Applications in Plant Sciences最新文献

{"title":"An efficient and effective RNA extraction protocol for ferns","authors":"Jessie A. Pelosi, Ruth Davenport, W. Brad Barbazuk, Emily B. Sessa, Li‐Yaung Kuo","doi":"10.1002/aps3.11617","DOIUrl":"https://doi.org/10.1002/aps3.11617","url":null,"abstract":"PremiseThe 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.MethodsWe 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 > 1.6, and RNA integrity numbers >7.ConclusionsThis 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.","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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":"https://doi.org/10.1002/aps3.11616","url":null,"abstract":"PremiseThe 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.Methods and Resultsflorabr 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.Conclusionsflorabr 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.","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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":null,"pages":null},"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":"<p>Methods for generating and analyzing data from polyploid species are not new to <i>Applications in Plant Sciences</i>, 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.</p><p>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., <span>2018</span>), measurements of spore sizes (Kuo et al., <span>2021</span>), and even spectroscopy (Buono and Albach, <span>2023</span>). 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. (<span>2024</span>) 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., <span>2014</span>), and the method of Ramirez-Castillo et al. continues this legacy. Moving from chromosomes to sequence data, Gaynor et al. (<span>2024</span>) 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":null,"pages":null},"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}

{"title":"Embryo excision in Compositae, with implications for combating biodiversity loss","authors":"Bruce G. Baldwin, Susan Fawcett, Dustin Wolkis","doi":"10.1002/aps3.11608","DOIUrl":"https://doi.org/10.1002/aps3.11608","url":null,"abstract":"PremiseEmbryo excision is an effective, under‐described means of promoting germination in the sunflower family and may help to ensure the survival of endangered taxa or lineages with limited seed availability.Methods and ResultsWe describe and illustrate a detailed method of embryo excision used successfully to stimulate germination in a diversity of composites and that requires minimal materials and expense, using <jats:italic>Layia platyglossa</jats:italic> as an example. We show how this procedure greatly increases germination compared to control treatments in <jats:italic>Madia elegans</jats:italic>, a close relative of Hawaiian silverswords that exhibits physiological dormancy.ConclusionsThis technique can be learned quickly and is highly effective. Embryo excision can aid conservation efforts dependent on minimal seed resources by enhancing germination and allowing evaluation of seed quality before or after storage, as well as synchronizing seedling development, thereby allowing for refinement of ex situ seed bank conditions and efficient use of horticultural resources.","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142199633","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":"Data‐driven guidelines for phylogenomic analyses using SNP data","authors":"J. Suissa, Gisel Y. De La Cerda, Leland C. Graber, Chloe Jelley, David Wickell, Heather R. Phillips, Ayress D. Grinage, C. S. Moreau, Chelsea D. Specht, Jeff J. Doyle, Jacob B. Landis","doi":"10.1002/aps3.11611","DOIUrl":"https://doi.org/10.1002/aps3.11611","url":null,"abstract":"There is a general lack of consensus on the best practices for filtering of single‐nucleotide polymorphisms (SNPs) and whether it is better to use SNPs or include flanking regions (full “locus”) in phylogenomic analyses and subsequent comparative methods.Using genotyping‐by‐sequencing data from 22 Glycine species, we assessed the effects of SNP vs. locus usage and SNP retention stringency. We compared branch length, node support, and divergence time estimation across 16 datasets with varying amounts of missing data and total size.Our results revealed five aspects of phylogenomic data usage that may be generally applicable: (1) tree topology is largely congruent across analyses; (2) filtering strictly for SNP retention (e.g., 90–100%) reduces support and can alter some inferred relationships; (3) absolute branch lengths vary by two orders of magnitude between SNP and locus datasets; (4) data type and branch length variation have little effect on divergence time estimation; and (5) phylograms alter the estimation of ancestral states and rates of morphological evolution.Using SNP or locus datasets does not alter phylogenetic inference significantly, unless researchers want or need to use absolute branch lengths. We recommend against using excessive filtering thresholds for SNP retention to reduce the risk of producing inconsistent topologies and generating low support.","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141921682","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":"The impact of extraction method and pollen concentration on community composition for pollen metabarcoding","authors":"Arne Devriese, Gerrit Peeters, Rein Brys, Hans Jacquemyn","doi":"10.1002/aps3.11601","DOIUrl":"https://doi.org/10.1002/aps3.11601","url":null,"abstract":"PremisePlants and pollinators closely interact with each other to form complex networks of species interactions. Metabarcoding of pollen collections has recently been proposed as an advantageous method for the construction of such networks, but the extent to which diversity and community analyses depend on the extraction method and pollen concentration used remains unclear.MethodsIn this study, we used a dilution series of two pollen mixtures (a mock community and pooled natural pollen loads from bumblebees) to assess the effect of mechanical homogenization and two DNA extraction kits (spin column DNA extraction kit and magnetic bead DNA extraction kit) on the detected pollen richness and community composition.ResultsAll species were successfully detected using the three methods, even in the most dilute samples. However, the extraction method had a significant effect on the detected pollen richness and community composition, with simple mechanical homogenization introducing an extraction bias.DiscussionOur findings suggest that all three methods are effective for detecting plant species in the pollen loads on insects, even in cases of very low pollen loads. However, our results also indicate that extraction methods can have a profound impact on the ability to correctly assess the community composition of the pollen loads on insects. The choice of extraction methodology should therefore be carefully considered to ensure reliable and unbiased results in pollen diversity and community analyses.","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141932620","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":"Guidelines for quantifying leaf chlorophyll content via non‐destructive spectrometry","authors":"Giancarlo M. Chiarenza, Eve Slavich, Angela T. Moles","doi":"10.1002/aps3.11610","DOIUrl":"https://doi.org/10.1002/aps3.11610","url":null,"abstract":"PremiseLeaf chlorophyll is a fundamental bioindicator used in several fields; however, we lack clear guidelines for optimizing sampling efforts and producing comparable studies.MethodsWe estimated the leaf chlorophyll content of 10 plant species using nondestructive spectrometry methods. We stored half of the leaves at 4°C and half at room temperature under similar light levels to assess the role of storage in the chlorophyll degradation rate.ResultsThe chilled mature leaves maintained a chlorophyll content within 5% of the original value for ~1.5 d, while the chlorophyll content of unrefrigerated mature leaves decreased rapidly, indicating that their chlorophyll content should be measured within 4 h. When refrigerated, the chlorophyll content of the expanding leaves remained within 5% of the original level for at least 5 d, but we suggest analyzing them within 3 d. In mature leaves, 73% of the variation in chlorophyll content is at the species level, 15% is between individuals, and the variation within leaves is negligible (&lt;1%). Measuring one mature leaf from eight individuals was sufficient to provide a species chlorophyll estimate within 5% of the true value at least 80% of the time.DiscussionWe advise researchers to prioritize sampling more individuals rather than repeating measures within leaves or individuals. Our findings will help researchers to optimize their time and research efforts, and to obtain more robust ecological data.","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141932621","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":"expowo: An R package for mining global plant diversity and distribution data","authors":"Débora C. Zuanny, Bruno Vilela, Peter W. Moonlight, Tiina E. Särkinen, Domingos Cardoso","doi":"10.1002/aps3.11609","DOIUrl":"https://doi.org/10.1002/aps3.11609","url":null,"abstract":"PremiseData on plant distribution and diversity from natural history collections and taxonomic databases are increasingly becoming available online as exemplified by the Royal Botanic Gardens, Kew's Plants of the World Online (POWO) database. This growing accumulation of biodiversity information requires an advance in bioinformatic tools for accessing and processing the massive data for use in downstream science. We present herein expowo, an open‐source package that facilitates extracting and using botanical data from POWO.Methods and ResultsThe expowo package is implemented in R and designed to handle the entire vascular plant tree of life. It includes functions to readily distill taxonomic and distributional information about all families, genera, or species of vascular plants. It outputs a complete list of species in each genus of any plant family, with the associated original publication, synonyms, and distribution, and plots global maps of species richness at the country and botanical country levels, as well as graphs displaying species‐discovery accumulation curves and nomenclatural changes over time. To demonstrate expowo's strengths in producing easy‐to‐handle outputs, we also show empirical examples from a set of biodiverse countries and representative species‐rich and ecologically important angiosperm families.ConclusionsBy harnessing bioinformatic tools that accommodate varying levels of R programming proficiency, expowo functions assist users who have limited R programming expertise in efficiently distilling specific botanical information from online sources and producing maps and graphics for the further interpretation of biogeographic and taxonomic patterns.","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141870157","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":"A machine learning algorithm for the automatic classification of Phytophthora infestans genotypes into clonal lineages","authors":"Camilo Patarroyo, Stéphane Dupas, Silvia Restrepo","doi":"10.1002/aps3.11603","DOIUrl":"https://doi.org/10.1002/aps3.11603","url":null,"abstract":"PremiseThe prompt categorization of <jats:italic>Phytophthora infestans</jats:italic> isolates into described clonal lineages is a key tool for the management of its associated disease, potato late blight. New isolates of this pathogen are currently classified by comparing their microsatellite genotypes with characterized clonal lineages, but an automated classification tool would greatly improve this process. Here, we developed a flexible machine learning–based classifier for <jats:italic>P. infestans</jats:italic> genotypes.MethodsThe performance of different machine learning algorithms in classifying <jats:italic>P. infestans</jats:italic> genotypes into its clonal lineages was preliminarily evaluated with decreasing amounts of training data. The four best algorithms were then evaluated using all collected genotypes.ResultsmlpML, cforest, nnet, and AdaBag performed best in the preliminary test, correctly classifying almost 100% of the genotypes. AdaBag performed significantly better than the others when tested using the complete data set (Tukey HSD <jats:italic>P</jats:italic> &lt; 0.001). This algorithm was then implemented in a web application for the automated classification of <jats:italic>P. infestans</jats:italic> genotypes, which is freely available at <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" xlink:href=\"https://github.com/cpatarroyo/genotypeclas\">https://github.com/cpatarroyo/genotypeclas</jats:ext-link>.DiscussionWe developed a gradient boosting–based tool to automatically classify <jats:italic>P. infestans</jats:italic> genotypes into its clonal lineages. This could become a valuable resource for the prompt identification of clonal lineages spreading into new regions.","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2024-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141778214","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}