During the COVID-19 pandemic lockdown, all laboratory work was suspended, and we were obliged to work from home, causing delays in our research. As the disruption to supply chains made it difficult to obtain our regular lab supplies, we were obliged to search for substitutes. We became familiar with a plastic material known as biaxially oriented polypropylene (BOPP) that is widely used in the food industry for wrapping or storing fruits, vegetables, and meat. BOPP is easily dissolved in organic solvents such as xylenes, acetone, or thinner, but these reagents are very toxic, flammable, and can cause nausea in some users. After testing several alternatives, we found a polyurethane remover that proved to be an effective and relatively harmless BOPP solvent.
Methods and Results
By dissolving thin slices of BOPP in a polyurethane solvent, we obtained a clean fluid that we used to obtain leaf surface prints that could be mounted on microscope slides with a coverslip. This fluid produced excellent bark and wood sections and can be used to obtain wood or charcoal surface prints. Our attempts to use it as a mounting medium were unsuccessful.
Conclusions
BOPP dissolved in a polyurethane remover is a handy, versatile resource for plant microtechniques. In addition to its economic advantages, it is useful in terms of reducing plastic pollution.
{"title":"Using disposable food packaging materials as printing, embedding, and sectioning media in the plant anatomy lab","authors":"Guillermo Angeles, Carolina Madero-Vega","doi":"10.1002/aps3.11570","DOIUrl":"10.1002/aps3.11570","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>During the COVID-19 pandemic lockdown, all laboratory work was suspended, and we were obliged to work from home, causing delays in our research. As the disruption to supply chains made it difficult to obtain our regular lab supplies, we were obliged to search for substitutes. We became familiar with a plastic material known as biaxially oriented polypropylene (BOPP) that is widely used in the food industry for wrapping or storing fruits, vegetables, and meat. BOPP is easily dissolved in organic solvents such as xylenes, acetone, or thinner, but these reagents are very toxic, flammable, and can cause nausea in some users. After testing several alternatives, we found a polyurethane remover that proved to be an effective and relatively harmless BOPP solvent.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>By dissolving thin slices of BOPP in a polyurethane solvent, we obtained a clean fluid that we used to obtain leaf surface prints that could be mounted on microscope slides with a coverslip. This fluid produced excellent bark and wood sections and can be used to obtain wood or charcoal surface prints. Our attempts to use it as a mounting medium were unsuccessful.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>BOPP dissolved in a polyurethane remover is a handy, versatile resource for plant microtechniques. In addition to its economic advantages, it is useful in terms of reducing plastic pollution.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11570","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139981077","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}
Jessica A. Savage, Sydney J. Hudzinski, Mady R. Olson
Premise
With growing interest in the impact of false springs on plant reproduction, there is the need to develop reliable, high-throughput methods for assessing floral freezing damage. Here we present a method for use with floral tissue that will facilitate more comparative work on floral freezing tolerance in the future.
Methods and Results
We examined the effectiveness of a modified electrolyte leakage protocol to assess floral freezing damage. By comparing data from temperature response curves to an estimate of visual tissue damage, we optimized the protocol for different floral types and improved the signal-to-noise ratio for floral data.
Conclusions
Our modified protocol provides a quick and straightforward method for quantifying floral freezing damage that can be standardized across floral types. This method allows for cross-species comparisons and can be a powerful tool for studying broad patterns in floral freezing tolerance.
{"title":"Use of electrolyte leakage to assess floral damage after freezing","authors":"Jessica A. Savage, Sydney J. Hudzinski, Mady R. Olson","doi":"10.1002/aps3.11569","DOIUrl":"10.1002/aps3.11569","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>With growing interest in the impact of false springs on plant reproduction, there is the need to develop reliable, high-throughput methods for assessing floral freezing damage. Here we present a method for use with floral tissue that will facilitate more comparative work on floral freezing tolerance in the future.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We examined the effectiveness of a modified electrolyte leakage protocol to assess floral freezing damage. By comparing data from temperature response curves to an estimate of visual tissue damage, we optimized the protocol for different floral types and improved the signal-to-noise ratio for floral data.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our modified protocol provides a quick and straightforward method for quantifying floral freezing damage that can be standardized across floral types. This method allows for cross-species comparisons and can be a powerful tool for studying broad patterns in floral freezing tolerance.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 5","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11569","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139923334","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 editors gratefully acknowledge our reviewers, who have generously given their time and expertise to review manuscripts submitted to Applications in Plant Sciences. The list includes those who reviewed manuscripts from December 31, 2022, to December 31, 2023. Thank you for helping APPS maintain a prompt and fair peer-review process.
Dewi Pramanik, Lotta Vaskimo, K. Joost Batenburg, Alexander Kostenko, Kevin Droppert, Erik Smets, Barbara Gravendeel
Premise
Most studies of the movement of orchid fruits and roots during plant development have focused on morphological observations; however, further genetic analysis is required to understand the molecular mechanisms underlying this phenomenon. A precise tool is required to observe these movements and harvest tissue at the correct position and time for transcriptomics research.
Methods
We utilized three-dimensional (3D) micro–computed tomography (CT) scans to capture the movement of fast-growing Erycina pusilla roots, and built an integrated bioinformatics pipeline to process 3D images into 3D time-lapse videos. To record the movement of slowly developing E. pusilla and Phalaenopsis equestris fruits, two-dimensional (2D) photographs were used.
Results
The E. pusilla roots twisted and resupinated multiple times from early development. The first period occurred in the early developmental stage (77–84 days after germination [DAG]) and the subsequent period occurred later in development (140–154 DAG). While E. pusilla fruits twisted 45° from 56–63 days after pollination (DAP), the fruits of P. equestris only began to resupinate a week before dehiscence (133 DAP) and ended a week after dehiscence (161 DAP).
Discussion
Our methods revealed that each orchid root and fruit had an independent direction and degree of torsion from the initial to the final position. Our innovative approaches produced detailed spatial and temporal information on the resupination of roots and fruits during orchid development.
{"title":"Orchid fruit and root movement analyzed using 2D photographs and a bioinformatics pipeline for processing sequential 3D scans","authors":"Dewi Pramanik, Lotta Vaskimo, K. Joost Batenburg, Alexander Kostenko, Kevin Droppert, Erik Smets, Barbara Gravendeel","doi":"10.1002/aps3.11567","DOIUrl":"10.1002/aps3.11567","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Most studies of the movement of orchid fruits and roots during plant development have focused on morphological observations; however, further genetic analysis is required to understand the molecular mechanisms underlying this phenomenon. A precise tool is required to observe these movements and harvest tissue at the correct position and time for transcriptomics research.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We utilized three-dimensional (3D) micro–computed tomography (CT) scans to capture the movement of fast-growing <i>Erycina pusilla</i> roots, and built an integrated bioinformatics pipeline to process 3D images into 3D time-lapse videos. To record the movement of slowly developing <i>E. pusilla</i> and <i>Phalaenopsis equestris</i> fruits, two-dimensional (2D) photographs were used.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The <i>E. pusilla</i> roots twisted and resupinated multiple times from early development. The first period occurred in the early developmental stage (77–84 days after germination [DAG]) and the subsequent period occurred later in development (140–154 DAG). While <i>E. pusilla</i> fruits twisted 45° from 56–63 days after pollination (DAP), the fruits of <i>P. equestris</i> only began to resupinate a week before dehiscence (133 DAP) and ended a week after dehiscence (161 DAP).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our methods revealed that each orchid root and fruit had an independent direction and degree of torsion from the initial to the final position. Our innovative approaches produced detailed spatial and temporal information on the resupination of roots and fruits during orchid development.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11567","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139750012","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}
Benjamin A. Lloyd, Richard S. Barclay, Regan E. Dunn, Ellen D. Currano, Ayuni I. Mohamaad, Kymbre Skersies, Surangi W. Punyasena
Premise
Leaf epidermal cell morphology is closely tied to the evolutionary history of plants and their growth environments and is therefore of interest to many plant biologists. However, cell measurement can be time consuming and restrictive with current methods. CuticleTrace is a suite of Fiji and R-based functions that streamlines and automates the segmentation and measurement of epidermal pavement cells across a wide range of cell morphologies and image qualities.
Methods and Results
We evaluated CuticleTrace-generated measurements against those from alternate automated methods and expert and undergraduate hand tracings across a taxonomically diverse 50-image data set of variable image qualities. We observed ~93% statistical agreement between CuticleTrace and expert hand-traced measurements, outperforming alternate methods.
Conclusions
CuticleTrace is a broadly applicable, modular, and customizable tool that integrates data visualization and cell shape measurement with image segmentation, lowering the barrier to high-throughput studies of epidermal morphology by vastly decreasing the labor investment required to generate high-quality cell shape data sets.
{"title":"CuticleTrace: A toolkit for capturing cell outlines from leaf cuticle with implications for paleoecology and paleoclimatology","authors":"Benjamin A. Lloyd, Richard S. Barclay, Regan E. Dunn, Ellen D. Currano, Ayuni I. Mohamaad, Kymbre Skersies, Surangi W. Punyasena","doi":"10.1002/aps3.11566","DOIUrl":"10.1002/aps3.11566","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Leaf epidermal cell morphology is closely tied to the evolutionary history of plants and their growth environments and is therefore of interest to many plant biologists. However, cell measurement can be time consuming and restrictive with current methods. CuticleTrace is a suite of Fiji and R-based functions that streamlines and automates the segmentation and measurement of epidermal pavement cells across a wide range of cell morphologies and image qualities.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We evaluated CuticleTrace-generated measurements against those from alternate automated methods and expert and undergraduate hand tracings across a taxonomically diverse 50-image data set of variable image qualities. We observed ~93% statistical agreement between CuticleTrace and expert hand-traced measurements, outperforming alternate methods.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>CuticleTrace is a broadly applicable, modular, and customizable tool that integrates data visualization and cell shape measurement with image segmentation, lowering the barrier to high-throughput studies of epidermal morphology by vastly decreasing the labor investment required to generate high-quality cell shape data sets.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11566","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139750068","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}
In this study, we use simulations to determine how pollen flow and sampling constraints can influence the genetic conservation found in seed collections.
Methods
We simulated genotypes of parental individuals and crossed the parentals based on three different ranges of pollen flow (panmictic, limited, and highly limited) to create new seed sets for sampling. We tested a variety of sampling scenarios modeled on those occurring in nature and calculated the proportion of alleles conserved in each scenario.
Results
We found that pollen flow greatly influences collection outcomes, with panmictic pollen flow resulting in seed sets containing 21.6% more alleles than limited pollen flow and 48.6% more alleles than highly limited pollen flow, although this impact diminishes when large numbers of maternal plants are sampled. Simulations of realistic seed sampling (sampling more seed from some plants and fewer from others) showed a relatively minor impact (<2.5%) on genetic diversity conserved compared to ideal sampling (uniform sampling across all maternal plants).
Discussion
We conclude that future work must consider limited pollen flow, but collectors can be flexible with their sampling in the field as long as many unique maternal plants are sampled. Simulations remain a fruitful method to advance ex situ sampling guidelines.
在这项研究中，我们通过模拟来确定花粉流动和取样限制如何影响种子采集中的遗传保护。
{"title":"Simulating pollen flow and field sampling constraints helps revise seed sampling recommendations for conserving genetic diversity","authors":"Kaylee J. Rosenberger, Sean Hoban","doi":"10.1002/aps3.11561","DOIUrl":"10.1002/aps3.11561","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>In this study, we use simulations to determine how pollen flow and sampling constraints can influence the genetic conservation found in seed collections.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We simulated genotypes of parental individuals and crossed the parentals based on three different ranges of pollen flow (panmictic, limited, and highly limited) to create new seed sets for sampling. We tested a variety of sampling scenarios modeled on those occurring in nature and calculated the proportion of alleles conserved in each scenario.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We found that pollen flow greatly influences collection outcomes, with panmictic pollen flow resulting in seed sets containing 21.6% more alleles than limited pollen flow and 48.6% more alleles than highly limited pollen flow, although this impact diminishes when large numbers of maternal plants are sampled. Simulations of realistic seed sampling (sampling more seed from some plants and fewer from others) showed a relatively minor impact (<2.5%) on genetic diversity conserved compared to ideal sampling (uniform sampling across all maternal plants).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>We conclude that future work must consider limited pollen flow, but collectors can be flexible with their sampling in the field as long as many unique maternal plants are sampled. Simulations remain a fruitful method to advance ex situ sampling guidelines.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 3","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11561","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139662266","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}
Natália Mossmann Koch, Raúl Díaz Dominguez, Ana Fávaro, Daniel Stanton
Premise
Methods to evaluate lichen thalli hydrophobicity have previously been described, but only recently has hydrophobicity been shown to be an important functional trait related to water regulation dynamics that could be used to predict future climate change effects. We describe a novel protocol to measure lichen thallus hydrophobicity that aims to be an easier and more affordable approach.
Methods and Results
Our protocol requires only a micropipette, distilled water, a tripod, and a smartphone or camera. Hydrophobicity is inferred from multiple metrics associated with the absorption times of standardized droplets (initial and total absorption time). We used a data set of 93 lichen taxa with different growth forms and from different biomes and demonstrated that this method is well suited for capturing different levels of hydrophobicity, including very hydrophilic species.
Conclusions
Our results show that this new protocol to measure lichen hydrophobicity is a rapid and low-cost method to assess an ecophysiologically based functional trait that can be used with almost no limitations, including in different climates, lichen species, and growth forms.
{"title":"Thallus hydrophobicity: A low-cost method for understanding lichen ecophysiological responses to environmental changes","authors":"Natália Mossmann Koch, Raúl Díaz Dominguez, Ana Fávaro, Daniel Stanton","doi":"10.1002/aps3.11565","DOIUrl":"10.1002/aps3.11565","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Methods to evaluate lichen thalli hydrophobicity have previously been described, but only recently has hydrophobicity been shown to be an important functional trait related to water regulation dynamics that could be used to predict future climate change effects. We describe a novel protocol to measure lichen thallus hydrophobicity that aims to be an easier and more affordable approach.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Our protocol requires only a micropipette, distilled water, a tripod, and a smartphone or camera. Hydrophobicity is inferred from multiple metrics associated with the absorption times of standardized droplets (initial and total absorption time). We used a data set of 93 lichen taxa with different growth forms and from different biomes and demonstrated that this method is well suited for capturing different levels of hydrophobicity, including very hydrophilic species.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our results show that this new protocol to measure lichen hydrophobicity is a rapid and low-cost method to assess an ecophysiologically based functional trait that can be used with almost no limitations, including in different climates, lichen species, and growth forms.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11565","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139587663","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}
Erika R. Moore-Pollard, Daniel S. Jones, Jennifer R. Mandel
Premise
A family-specific probe set for sunflowers, Compositae-1061, enables family-wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization.
Methods
We developed a Hyb-Seq probe set, Compositae-ParaLoss-1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus Packera. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 Packera taxa that were previously studied using Compositae-1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support.
Results
We report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae-1061. Most notably, Compositae-ParaLoss-1272 recovered substantially fewer paralogous sequences than Compositae-1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae-1061.
Discussion
Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae-ParaLoss-1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.
{"title":"Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems","authors":"Erika R. Moore-Pollard, Daniel S. Jones, Jennifer R. Mandel","doi":"10.1002/aps3.11568","DOIUrl":"10.1002/aps3.11568","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>A family-specific probe set for sunflowers, Compositae-1061, enables family-wide phylogenomic studies and investigations at lower taxonomic levels, but may lack resolution at genus to species levels, especially in groups complicated by polyploidy and hybridization.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We developed a Hyb-Seq probe set, Compositae-ParaLoss-1272, that targets orthologous loci in Asteraceae. We tested its efficiency across the family by simulating target enrichment sequencing in silico. Additionally, we tested its effectiveness at lower taxonomic levels in the historically complex genus <i>Packera</i>. We performed Hyb-Seq with Compositae-ParaLoss-1272 for 19 <i>Packera</i> taxa that were previously studied using Compositae-1061. The resulting sequences from each probe set, plus a combination of both, were used to generate phylogenies, compare topologies, and assess node support.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We report that Compositae-ParaLoss-1272 captured loci across all tested Asteraceae members, had less gene tree discordance, and retained longer loci than Compositae-1061. Most notably, Compositae-ParaLoss-1272 recovered substantially fewer paralogous sequences than Compositae-1061, with only ~5% of the recovered loci reporting as paralogous, compared to ~59% with Compositae-1061.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Given the complexity of plant evolutionary histories, assigning orthology for phylogenomic analyses will continue to be challenging. However, we anticipate Compositae-ParaLoss-1272 will provide improved resolution and utility for studies of complex groups and lower taxonomic levels in the sunflower family.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11568","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139587590","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}
A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae.
Methods
In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version.
Results
The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery.
Discussion
This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant-targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.
{"title":"An updated and extended version of the Melastomataceae probe set for target capture","authors":"Léo-Paul M. J. Dagallier, Fabián A. Michelangeli","doi":"10.1002/aps3.11564","DOIUrl":"10.1002/aps3.11564","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>A probe set was previously designed to target 384 nuclear loci in the Melastomataceae family; however, when trying to use it, we encountered several practical and conceptual problems, such as the presence of sequences in reverse complement, intronic regions with stop codons, and other issues. This raised concerns regarding the use of this probe set for sequence recovery in Melastomataceae.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>In order to correct these issues, we cleaned the Melastomataceae probe set, extended it with additional sequences, and compared its performance with the original version.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The final probe set targets 396 putative nuclear loci represented by 6009 template sequences. The probe set has been made available, along with details on the cleaning process, for reproducibility. We show that the new probe set performs better than the original version in terms of sequence recovery.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>This updated, extended, and cleaned probe set will improve the availability of phylogenomic resources across the Melastomataceae family. It is fully compatible with sequence recovery and extraction pipelines. The cleaning process can also be applied to any plant-targeting probe set that would need to be cleaned or updated if new genomic resources for the targeted taxa become available.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11564","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139495487","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}
Ryan A. Folk, Robert P. Guralnick, Raphael T. LaFrance
Premise
Plant trait data are essential for quantifying biodiversity and function across Earth, but these data are challenging to acquire for large studies. Diverse strategies are needed, including the liberation of heritage data locked within specialist literature such as floras and taxonomic monographs. Here we report FloraTraiter, a novel approach using rule-based natural language processing (NLP) to parse computable trait data from biodiversity literature.
Methods
FloraTraiter was implemented through collaborative work between programmers and botanical experts and customized for both online floras and scanned literature. We report a strategy spanning optical character recognition, recognition of taxa, iterative building of traits, and establishing linkages among all of these, as well as curational tools and code for turning these results into standard morphological matrices.
Results
Over 95% of treatment content was successfully parsed for traits with <1% error. Data for more than 700 taxa are reported, including a demonstration of common downstream uses.
Conclusions
We identify strategies, applications, tips, and challenges that we hope will facilitate future similar efforts to produce large open-source trait data sets for broad community reuse. Largely automated tools like FloraTraiter will be an important addition to the toolkit for assembling trait data at scale.
{"title":"FloraTraiter: Automated parsing of traits from descriptive biodiversity literature","authors":"Ryan A. Folk, Robert P. Guralnick, Raphael T. LaFrance","doi":"10.1002/aps3.11563","DOIUrl":"10.1002/aps3.11563","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Plant trait data are essential for quantifying biodiversity and function across Earth, but these data are challenging to acquire for large studies. Diverse strategies are needed, including the liberation of heritage data locked within specialist literature such as floras and taxonomic monographs. Here we report FloraTraiter, a novel approach using rule-based natural language processing (NLP) to parse computable trait data from biodiversity literature.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>FloraTraiter was implemented through collaborative work between programmers and botanical experts and customized for both online floras and scanned literature. We report a strategy spanning optical character recognition, recognition of taxa, iterative building of traits, and establishing linkages among all of these, as well as curational tools and code for turning these results into standard morphological matrices.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Over 95% of treatment content was successfully parsed for traits with <1% error. Data for more than 700 taxa are reported, including a demonstration of common downstream uses.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>We identify strategies, applications, tips, and challenges that we hope will facilitate future similar efforts to produce large open-source trait data sets for broad community reuse. Largely automated tools like FloraTraiter will be an important addition to the toolkit for assembling trait data at scale.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11563","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139495519","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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