Robert P. Guralnick, Raphael LaFrance, Julie M. Allen, Michael W. Denslow
Premise
One of the slowest steps in digitizing natural history collections is converting labels associated with specimens into a digital data record usable for collections management and research. Here, we address how herbarium specimen labels can be converted into digital data records via extraction into standardized Darwin Core fields.
Methods
We first showcase the development of a rule-based approach and compare outcomes with a large language model–based approach, in particular ChatGPT4. We next quantified omission and commission error rates across target fields for a set of labels transcribed using optical character recognition (OCR) for both approaches. For example, we find that ChatGPT4 often creates field names that are not Darwin Core compliant while rule-based approaches often have high commission error rates.
Results
Our results suggest that these approaches each have different strengths and limitations. We therefore developed an ensemble approach that leverages the strengths of each individual method and documented that ensembling strongly reduced overall information extraction errors.
Discussion
This work shows that an ensemble approach has particular value for creating high-quality digital data records, even for complicated label content. While human validation is still needed to ensure the best possible quality, automated approaches can speed digitization of herbarium specimen labels and are likely to be broadly usable for all natural history collection types.
{"title":"Ensemble automated approaches for producing high-quality herbarium digital records","authors":"Robert P. Guralnick, Raphael LaFrance, Julie M. Allen, Michael W. Denslow","doi":"10.1002/aps3.11623","DOIUrl":"10.1002/aps3.11623","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>One of the slowest steps in digitizing natural history collections is converting labels associated with specimens into a digital data record usable for collections management and research. Here, we address how herbarium specimen labels can be converted into digital data records via extraction into standardized Darwin Core fields.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We first showcase the development of a rule-based approach and compare outcomes with a large language model–based approach, in particular ChatGPT4. We next quantified omission and commission error rates across target fields for a set of labels transcribed using optical character recognition (OCR) for both approaches. For example, we find that ChatGPT4 often creates field names that are not Darwin Core compliant while rule-based approaches often have high commission error rates.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our results suggest that these approaches each have different strengths and limitations. We therefore developed an ensemble approach that leverages the strengths of each individual method and documented that ensembling strongly reduced overall information extraction errors.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>This work shows that an ensemble approach has particular value for creating high-quality digital data records, even for complicated label content. While human validation is still needed to ensure the best possible quality, automated approaches can speed digitization of herbarium specimen labels and are likely to be broadly usable for all natural history collection types.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11623","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143112425","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}
Aarón I. Vélez-Ramírez, Juan de Dios Moreno, Uriel G. Pérez-Guerrero, Antonio M. Juarez, Hector Castillo-Arriaga, Josefina Vázquez-Medrano, Ilane Hernández-Morales
Premise
Controlling light flux density during carbon dioxide assimilation measurements is essential in photosynthesis research. Commercial lamps are expensive and are based on monochromatic light-emitting diodes (LEDs), which deviate significantly in their spectral distribution compared to sunlight.
Methods and Results
Using LED-emitted white light with a color temperature similar to sunlight, we developed a cost-effective lamp compatible with the LI-6800 Portable Photosynthesis System. When coupled with customized software, the lamp can be controlled via the LI-6800 console by a user or Python scripts. Testing and calibration show that the lamp meets the quality needed to estimate photosynthesis parameters.
Conclusions
The lamp can be built using a basic electronics lab and a 3D printer. Calibration instructions are supplied and only require equipment commonly available at plant science laboratories. The lamp is a cost-effective alternative to perform photosynthesis research coupled with the popular LI-6800 photosynthesis measuring system.
{"title":"An open-source LED lamp for use with the LI-6800 photosynthesis system","authors":"Aarón I. Vélez-Ramírez, Juan de Dios Moreno, Uriel G. Pérez-Guerrero, Antonio M. Juarez, Hector Castillo-Arriaga, Josefina Vázquez-Medrano, Ilane Hernández-Morales","doi":"10.1002/aps3.11622","DOIUrl":"10.1002/aps3.11622","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Controlling light flux density during carbon dioxide assimilation measurements is essential in photosynthesis research. Commercial lamps are expensive and are based on monochromatic light-emitting diodes (LEDs), which deviate significantly in their spectral distribution compared to sunlight.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Using LED-emitted white light with a color temperature similar to sunlight, we developed a cost-effective lamp compatible with the LI-6800 Portable Photosynthesis System. When coupled with customized software, the lamp can be controlled via the LI-6800 console by a user or Python scripts. Testing and calibration show that the lamp meets the quality needed to estimate photosynthesis parameters.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The lamp can be built using a basic electronics lab and a 3D printer. Calibration instructions are supplied and only require equipment commonly available at plant science laboratories. The lamp is a cost-effective alternative to perform photosynthesis research coupled with the popular LI-6800 photosynthesis measuring system.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11622","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143119431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jamie R. Sykes, Katherine J. Denby, Daniel W. Franks
Premise
Automated disease, weed, and crop classification with computer vision will be invaluable in the future of agriculture. However, existing model architectures like ResNet, EfficientNet, and ConvNeXt often underperform on smaller, specialised datasets typical of such projects.
Methods
We address this gap with informed data collection and the development of a new convolutional neural network architecture, PhytNet. Utilising a novel dataset of infrared cocoa tree images, we demonstrate PhytNet's development and compare its performance with existing architectures. Data collection was informed by spectroscopy data, which provided useful insights into the spectral characteristics of cocoa trees. Cocoa was chosen as a focal species due to the diverse pathology of its diseases, which pose significant challenges for detection.
Results
ResNet18 showed some signs of overfitting, while EfficientNet variants showed distinct signs of overfitting. By contrast, PhytNet displayed excellent attention to relevant features, almost no overfitting, and an exceptionally low computation cost of 1.19 GFLOPS.
Conclusions
We show that PhytNet is a promising candidate for rapid disease or plant classification and for precise localisation of disease symptoms for autonomous systems. We also show that the most informative light spectra for detecting cocoa disease are outside the visible spectrum and that efforts to detect disease in cocoa should be focused on local symptoms, rather than the systemic effects of disease.
{"title":"Tailoring convolutional neural networks for custom botanical data","authors":"Jamie R. Sykes, Katherine J. Denby, Daniel W. Franks","doi":"10.1002/aps3.11620","DOIUrl":"10.1002/aps3.11620","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Automated disease, weed, and crop classification with computer vision will be invaluable in the future of agriculture. However, existing model architectures like ResNet, EfficientNet, and ConvNeXt often underperform on smaller, specialised datasets typical of such projects.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We address this gap with informed data collection and the development of a new convolutional neural network architecture, PhytNet. Utilising a novel dataset of infrared cocoa tree images, we demonstrate PhytNet's development and compare its performance with existing architectures. Data collection was informed by spectroscopy data, which provided useful insights into the spectral characteristics of cocoa trees. Cocoa was chosen as a focal species due to the diverse pathology of its diseases, which pose significant challenges for detection.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>ResNet18 showed some signs of overfitting, while EfficientNet variants showed distinct signs of overfitting. By contrast, PhytNet displayed excellent attention to relevant features, almost no overfitting, and an exceptionally low computation cost of 1.19 GFLOPS.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>We show that PhytNet is a promising candidate for rapid disease or plant classification and for precise localisation of disease symptoms for autonomous systems. We also show that the most informative light spectra for detecting cocoa disease are outside the visible spectrum and that efforts to detect disease in cocoa should be focused on local symptoms, rather than the systemic effects of disease.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11620","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143117682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sourabh Palande, Jeremy Arsenault, Patricia Basurto-Lozada, Andrew Bleich, Brianna N. I. Brown, Sophia F. Buysse, Noelle A. Connors, Sikta Das Adhikari, Kara C. Dobson, Francisco Xavier Guerra-Castillo, Maria F. Guerrero-Carrillo, Sophia Harlow, Héctor Herrera-Orozco, Asia T. Hightower, Paulo Izquierdo, MacKenzie Jacobs, Nicholas A. Johnson, Wendy Leuenberger, Alessandro Lopez-Hernandez, Alicia Luckie-Duque, Camila Martínez-Avila, Eddy J. Mendoza-Galindo, David Cruz Plancarte, Jenny M. Schuster, Harry Shomer, Sidney C. Sitar, Anne K. Steensma, Joanne Elise Thomson, Damián Villaseñor-Amador, Robin Waterman, Brandon M. Webster, Madison Whyte, Sofía Zorilla-Azcué, Beronda L. Montgomery, Aman Y. Husbands, Arjun Krishnan, Sarah Percival, Elizabeth Munch, Robert VanBuren, Daniel H. Chitwood, Alejandra Rougon-Cardoso
Premise
The selection of Arabidopsis as a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural- or ecological-based model species were rejected, in favor of building knowledge in a species that would facilitate genome-enabled research.
Methods
Here, we examine the ability of models based on Arabidopsis gene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested on Arabidopsis data achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained on Arabidopsis data, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64.
Results
The identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance from Arabidopsis. k-nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants.
Discussion
Our data-driven results highlight that the assertion that knowledge from Arabidopsis is translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis on Arabidopsis and prioritize plant diversity.
{"title":"Expression-based machine learning models for predicting plant tissue identity","authors":"Sourabh Palande, Jeremy Arsenault, Patricia Basurto-Lozada, Andrew Bleich, Brianna N. I. Brown, Sophia F. Buysse, Noelle A. Connors, Sikta Das Adhikari, Kara C. Dobson, Francisco Xavier Guerra-Castillo, Maria F. Guerrero-Carrillo, Sophia Harlow, Héctor Herrera-Orozco, Asia T. Hightower, Paulo Izquierdo, MacKenzie Jacobs, Nicholas A. Johnson, Wendy Leuenberger, Alessandro Lopez-Hernandez, Alicia Luckie-Duque, Camila Martínez-Avila, Eddy J. Mendoza-Galindo, David Cruz Plancarte, Jenny M. Schuster, Harry Shomer, Sidney C. Sitar, Anne K. Steensma, Joanne Elise Thomson, Damián Villaseñor-Amador, Robin Waterman, Brandon M. Webster, Madison Whyte, Sofía Zorilla-Azcué, Beronda L. Montgomery, Aman Y. Husbands, Arjun Krishnan, Sarah Percival, Elizabeth Munch, Robert VanBuren, Daniel H. Chitwood, Alejandra Rougon-Cardoso","doi":"10.1002/aps3.11621","DOIUrl":"10.1002/aps3.11621","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The selection of <i>Arabidopsis</i> as a model organism played a pivotal role in advancing genomic science. The competing frameworks to select an agricultural- or ecological-based model species were rejected, in favor of building knowledge in a species that would facilitate genome-enabled research.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here, we examine the ability of models based on <i>Arabidopsis</i> gene expression data to predict tissue identity in other flowering plants. Comparing different machine learning algorithms, models trained and tested on <i>Arabidopsis</i> data achieved near perfect precision and recall values, whereas when tissue identity is predicted across the flowering plants using models trained on <i>Arabidopsis</i> data, precision values range from 0.69 to 0.74 and recall from 0.54 to 0.64.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The identity of belowground tissue can be predicted more accurately than other tissue types, and the ability to predict tissue identity is not correlated with phylogenetic distance from <i>Arabidopsis</i>. <i>k</i>-nearest neighbors is the most successful algorithm, suggesting that gene expression signatures, rather than marker genes, are more valuable to create models for tissue and cell type prediction in plants.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our data-driven results highlight that the assertion that knowledge from <i>Arabidopsis</i> is translatable to other plants is not always true. Considering the current landscape of abundant sequencing data, we should reevaluate the scientific emphasis on <i>Arabidopsis</i> and prioritize plant diversity.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"13 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11621","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143116963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Violeta Simón-Porcar, A. Jesús Muñoz-Pajares, Juan Arroyo, Steven D. Johnson
Premise
Heterostyly in plants promotes pollen transfer between floral morphs, because female and male sex organs are located at roughly reciprocal heights within the flowers of each morph. Reciprocity indices, which assess the one-dimensional variation in the height of sex organs, are used to define the phenotypic structure of heterostyly in plant populations and to make inferences about selection. Other reciprocal stylar polymorphisms (e.g., enantiostyly) may function in a similar manner to heterostyly. In-depth assessment of their potential fit with pollinators requires accounting for the multidimensional variation in the location of sex organs.
Methods and Results
We have adapted the existing reciprocity indices used for heterostylous plant populations to incorporate multidimensional data. We illustrate the computation of the adapted and original indices in the freely available R package FlowerMate.
Conclusions
FlowerMate provides fast computation of reliable indices to facilitate understanding of the evolution and function of the full diversity of reciprocal polymorphisms.
{"title":"FlowerMate: Multidimensional reciprocity and inaccuracy indices for style-polymorphic plant populations","authors":"Violeta Simón-Porcar, A. Jesús Muñoz-Pajares, Juan Arroyo, Steven D. Johnson","doi":"10.1002/aps3.11618","DOIUrl":"10.1002/aps3.11618","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Heterostyly in plants promotes pollen transfer between floral morphs, because female and male sex organs are located at roughly reciprocal heights within the flowers of each morph. Reciprocity indices, which assess the one-dimensional variation in the height of sex organs, are used to define the phenotypic structure of heterostyly in plant populations and to make inferences about selection. Other reciprocal stylar polymorphisms (e.g., enantiostyly) may function in a similar manner to heterostyly. In-depth assessment of their potential fit with pollinators requires accounting for the multidimensional variation in the location of sex organs.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We have adapted the existing reciprocity indices used for heterostylous plant populations to incorporate multidimensional data. We illustrate the computation of the adapted and original indices in the freely available R package FlowerMate.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>FlowerMate provides fast computation of reliable indices to facilitate understanding of the evolution and function of the full diversity of reciprocal polymorphisms.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"12 6","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11618","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142758745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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":"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":2.4,"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":"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":2.4,"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":2.4,"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":2.4,"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":"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":2.4,"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}
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