Applications in Plant Sciences最新文献

筛选
英文 中文
Efficient homology-based annotation of transposable elements using minimizers 利用最小化器高效的基于同构的转座元素注释
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-05-11 DOI: 10.1002/aps3.11520
Laura Natalia Gonzalez-García, Daniela Lozano-Arce, Juan Pablo Londoño, Romain Guyot, Jorge Duitama
{"title":"Efficient homology-based annotation of transposable elements using minimizers","authors":"Laura Natalia Gonzalez-García,&nbsp;Daniela Lozano-Arce,&nbsp;Juan Pablo Londoño,&nbsp;Romain Guyot,&nbsp;Jorge Duitama","doi":"10.1002/aps3.11520","DOIUrl":"10.1002/aps3.11520","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Transposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long-read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. Unfortunately, TE annotation currently represents a bottleneck in the annotation of genome assemblies.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We present a new functionality of the Next-Generation Sequencing Experience Platform (NGSEP) to perform efficient homology-based TE annotation. Sequences in a reference library are treated as long reads and mapped to an input genome assembly. A hierarchical annotation is then assigned by homology using the annotation of the reference library. We tested the performance of our algorithm on genome assemblies of different plant species, including <i>Arabidopsis thaliana</i>, <i>Oryza sativa, Coffea humblotiana</i>, and <i>Triticum aestivum</i> (bread wheat). Our algorithm outperforms traditional homology-based annotation tools in speed by a factor of three to &gt;20, reducing the annotation time of the <i>T. aestivum</i> genome from months to hours, and recovering up to 80% of TEs annotated with RepeatMasker with a precision of up to 0.95.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>NGSEP allows rapid analysis of TEs, especially in very large and TE-rich plant genomes.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 4","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11520","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10052135","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}
引用次数: 2
An optimized RNA extraction method for diverse leaves of Hawaiian Metrosideros, a hypervariable tree species complex 一种优化的高变树种复合体夏威夷Metrosideros不同叶片RNA提取方法
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-04-27 DOI: 10.1002/aps3.11518
Maryam Hadi, Elizabeth A. Stacy
{"title":"An optimized RNA extraction method for diverse leaves of Hawaiian Metrosideros, a hypervariable tree species complex","authors":"Maryam Hadi,&nbsp;Elizabeth A. Stacy","doi":"10.1002/aps3.11518","DOIUrl":"https://doi.org/10.1002/aps3.11518","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The isolation of RNA from trees is challenging due to the interference of polyphenols and polysaccharides with downstream processes. Furthermore, many RNA extraction protocols are time consuming and involve hazardous chemicals. To address these issues, we aimed to develop a safe protocol for high-quality RNA extraction from diverse <i>Metrosideros</i> taxa representing a broad range of leaf toughness, pubescence, and secondary metabolites.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We tested popular RNA isolation kits and protocols that were effective on other recalcitrant trees, including a broad range of optimization and purification steps. We optimized a protocol involving two silica-membrane column-based kits that yielded high-quantity RNA with an RNA integrity number &gt;7 and without DNA contamination. All RNA samples were used successfully in a follow-on RNA-Seq experiment.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>We present an optimized high-throughput RNA extraction protocol that yielded high-quality and high-quantity RNA from three contrasting leaf phenotypes within a hyperdiverse woody species complex.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 3","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11518","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50154786","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}
引用次数: 2
Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens 红外光谱用于倍性估计:以两种Veronica为例,使用新鲜标本和植物标本
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-04-03 DOI: 10.1002/aps3.11516
Daniele Buono, Dirk C. Albach
{"title":"Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens","authors":"Daniele Buono,&nbsp;Dirk C. Albach","doi":"10.1002/aps3.11516","DOIUrl":"https://doi.org/10.1002/aps3.11516","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Polyploidy has become a central factor in plant evolutionary biological research in recent decades. Methods such as flow cytometry have revealed the widespread occurrence of polyploidy; however, its inference relies on expensive lab equipment and is largely restricted to fresh or recently dried material.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here, we assess the applicability of infrared spectroscopy to infer ploidy in two related species of <i>Veronica</i> (Plantaginaceae). Infrared spectroscopy relies on differences in the absorbance of tissues, which could be affected by primary and secondary metabolites related to polyploidy. We sampled 33 living plants from the greenhouse and 74 herbarium specimens with ploidy known through flow cytometrical measurements and analyzed the resulting spectra using discriminant analysis of principal components (DAPC) and neural network (NNET) classifiers.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Living material of both species combined was classified with 70% (DAPC) to 75% (NNET) accuracy, whereas herbarium material was classified with 84% (DAPC) to 85% (NNET) accuracy. Analyzing both species separately resulted in less clear results.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Infrared spectroscopy is quite reliable but is not a certain method for assessing intraspecific ploidy level differences in two species of <i>Veronica</i>. More accurate inferences rely on large training data sets and herbarium material. This study demonstrates an important way to expand the field of polyploid research to herbaria.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11516","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50118844","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}
引用次数: 0
Does sorting by color using visible and high-energy violet light improve classification of taxa in honey bee pollen pellets? 利用可见光和高能紫外光进行颜色分类是否能改善蜜蜂花粉粒的分类?
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-03-28 DOI: 10.1002/aps3.11514
Charlie P. Bailey, Carolyn A. Sonter, Jeremy L. Jones, Sabu Pandey, Simon Haberle, Karen C. B. S. Santos, Maria L. Absy, Romina Rader
{"title":"Does sorting by color using visible and high-energy violet light improve classification of taxa in honey bee pollen pellets?","authors":"Charlie P. Bailey,&nbsp;Carolyn A. Sonter,&nbsp;Jeremy L. Jones,&nbsp;Sabu Pandey,&nbsp;Simon Haberle,&nbsp;Karen C. B. S. Santos,&nbsp;Maria L. Absy,&nbsp;Romina Rader","doi":"10.1002/aps3.11514","DOIUrl":"10.1002/aps3.11514","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Pollen collected by honey bees from different plant species often differs in color, and this has been used as a basis for plant identification. The objective of this study was to develop a new, low-cost protocol to sort pollen pellets by color using high-energy violet light and visible light to determine whether pollen pellet color is associated with variations in plant species identity.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We identified 35 distinct colors and found that 52% of pollen subsamples (<i>n</i> = 200) were dominated by a single taxon. Among these near-pure pellets, only one color consistently represented a single pollen taxon (Asteraceae: Cichorioideae). Across the spectrum of colors spanning yellows, oranges, and browns, similarly colored pollen pellets contained pollen from multiple plant families ranging from two to 13 families per color.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Sorting pollen pellets illuminated under high-energy violet light lit from four directions within a custom-made light box aided in distinguishing pellet composition, especially in pellets within the same color.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e5/98/APS3-11-e11514.PMC10083439.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9359451","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}
引用次数: 1
Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies 多叶样品提取系统(MuLES):一个工具,以提高自动化形态测量叶片研究
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-03-21 DOI: 10.1002/aps3.11513
Christian S. Bowman, Ryan Traband, Xuesong Wang, Sara P. Knowles, Sassoum Lo, Zhenyu Jia, Nicholi Vorsa, Ira A. Herniter
{"title":"Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies","authors":"Christian S. Bowman,&nbsp;Ryan Traband,&nbsp;Xuesong Wang,&nbsp;Sara P. Knowles,&nbsp;Sassoum Lo,&nbsp;Zhenyu Jia,&nbsp;Nicholi Vorsa,&nbsp;Ira A. Herniter","doi":"10.1002/aps3.11513","DOIUrl":"10.1002/aps3.11513","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The measurement of leaf morphometric parameters from digital images can be time-consuming or restrictive when using digital image analysis softwares. The Multiple Leaf Sample Extraction System (MuLES) is a new tool that enables high-throughput leaf shape analysis with minimal user input or prerequisites, such as coding knowledge or image modification.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>MuLES uses contrasting pixel color values to distinguish between leaf objects and their background area, eliminating the need for color threshold–based methods or color correction cards typically required in other software methods. The leaf morphometric parameters measured by this software, especially leaf aspect ratio, were able to distinguish between large populations of different accessions for the same species in a high-throughput manner.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>MuLES provides a simple method for the rapid measurement of leaf morphometric parameters in large plant populations from digital images and demonstrates the ability of leaf aspect ratio to distinguish between closely related plant types.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/8d/19/APS3-11-e11513.PMC10083438.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9359453","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}
引用次数: 1
DNA assays for genetic discrimination of three Phragmites australis subspecies in the United States 美国三个芦苇亚种遗传鉴别的DNA分析
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-03-08 DOI: 10.1002/aps3.11512
Denise L. Lindsay, Xin Guan, Nathan E. Harms, James T. Cronin, Laura A. Meyerson, Richard F. Lance
{"title":"DNA assays for genetic discrimination of three Phragmites australis subspecies in the United States","authors":"Denise L. Lindsay,&nbsp;Xin Guan,&nbsp;Nathan E. Harms,&nbsp;James T. Cronin,&nbsp;Laura A. Meyerson,&nbsp;Richard F. Lance","doi":"10.1002/aps3.11512","DOIUrl":"https://doi.org/10.1002/aps3.11512","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>To genetically discriminate subspecies of the common reed (<i>Phragmites australis</i>), we developed real-time quantitative (qPCR) assays for identifying <i>P. australis</i> subsp. <i>americanus</i>, <i>P. australis</i> subsp. <i>australis</i>, and <i>P. australis</i> subsp. <i>berlandieri</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Utilizing study-generated chloroplast DNA sequences, we developed three novel qPCR assays. Assays were verified on individuals of each subspecies and against two non-target species, <i>Arundo donax</i> and <i>Phalaris arundinacea</i>. One assay amplifies only <i>P. australis</i> subsp. <i>americanus</i>, one amplifies <i>P. australis</i> subsp. <i>australis</i> and/or <i>P. australis</i> subsp. <i>berlandieri</i>, and one amplifies <i>P. australis</i> subsp. <i>americanus</i> and/or <i>P. australis</i> subsp. <i>australis</i>. This protocol enhances currently available rapid identification methods by providing genetic discrimination of all three subspecies.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The newly developed assays were validated using <i>P. australis</i> samples from across the United States. Application of these assays outside of this geographic range should be preceded by additional testing.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11512","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50140455","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}
引用次数: 0
Acclimation and hardening of a slow-growing woody species emblematic to western North America from in vitro plantlets 驯化和硬化一种生长缓慢的木本物种象征着北美西部从离体植株
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-03-02 DOI: 10.1002/aps3.11515
Peggy Martinez, Marcelo Serpe, Rachael Barron, Sven Buerki
{"title":"Acclimation and hardening of a slow-growing woody species emblematic to western North America from in vitro plantlets","authors":"Peggy Martinez,&nbsp;Marcelo Serpe,&nbsp;Rachael Barron,&nbsp;Sven Buerki","doi":"10.1002/aps3.11515","DOIUrl":"10.1002/aps3.11515","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Determining the tolerance of plant populations to climate change requires the development of biotechnological protocols producing genetically identical individuals used for genotype-by-environment experiments. Such protocols are missing for slow-growth, woody plants; to address this gap, this study uses <i>Artemisia tridentata</i>, a western North American keystone shrub, as model.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>The production of individual lines is a two-step process: in vitro propagation under aseptic conditions followed by ex vitro acclimation and hardening. Due to aseptic growth conditions, in vitro plantlets exhibit maladapted phenotypes, and this protocol focuses on presenting an approach promoting morphogenesis for slow-growth, woody species. Survival was used as the main criterion determining successful acclimation and hardening. Phenotypic changes were confirmed by inspecting leaf anatomy, and shoot water potential was used to ensure that plantlets were not water stressed.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Although our protocol has lower survival rates (11–41%) compared to protocols developed for herbaceous, fast-growing species, it provides a benchmark for slow-growth, woody species occurring in dry ecosystems.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 2","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a6/24/APS3-11-e11515.PMC10083460.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9359456","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}
引用次数: 0
Acknowledgment of Reviewers 审稿人致谢
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-02-04 DOI: 10.1002/aps3.11511
{"title":"Acknowledgment of Reviewers","authors":"","doi":"10.1002/aps3.11511","DOIUrl":"10.1002/aps3.11511","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, 2021, to December 31, 2022. 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;Anderson, Craig&lt;/p&gt;&lt;p&gt;Arseneau, Jean-Rene&lt;/p&gt;&lt;p&gt;Aucique, Carlos&lt;/p&gt;&lt;p&gt;Ávila-Lovera, Eleinis&lt;/p&gt;&lt;p&gt;Bachle, Seton&lt;/p&gt;&lt;p&gt;Banerjee, Sagnik&lt;/p&gt;&lt;p&gt;Barve, Vijay&lt;/p&gt;&lt;p&gt;Bieker, Vanessa&lt;/p&gt;&lt;p&gt;Blischak, Paul&lt;/p&gt;&lt;p&gt;Blonder, Benjamin&lt;/p&gt;&lt;p&gt;Bonnet, Pierre&lt;/p&gt;&lt;p&gt;Boquete Seoane, Teresa&lt;/p&gt;&lt;p&gt;Borràs, Joshua&lt;/p&gt;&lt;p&gt;Breman, Elinor&lt;/p&gt;&lt;p&gt;Brennan, Andrea&lt;/p&gt;&lt;p&gt;Brolly, Matthew&lt;/p&gt;&lt;p&gt;Bunn, Eric&lt;/p&gt;&lt;p&gt;Butler, Christopher&lt;/p&gt;&lt;p&gt;Cai, Liming&lt;/p&gt;&lt;p&gt;Carneiro de Melo Moura, Carina&lt;/p&gt;&lt;p&gt;Chano, Victor&lt;/p&gt;&lt;p&gt;Chen, Jeffery&lt;/p&gt;&lt;p&gt;Cohen, James&lt;/p&gt;&lt;p&gt;Colin, Ricardo&lt;/p&gt;&lt;p&gt;Contreras, Dori&lt;/p&gt;&lt;p&gt;Copetti, Dario&lt;/p&gt;&lt;p&gt;Del-Bem, Luiz Eduardo&lt;/p&gt;&lt;p&gt;Derkarabetian, Shahan&lt;/p&gt;&lt;p&gt;dos Santos, Renato&lt;/p&gt;&lt;p&gt;Dowell, Jordan&lt;/p&gt;&lt;p&gt;Downing, Jason&lt;/p&gt;&lt;p&gt;Duitama, Jorge&lt;/p&gt;&lt;p&gt;Elser, Justin&lt;/p&gt;&lt;p&gt;Fahlgren, Noah&lt;/p&gt;&lt;p&gt;Feltus, Frank&lt;/p&gt;&lt;p&gt;Feng, Xianzhong&lt;/p&gt;&lt;p&gt;Fetter, Karl&lt;/p&gt;&lt;p&gt;Goke, Alex&lt;/p&gt;&lt;p&gt;Gole, Pushkar&lt;/p&gt;&lt;p&gt;Gorai, Mustapha&lt;/p&gt;&lt;p&gt;Gratzfeld, Joachim&lt;/p&gt;&lt;p&gt;Griffiths, Marcus&lt;/p&gt;&lt;p&gt;Gueta, Tomer&lt;/p&gt;&lt;p&gt;Haque, Taslima&lt;/p&gt;&lt;p&gt;Herrera, Cayetano&lt;/p&gt;&lt;p&gt;Hodel, Richard&lt;/p&gt;&lt;p&gt;Hoff, Katharina&lt;/p&gt;&lt;p&gt;Ijaz, Muhammad Fazal&lt;/p&gt;&lt;p&gt;Inouye, David&lt;/p&gt;&lt;p&gt;James, Ryan&lt;/p&gt;&lt;p&gt;Jernstedt, Judy&lt;/p&gt;&lt;p&gt;Jin, Xiao-Hua&lt;/p&gt;&lt;p&gt;Johnson, Gabriel&lt;/p&gt;&lt;p&gt;Johnson, Mark&lt;/p&gt;&lt;p&gt;Johnson, Matthew&lt;/p&gt;&lt;p&gt;Jud, Nathan&lt;/p&gt;&lt;p&gt;Kim, Sangtae&lt;/p&gt;&lt;p&gt;Klymiuk, Ashley&lt;/p&gt;&lt;p&gt;Krieg, Christopher&lt;/p&gt;&lt;p&gt;Landis, Jacob&lt;/p&gt;&lt;p&gt;Landoni, Beatrice&lt;/p&gt;&lt;p&gt;Lara-Mondragón, Cecilia&lt;/p&gt;&lt;p&gt;Larridon, Isabel&lt;/p&gt;&lt;p&gt;Legland, David&lt;/p&gt;&lt;p&gt;Leroy, Thibault&lt;/p&gt;&lt;p&gt;Liang, Zhikai&lt;/p&gt;&lt;p&gt;Liesenberg, Veraldo&lt;/p&gt;&lt;p&gt;Lobdell, Matthew&lt;/p&gt;&lt;p&gt;Lücking, Robert&lt;/p&gt;&lt;p&gt;Machado-Neto, Nelson&lt;/p&gt;&lt;p&gt;Marchant, Blaine&lt;/p&gt;&lt;p&gt;Marimuthu, MohanPremAnand&lt;/p&gt;&lt;p&gt;Marks, Elias&lt;/p&gt;&lt;p&gt;Maruthachalam, Ravi&lt;/p&gt;&lt;p&gt;Mata Rosas, Martin&lt;/p&gt;&lt;p&gt;Mathys, Aurore&lt;/p&gt;&lt;p&gt;McCormick, Melissa&lt;/p&gt;&lt;p&gt;McDaniel, Stuart&lt;/p&gt;&lt;p&gt;Mehta, Angela&lt;/p&gt;&lt;p&gt;Meng, Xiaoxi&lt;/p&gt;&lt;p&gt;Monks, Leonie&lt;/p&gt;&lt;p&gt;Moyers, Brook&lt;/p&gt;&lt;p&gt;Mseddi, Khalil&lt;/p&gt;&lt;p&gt;Nath, Onkar&lt;/p&gt;&lt;p&gt;O'Connor, Rory&lt;/p&gt;&lt;p&gt;Olsson, Sanna&lt;/p&gt;&lt;p&gt;Oraby, Hanaa A. S.&lt;/p&gt;&lt;p&gt;Osmundson, Todd&lt;/p&gt;&lt;p&gt;Oso, Oluwatobi&lt;/p&gt;&lt;p&gt;Padilla-García, Nélida&lt;/p&gt;&lt;p&gt;Pelosi, Jessie&lt;/p&gt;&lt;p&gt;Pence, Valerie&lt;/p&gt;&lt;p&gt;Phartyal, Shyam&lt;/p&gt;&lt;p&gt;Popova, Elena&lt;/p&gt;&lt;p&gt;Pritchard, Hugh&lt;/p&gt;&lt;p&gt;Przelomska, Natalia&lt;/p&gt;&lt;p&gt;Pucker, Boas&lt;/p&gt;&lt;p&gt;Rezadoost, Mohammad Hossein&lt;/p&gt;&lt;p&gt;Royer, Anne&lt;/p&gt;&lt;p&gt;Rzanny, Michael&lt;/p&gt;&lt;p&gt;Saggiomo, Vittorio&lt;/p&gt;&lt;p&gt;Saroja, Seethapathy G.&lt;/p&gt;&lt;p&gt;Sassone, Agostina&lt;/p&gt;&lt;p&gt;Schmitt, Sylvain&lt;/p&gt;&lt;p&gt;Scott, Michael&lt;/p&gt;&lt;p&gt;Sedio, Brian&lt;/p&gt;&lt;p&gt;Shan, Shengchen&lt;/p&gt;&lt;p&gt;Shi, Rui&lt;/p&gt;&lt;p&gt;Siniscalchi, Carolina M.&lt;/p&gt;&lt;p&gt;Smith, Stacey&lt;/p&gt;&lt;p&gt;Stutz, Samantha&lt;/p&gt;&lt;p&gt;Sudianto, Edi&lt;/p&gt;&lt;p&gt;Takekawa, John&lt;/p&gt;&lt;p&gt;Teixeira-Costa, Luiza&lt;/p&gt;&lt;p&gt;Thybring, Emil Engelund&lt;/p&gt;&lt;p&gt;Tippery, Nicholas&lt;/p&gt;&lt;p&gt;Van De Verg, Scott&lt;/p&gt;&lt;p&gt;Walle","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11511","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10755294","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}
引用次数: 0
Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections 应用改良元条形码方法对真菌标本进行测序
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-02-02 DOI: 10.1002/aps3.11508
C. Gary Olds, Jessie W. Berta-Thompson, Justin J. Loucks, Richard A. Levy, Andrew W. Wilson
{"title":"Applying a modified metabarcoding approach for the sequencing of macrofungal specimens from fungarium collections","authors":"C. Gary Olds,&nbsp;Jessie W. Berta-Thompson,&nbsp;Justin J. Loucks,&nbsp;Richard A. Levy,&nbsp;Andrew W. Wilson","doi":"10.1002/aps3.11508","DOIUrl":"10.1002/aps3.11508","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Fungaria are an underutilized resource for understanding fungal biodiversity. The effort and cost of producing DNA barcode sequence data for large numbers of fungal specimens can be prohibitive. This study applies a modified metabarcoding approach that provides a labor-efficient and cost-effective solution for sequencing the fungal DNA barcodes of hundreds of specimens at once.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We applied a two-step PCR approach using nested, barcoded primers to sequence the fungal nrITS2 region of 766 macrofungal specimens using the Illumina platform. The specimens represent a broad taxonomic sampling of the Dikarya. Of these, 382 <i>Lactarius</i> specimens were analyzed to identify molecular operational taxonomic units (MOTUs) using a phylogenetic approach. The raw sequences were trimmed, filtered, assessed, and analyzed using the DADA2 amplicon de-noising toolkit and Biopython. The sequences were compared to the NCBI and UNITE databases and Sanger nrITS sequences from the same specimens.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The taxonomic identities derived from the nrITS2 sequence data were &gt;90% accurate across all specimens sampled. A phylogenetic analysis of the <i>Lactarius</i> sequences identified 20 MOTUs.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>The results demonstrate the capacity of these methods to produce nrITS2 sequences from large numbers of fungarium specimens. This provides an opportunity to more effectively use fungarium collections to advance fungal diversity identification and documentation.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11508","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10768797","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}
引用次数: 0
DNA release from plant tissue using focused ultrasound extraction (FUSE) 聚焦超声提取(FUSE)技术从植物组织中释放DNA
IF 3.6 3区 生物学
Applications in Plant Sciences Pub Date : 2023-01-28 DOI: 10.1002/aps3.11510
Alexia Stettinius, Hal Holmes, Qian Zhang, Isabelle Mehochko, Misa Winters, Ruby Hutchison, Adam Maxwell, Jason Holliday, Eli Vlaisavljevich
{"title":"DNA release from plant tissue using focused ultrasound extraction (FUSE)","authors":"Alexia Stettinius,&nbsp;Hal Holmes,&nbsp;Qian Zhang,&nbsp;Isabelle Mehochko,&nbsp;Misa Winters,&nbsp;Ruby Hutchison,&nbsp;Adam Maxwell,&nbsp;Jason Holliday,&nbsp;Eli Vlaisavljevich","doi":"10.1002/aps3.11510","DOIUrl":"10.1002/aps3.11510","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Sample preparation in genomics is a critical step that is often overlooked in molecular workflows and impacts the success of downstream genetic applications. This study explores the use of a recently developed focused ultrasound extraction (FUSE) technique to enable the rapid release of DNA from plant tissues for genetic analysis.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>FUSE generates a dense acoustic cavitation bubble cloud that pulverizes targeted tissue into acellular debris. This technique was applied to leaf samples of American chestnut (<i>Castanea dentata</i>), tulip poplar (<i>Liriodendron tulipifera</i>), red maple (<i>Acer rubrum</i>), and chestnut oak (<i>Quercus montana</i>).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We observed that FUSE can extract high quantities of DNA in 9–15 min, compared to the 30 min required for control DNA extraction methods. FUSE extracted DNA quantities of 24.33 ± 6.51 ng/mg and 35.32 ± 9.21 ng/mg from American chestnut and red maple, respectively, while control methods yielded 6.22 ± 0.87 ng/mg and 11.51 ± 1.95 ng/mg, respectively. The quality of the DNA released by FUSE allowed for successful amplification and next-generation sequencing.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>These results indicate that FUSE can improve DNA extraction efficiency for leaf tissues. Continued development of this technology aims to adapt to field-deployable systems to increase the cataloging of genetic biodiversity, particularly in low-resource biodiversity hotspots.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"11 1","pages":""},"PeriodicalIF":3.6,"publicationDate":"2023-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/df/34/APS3-11-e11510.PMC9934592.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10768800","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}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信