Luiz Henrique M. Fonseca, Pieter Asselman, Katherine R. Goodrich, Francis J. Nge, Vincent Soulé, Kathryn Mercier, Thomas L. P. Couvreur, Lars W. Chatrou
Premise
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.
Methods
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 Asimina and Deeringothamnus.
Results
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.
Discussion
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.
{"title":"Truly the best of both worlds: Merging lineage-specific and universal probe kits to maximize phylogenomic inference","authors":"Luiz Henrique M. Fonseca, Pieter Asselman, Katherine R. Goodrich, Francis J. Nge, Vincent Soulé, Kathryn Mercier, Thomas L. P. Couvreur, 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}
Nelson R. Salinas, Gil Eshel, Gloria M. Coruzzi, Rob DeSalle, Michael Tessler, Damon P. Little
Premise
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.
Methods and Results
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).
Conclusions
BAD2matrix helps simplify phylogenomic pipelines and can be downloaded from https://github.com/dpl10/BAD2matrix/tree/master under a GNU General Public License v2.
系统基因组矩阵生成的常见步骤包括生物序列拼接、形态学数据拼接、插入/删除（indel）编码、基因内容（存在/不存在）编码、去除无信息字符进行简约分析、用还原氨基酸字母记录和占用过滤。现有的软件不能使用单个程序在系统基因组规模上完成这些任务。方法和结果BAD2matrix是一个Python脚本，可以执行上述步骤，构建DNA或氨基酸序列以及形态数据的系统基因组矩阵。该脚本工作在类unix环境中（例如，LINUX, MacOS, Windows Subsystem for LINUX）。BAD2matrix有助于简化系统基因组学管道，可以在GNU通用公共许可证v2下从https://github.com/dpl10/BAD2matrix/tree/master下载。
{"title":"BAD2matrix: Phylogenomic matrix concatenation, indel coding, and more","authors":"Nelson R. Salinas, Gil Eshel, Gloria M. Coruzzi, Rob DeSalle, Michael Tessler, 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}
Jessie A. Pelosi, Ruth Davenport, W. Brad Barbazuk, Emily B. Sessa, Li-Yaung Kuo
Premise
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.
Methods
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 > 1.6, and RNA integrity numbers >7.
Conclusions
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.
{"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":"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 > 1.6, and RNA integrity numbers >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}
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.
Methods and Results
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.
Conclusions
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.
前提条件Flora e Funga do Brasil 项目是可靠记录巴西植物和真菌多样性的最全面的工作。该项目涉及数百名分类学家的合作工作，整合了在巴西各地收集到的植物、藻类和真菌的详细和标准化形态描述、命名状况和地理分布信息。方法和结果florabr是一个R软件包，开发它的目的是为了方便探索和地理分析来自巴西植物志的物种信息。florabr 的独特之处在于它能够与每周更新的最新版数据集或任何其他版本的数据集进行交互。我说明了 florabr 在生物地理学和保护研究的常见任务中的实际应用。结论预计生物地理学家、生态学家、生物收藏馆馆长以及积极为巴西植物志做出贡献的分类学家会对 florabr 产生浓厚的兴趣。
{"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}
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.
Methods
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.
Results
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.
Discussion
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.
前提杂交和多倍体化在维管束植物中很常见，通过促进物种分化和生态多样化而成为生物多样性的重要驱动力。在杂交和全多倍体生物多样性研究中进行广泛合成发现的一个主要限制因素是缺乏一个标准化框架来比较不同研究和生物尺度的数据。 方法 在这里，我提出了一种新的定量框架，用于研究和解释杂交种和异源多倍体生物学中的模式，即分歧指数（DI）。分歧指数框架产生的标准化数据在不同研究和变量之间具有可比性。为了展示如何利用 DI 框架综合数据，我分析了已发表的杂交种和异源多倍体的生化、生理和生态性状数据。我还应用了杂交种和多倍体生物学中的关键生态学和进化概念，在连续的 DI 空间中转化名义结果，包括跃迁、中间性、扩展和收缩。 结果 生化、生理、生态和进化数据都可以在 DI 框架内进行分析、可视化和解释。DI 框架尤其适用于标准化和比较不同尺度的变量。在使用 DI 框架了解生态位分异时，可以使用生态位重叠度量来补充对中心点和广度变化的认识。 讨论 DI 框架是杂交种和异源多倍体生物学的一个简单易行的框架，是一个灵活直观的工具，可用于解决植物生物多样性研究中的突出问题。
{"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}
Michael R. McKain, Ya Yang, Agnieszka Golicz, Briana L. Gross
<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
{"title":"Charting the course for new discoveries in polyploid lineages","authors":"Michael R. McKain, Ya Yang, Agnieszka Golicz, 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":"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}
Embryo 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 Results
We 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 Layia platyglossa as an example. We show how this procedure greatly increases germination compared to control treatments in Madia elegans, a close relative of Hawaiian silverswords that exhibits physiological dormancy.
Conclusions
This 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.
{"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":"10.1002/aps3.11608","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Embryo 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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We 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 <i>Layia platyglossa</i> as an example. We show how this procedure greatly increases germination compared to control treatments in <i>Madia elegans</i>, a close relative of Hawaiian silverswords that exhibits physiological dormancy.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This 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.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11608","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jacob S. Suissa, Gisel Y. De La Cerda, Leland C. Graber, Chloe Jelley, David Wickell, Heather R. Phillips, Ayress D. Grinage, Corrie S. Moreau, Chelsea D. Specht, Jeff J. Doyle, Jacob B. Landis
Premise
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.
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.
Results
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.
Discussion
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.
关于过滤单核苷酸多态性（SNP）的最佳方法，以及在系统发生组分析和后续比较方法中使用 SNP 还是包括侧翼区域（完整的 "位点"）更好，目前普遍缺乏共识。我们比较了 16 个数据集的分支长度、节点支持率和分化时间估计，这些数据集的缺失数据量和总规模各不相同。我们的结果揭示了系统发生组数据使用的五个方面，这些方面可能具有普遍适用性：（1）树拓扑结构在不同分析中基本一致；（2）严格筛选 SNP 保留率（如 90%-100%）会降低支持率，并且会影响树的分化时间、(3) SNP 数据集和基因座数据集的绝对分支长度相差两个数量级；(4) 数据类型和分支长度的变化对分歧时间的估计影响不大；(5) 系统图会改变对祖先状态和形态进化速率的估计。我们建议不要使用过高的 SNP 保留过滤阈值，以降低产生不一致拓扑和低支持度的风险。
{"title":"Data-driven guidelines for phylogenomic analyses using SNP data","authors":"Jacob S. Suissa, Gisel Y. De La Cerda, Leland C. Graber, Chloe Jelley, David Wickell, Heather R. Phillips, Ayress D. Grinage, Corrie S. Moreau, Chelsea D. Specht, Jeff J. Doyle, Jacob B. Landis","doi":"10.1002/aps3.11611","DOIUrl":"10.1002/aps3.11611","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Using genotyping-by-sequencing data from 22 <i>Glycine</i> 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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>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.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11611","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Arne Devriese, Gerrit Peeters, Rein Brys, Hans Jacquemyn
Premise
Plants 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.
Methods
In 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.
Results
All 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.
Discussion
Our 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.
前言植物与传粉昆虫之间密切互动，形成复杂的物种互动网络。最近有人提出，花粉采集的元条码是构建此类网络的一种有利方法，但多样性和群落分析在多大程度上取决于所使用的提取方法和花粉浓度仍不清楚。方法在这项研究中，我们使用了两种花粉混合物的稀释系列（模拟群落和来自熊蜂的汇集天然花粉量）来评估机械均质和两种 DNA 提取试剂盒（旋柱 DNA 提取试剂盒和磁珠 DNA 提取试剂盒）对检测到的花粉丰富度和群落组成的影响。讨论 我们的研究结果表明，这三种方法都能有效地检测昆虫花粉负载中的植物物种，即使在花粉负载量很低的情况下也是如此。然而，我们的研究结果也表明，提取方法会对正确评估昆虫花粉载荷群落组成的能力产生深远影响。因此，应仔细考虑提取方法的选择，以确保花粉多样性和群落分析结果的可靠性和公正性。
{"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":"10.1002/aps3.11601","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Plants 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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>In 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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>All 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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our 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.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11601","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Giancarlo M. Chiarenza, Eve Slavich, Angela T. Moles
Premise
Leaf chlorophyll is a fundamental bioindicator used in several fields; however, we lack clear guidelines for optimizing sampling efforts and producing comparable studies.
Methods
We 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.
Results
The 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 (<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.
Discussion
We 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.
前言叶片叶绿素是多个领域使用的基本生物指标；然而，我们缺乏明确的指导方针来优化取样工作并进行可比研究。方法我们使用无损光谱法估算了 10 种植物的叶片叶绿素含量。结果冷藏成熟叶片的叶绿素含量在约 1.5 d 内保持在原始值的 5%以内，而未冷藏成熟叶片的叶绿素含量迅速下降，这表明叶绿素含量应在 4 h 内测量。成熟叶片叶绿素含量的变化，73%在物种水平，15%在个体间，叶片内部的变化可以忽略不计（<1%）。我们建议研究人员优先对更多个体进行取样，而不是在叶片或个体内部重复测量。我们的发现将有助于研究人员优化时间和研究工作，并获得更可靠的生态数据。
{"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":"10.1002/aps3.11610","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Leaf chlorophyll is a fundamental bioindicator used in several fields; however, we lack clear guidelines for optimizing sampling efforts and producing comparable studies.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We 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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The 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 (<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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We 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.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.7,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11610","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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