle,&nbsp;Michael Tessler,&nbsp;Damon P. Little","doi":"10.1002/aps3.11604","DOIUrl":"https://doi.org/10.1002/aps3.11604","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Common steps in phylogenomic matrix production include biological sequence concatenation, morphological data concatenation, insertion/deletion (indel) coding, gene content (presence/absence) coding, removing uninformative characters for parsimony analysis, recording with reduced amino acid alphabets, and occupancy filtering. Existing software does not accomplish these tasks on a phylogenomic scale using a single program.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>BAD2matrix is a Python script that performs the above-mentioned steps in phylogenomic matrix construction for DNA or amino acid sequences as well as morphological data. The script works in UNIX-like environments (e.g., LINUX, MacOS, Windows Subsystem for LINUX).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>BAD2matrix helps simplify phylogenomic pipelines and can be downloaded from https://github.com/dpl10/BAD2matrix/tree/master under a GNU General Public License v2.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11604","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142762633","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 efficient and effective RNA extraction protocol for ferns","authors":"Jessie A. Pelosi,&nbsp;Ruth Davenport,&nbsp;W. Brad Barbazuk,&nbsp;Emily B. Sessa,&nbsp;Li-Yaung Kuo","doi":"10.1002/aps3.11617","DOIUrl":"10.1002/aps3.11617","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The extraction of high-quality RNA is the critical first step for the analysis of gene expression and gene space. This remains particularly challenging in plants, and especially in ferns, where the disruption of the cell wall and separation of organic compounds from nucleic acids is not trivial.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We developed a cetyltrimethylammonium bromide (CTAB)-based RNA extraction protocol that consistently performs well across a large phylogenetic breadth of ferns—a lineage of plants high in secondary compounds—and in an array of tissue types. Two alternative options (precipitation vs. clean-up without intermediate precipitation) are presented, both of which yield high-quality RNA extracts with optical density (OD) ratios of OD 260/280 = 1.9–2.1 and OD 260/230 &gt; 1.6, and RNA integrity numbers &gt;7.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This study presents an efficient protocol for the extraction of high-quality RNA from multiple tissues and across the fern phylogeny, a clade of plants that still lags behind other major lineages in the development of genomic resources. We hope that this method can be used to help facilitate the closing of this gap.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11617","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142199631","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":"florabr: An R package to explore and spatialize species distribution using Flora e Funga do Brasil","authors":"Weverton C. F. Trindade","doi":"10.1002/aps3.11616","DOIUrl":"10.1002/aps3.11616","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The Flora e Funga do Brasil project is the most comprehensive effort to reliably document Brazilian plant and fungal diversity. It involves the collaborative work of hundreds of taxonomists, integrating detailed and standardized morphological descriptions, nomenclatural status, and geographic distribution information of plants, algae, and fungi collected throughout Brazil. Despite the extensive information available, managing the information from the Flora e Funga do Brasil website poses certain challenges.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>florabr is an R package developed to facilitate the exploration and geographical analysis of species information derived from the Flora e Funga do Brasil. Unique to florabr is its ability to interact with the latest, or any other version of the dataset, which undergoes weekly updates. I illustrate the practical application of florabr in common tasks in biogeography and conservation studies.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>florabr is anticipated to be of significant interest to biogeographers, ecologists, curators of biological collections, and taxonomists actively contributing to the Flora e Funga do Brasil.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11616","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142199632","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 unified framework to investigate and interpret hybrid and allopolyploid biodiversity across biological scales","authors":"Christopher P. Krieg","doi":"10.1002/aps3.11612","DOIUrl":"https://doi.org/10.1002/aps3.11612","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Hybridization and polyploidization are common in vascular plants and important drivers of biodiversity by facilitating speciation and ecological diversification. A primary limitation to making broad synthetic discoveries in hybrid and allopolyploid biodiversity research is the absence of a standardized framework to compare data across studies and biological scales.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here, I present a new quantitative framework to investigate and interpret patterns in hybrid and allopolyploid biology called the divergence index (DI). The DI framework produces standardized data that are comparable across studies and variables. To show how the DI framework can be used to synthesize data, I analyzed published biochemical, physiological, and ecological trait data of hybrids and allopolyploids. I also apply key ecological and evolutionary concepts in hybrid and polyploid biology to translate nominal outcomes, including transgression, intermediacy, expansion, and contraction, in continuous DI space.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Biochemical, physiological, ecological, and evolutionary data can all be analyzed, visualized, and interpreted in the DI framework. The DI framework is particularly suited to standardize and compare variables with very different scales. When using the DI framework to understand niche divergence, a metric of niche overlap can be used to complement insights to centroid and breadth changes.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The DI framework is an accessible framework for hybrid and allopolyploid biology and represents a flexible and intuitive tool that can be used to reconcile outstanding problems in plant biodiversity research.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 4","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11612","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142045308","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":"Charting the course for new discoveries in polyploid lineages","authors":"Michael R. McKain,&nbsp;Ya Yang,&nbsp;Agnieszka Golicz,&nbsp;Briana L. Gross","doi":"10.1002/aps3.11613","DOIUrl":"https://doi.org/10.1002/aps3.11613","url":null,"abstract":"&lt;p&gt;Methods for generating and analyzing data from polyploid species are not new to &lt;i&gt;Applications in Plant Sciences&lt;/i&gt;, yet a special issue on the topic still presents an exciting opportunity to explore newly emerging research techniques. The complexity associated with the existence of multiple genomes in a single nucleus has meant that despite decades of research, there are still unexplored frontiers at the molecular, phylogenetic, ecological, and evolutionary levels. Some uncharted areas persist despite the forays of excellent research by dedicated scientists, and some remain unmapped because the community avoids polyploid species due to a lack of tools or data. The eight articles in this special issue provide new waypoints and allow us to push the boundaries of our knowledge of polyploid lineages. The tools and applications offered here range from critical techniques for determining the ploidy level of an organism, through synthetic reviews of the optimal treatment of polyploid data for phylogenomics and population genomics, to leveraging and developing new tools to further our understanding of genome dynamics and whole-plant responses to polyploidy. We look forward to the impact that these tools and innovative approaches will have in accelerating the expansion of research into the nature and impact of polyploidy across plant taxa in the coming years.&lt;/p&gt;&lt;p&gt;Despite the generally acknowledged prevalence of polyploidy across plants, determining the ploidy of any given species or specimen is far from trivial. Techniques for answering this question include direct chromosome counts, but also indirect measures through flow cytometry (Smith et al., &lt;span&gt;2018&lt;/span&gt;), measurements of spore sizes (Kuo et al., &lt;span&gt;2021&lt;/span&gt;), and even spectroscopy (Buono and Albach, &lt;span&gt;2023&lt;/span&gt;). This issue features two new tools to facilitate the accurate assessment of ploidy—one method with a long tradition in plant science, and another that takes advantage of modern sequencing data. Ramirez-Castillo et al. (&lt;span&gt;2024&lt;/span&gt;) developed a method using croziers, or fiddleheads, to count chromosomes in different fern species. Although roots are typically used for mitotic chromosome counts, the ability to incorporate croziers as potential sources of material allows for a wider array of availability for samples. Ramirez-Castillo et al. use an enzyme pretreatment with a cellulose–pectinase solution to improve permeability of the tissue for the uptake of colchicine to arrest chromosomes at metaphase. Chromosome counting is the original method by which polyploidy was first described in plants (reviewed in Soltis et al., &lt;span&gt;2014&lt;/span&gt;), and the method of Ramirez-Castillo et al. continues this legacy. Moving from chromosomes to sequence data, Gaynor et al. (&lt;span&gt;2024&lt;/span&gt;) present nQuack, an R package that allows for ploidy estimation from sequence data ranging from whole-genome resequencing to target enrichment. Building on the methodology of nQuire (Weiß ","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 4","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11613","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142045160","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}