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Sequencing vs. amplification for the estimation of allele dosages in sugarcane (Saccharum spp.) Appl. Plant Sci. (IF 3.6) Pub Date : 2024-03-14 Hugo Jaimes, Alejandra Londoño, Carolina Saavedra‐Diaz, Jhon Henry Trujillo‐Montenegro, Jershon López‐Gerena, John J. Riascos, Fernando S. Aguilar
PremiseDetecting single‐nucleotide polymorphisms (SNPs) in a cost‐effective way is fundamental in any plant breeding pipeline. Here, we compare three genotyping techniques for their ability to reproduce the allele dosage of SNPs of interest in sugarcane (Saccharum spp.).MethodsTo identify a reproducible technique to estimate allele dosage for the validation of SNP markers, the correlation between Flex‐Seq
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Data‐centric species distribution modeling: Impacts of modeler decisions in a case study of invasive European frog‐bit Appl. Plant Sci. (IF 3.6) Pub Date : 2024-03-12 Sara E. Hansen, Michael J. Monfils, Rachel A. Hackett, Ryan T. Goebel, Anna K. Monfils
PremiseSpecies distribution models (SDMs) are widely utilized to guide conservation decisions. The complexity of available data and SDM methodologies necessitates considerations of how data are chosen and processed for modeling to enhance model accuracy and support biological interpretations and ecological applications.MethodsWe built SDMs for the invasive aquatic plant European frog‐bit using aggregated
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Using disposable food packaging materials as printing, embedding, and sectioning media in the plant anatomy lab Appl. Plant Sci. (IF 3.6) Pub Date : 2024-02-26 Guillermo Angeles, Carolina Madero‐Vega
PremiseDuring 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
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Acknowledgment of Reviewers Appl. Plant Sci. (IF 3.6) Pub Date : 2024-02-17
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. Adit, Arjun Arora, Rajeev Arstingstall, Katherine Ávila-Lovera
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Use of electrolyte leakage to assess floral damage after freezing Appl. Plant Sci. (IF 3.6) Pub Date : 2024-02-20 Jessica A. Savage, Sydney J. Hudzinski, Mady R. Olson
PremiseWith 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 ResultsWe examined the effectiveness of a modified electrolyte leakage
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Orchid fruit and root movement analyzed using 2D photographs and a bioinformatics pipeline for processing sequential 3D scans Appl. Plant Sci. (IF 3.6) Pub Date : 2024-02-09 Dewi Pramanik, Lotta Vaskimo, K. Joost Batenburg, Alexander Kostenko, Kevin Droppert, Erik Smets, Barbara Gravendeel
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.
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Simulating pollen flow and field sampling constraints helps revise seed sampling recommendations for conserving genetic diversity Appl. Plant Sci. (IF 3.6) Pub Date : 2024-02-02 Kaylee J. Rosenberger, Sean Hoban
In this study, we use simulations to determine how pollen flow and sampling constraints can influence the genetic conservation found in seed collections.
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CuticleTrace: A toolkit for capturing cell outlines from leaf cuticle with implications for paleoecology and paleoclimatology Appl. Plant Sci. (IF 3.6) Pub Date : 2024-02-02 Benjamin A. Lloyd, Richard S. Barclay, Regan E. Dunn, Ellen D. Currano, Ayuni I. Mohamaad, Kymbre Skersies, Surangi W. Punyasena
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
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Thallus hydrophobicity: A low-cost method for understanding lichen ecophysiological responses to environmental changes Appl. Plant Sci. (IF 3.6) Pub Date : 2024-01-28 Natália Mossmann Koch, Raúl Díaz Dominguez, Ana Fávaro, Daniel Stanton
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.
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Compositae-ParaLoss-1272: A complementary sunflower-specific probe set reduces paralogs in phylogenomic analyses of complex systems Appl. Plant Sci. (IF 3.6) Pub Date : 2024-01-27 Erika R. Moore-Pollard, Daniel S. Jones, Jennifer R. Mandel
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.
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Toward an open-source 3D-printable laboratory Appl. Plant Sci. (IF 3.6) Pub Date : 2024-01-18 Mason C. McNair, Sebastian C. Cocioba, Peter Pietrzyk, Trevor W. Rife
Low-cost, repairable lab equipment is rare within the biological sciences. By lowering the costs of entry using 3D printing and open-source hardware, our goal is to empower both amateur and professional scientists to conduct research.
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An updated and extended version of the Melastomataceae probe set for target capture Appl. Plant Sci. (IF 3.6) Pub Date : 2024-01-18 Léo-Paul M. J. Dagallier, Fabián A. Michelangeli
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.
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FloraTraiter: Automated parsing of traits from descriptive biodiversity literature Appl. Plant Sci. (IF 3.6) Pub Date : 2024-01-18 Ryan A. Folk, Robert P. Guralnick, Raphael T. LaFrance
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
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Humans in the loop: Community science and machine learning synergies for overcoming herbarium digitization bottlenecks Appl. Plant Sci. (IF 3.6) Pub Date : 2024-01-03 Robert Guralnick, Raphael LaFrance, Michael Denslow, Samantha Blickhan, Mark Bouslog, Sean Miller, Jenn Yost, Jason Best, Deborah L. Paul, Elizabeth Ellwood, Edward Gilbert, Julie Allen
Among the slowest steps in the digitization of natural history collections is converting imaged labels into digital text. We present here a working solution to overcome this long-recognized efficiency bottleneck that leverages synergies between community science efforts and machine learning approaches.
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Computer vision for plant pathology: A review with examples from cocoa agriculture Appl. Plant Sci. (IF 3.6) Pub Date : 2023-12-19 Jamie R. Sykes, Katherine J. Denby, Daniel W. Franks
Plant pathogens can decimate crops and render the local cultivation of a species unprofitable. In extreme cases this has caused famine and economic collapse. Timing is vital in treating crop diseases, and the use of computer vision for precise disease detection and timing of pesticide application is gaining popularity. Computer vision can reduce labour costs, prevent misdiagnosis of disease, and prevent
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Correction to Development and characterization of microsatellite primers in the federally endangered Astragalus bibullatus (Fabaceae) Appl. Plant Sci. (IF 3.6) Pub Date : 2023-12-05
Morris, A. B., C. Scalf, A. Burleyson, L. T. Johnson, and K. Trostel. 2016. Development and characterization of microsatellite primers in the federally endangered Astragalus bibullatus (Fabaceae). Applications in Plant Sciences 4(4): e1500126. In Table 1, the reverse primer sequences for loci Abib051, Abib156, and Abib170 were incorrect. Table 1 is provided here with the corrected sequences shown in
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Candidate pathway association and genome-wide association approaches reveal alternative genetic architectures of carotenoid content in cultivated sunflower (Helianthus annuus) Appl. Plant Sci. (IF 3.6) Pub Date : 2023-12-02 Jordan A. Dowell, Chase Mason
The explosion of available genomic data poses significant opportunities and challenges for genome-wide association studies. Current approaches via linear mixed models (LMM) are straightforward but prevent flexible assumptions of an a priori genomic architecture, while Bayesian sparse LMMs (BSLMMs) allow this flexibility. Complex traits, such as specialized metabolites, are subject to various hierarchical
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Calceolariaceae809: A bait set for targeted sequencing of nuclear loci Appl. Plant Sci. (IF 3.6) Pub Date : 2023-12-02 Nicolas Medina, David C. Tank, Anahí Espíndola
The genus Calceolaria (Calceolariaceae) is emblematic of the Andes, is hypothesized to have originated as a recent, rapid radiation, and has important taxonomic needs. Additionally, the genus is a model for the study of specialized pollination systems, as its flowers are nectarless and many offer floral oils as a pollination reward collected by specialist bees. Despite their evolutionary and ecological
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Review of the cellulose acetate peel method and the physical and digital curation of coal balls Appl. Plant Sci. (IF 3.6) Pub Date : 2023-11-29 Scott R. Lakeram, Scott Elrick, Surangi W. Punyasena
Coal balls, in which fossil plants are preserved in permineralized peat deposits, have widely been described from coal deposits representing the tropical forest of the Carboniferous. Coal ball preparation techniques have evolved over the past century, with the cellulose acetate peel method becoming the standard in the 1950s. While coal ball research is not as active as it has been in the past, large
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A target enrichment probe set for resolving phylogenetic relationships in the coffee family, Rubiaceae Appl. Plant Sci. (IF 3.6) Pub Date : 2023-11-17 Laymon D. Ball, Ana M. Bedoya, Charlotte M. Taylor, Laura P. Lagomarsino
Rubiaceae is among the most species-rich plant families, as well as one of the most morphologically and geographically diverse. Currently available phylogenies have mostly relied on few genomic and plastid loci, as opposed to large-scale genomic data. Target enrichment provides the ability to generate sequence data for hundreds to thousands of phylogenetically informative, single-copy loci, which often
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Correction to Welcome to the big leaves: Best practices for improving genome annotation in non-model plant genomes Appl. Plant Sci. (IF 3.6) Pub Date : 2023-11-07
Vuruputoor, V. S., D. Monyak, K. C. Fetter, C. Webster, A. Bhattarai, B. Shrestha, S. Zaman, et al. 2023. Welcome to the big leaves: Best practices for improving genome annotation in non-model plant genomes. Applications in Plant Sciences 11(4): e11533. Figure 4 in the published manuscript contained the following errors. Figure 4A and 4B were missing violin plots for MAKER, which should have been colored
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A standardized and efficient technique to estimate seed traits in plants with numerous small propagules Appl. Plant Sci. (IF 3.6) Pub Date : 2023-10-31 Christina Steinecke, Jeremiah Lee, Jannice Friedman
Variation in seed traits is common within and among populations of plant species and often has ecological and evolutionary implications. However, due to the time-consuming nature of manual seed measurements and the level of variability in imaging techniques, quantifying and interpreting the extent of seed variation can be challenging.
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How dense can you be? New automatic measures of vein density in angiosperm leaves Appl. Plant Sci. (IF 3.6) Pub Date : 2023-10-31 Walton A. Green, Juan M. Losada
Because of the trade-off between water loss and carbon dioxide assimilation, the conductivity of the transpiration path in a leaf is an important limit on photosynthesis. Closely packed veins correspond to short paths and high assimilation rates while widely spaced veins are associated with higher resistance to flow and lower maximum photosynthetic rates. Vein length per area (VLA) has become the standard
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Advances in plant imaging across scales Appl. Plant Sci. (IF 3.6) Pub Date : 2023-10-18 Pamela S. Soltis, Luiza Teixeira-Costa, Pierre Bonnet, R. Gil Nelson
New imaging technologies are dramatically transforming all of biology. From remote sensing of continents to computed tomography (CT) scanning of individual organisms or parts of organisms, novel views are emerging that span planetary to suborganismal scales. In plant biology, observations from satellites (e.g., Deneu et al., 2021; Cavender-Bares et al., 2022) and airborne instruments (e.g., Sun et
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3D pollination biology using micro-computed tomography and geometric morphometrics in Theobroma cacao Appl. Plant Sci. (IF 3.6) Pub Date : 2023-10-17 Katherine A. Wolcott, Edward L. Stanley, Osman A. Gutierrez, Stefan Wuchty, Barbara Ann Whitlock
Imaging technologies that capture three-dimensional (3D) variation in floral morphology at micro- and nano-resolutions are increasingly accessible. In herkogamous flowers, such as those of Theobroma cacao, structural barriers between anthers and stigmas represent bottlenecks that restrict pollinator size and access to reproductive organs. To study the unresolved pollination biology of cacao, we present
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Rapid imaging in the field followed by photogrammetry digitally captures the otherwise lost dimensions of plant specimens Appl. Plant Sci. (IF 3.6) Pub Date : 2023-10-16 Nicole James, Alex Adkinson, Austin Mast
We recognized the need for a customized imaging protocol for plant specimens at the time of collection for the purpose of three-dimensional (3D) modeling, as well as the lack of a broadly applicable photogrammetry protocol that encompasses the heterogeneity of plant specimen geometries and the challenges introduced by processes such as wilting.
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From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2 Appl. Plant Sci. (IF 3.6) Pub Date : 2023-10-16 William N. Weaver, Stephen A. Smith
Quantitative plant traits play a crucial role in biological research. However, traditional methods for measuring plant morphology are time consuming and have limited scalability. We present LeafMachine2, a suite of modular machine learning and computer vision tools that can automatically extract a base set of leaf traits from digital plant data sets.
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A pipeline for the rapid collection of color data from photographs Appl. Plant Sci. (IF 3.6) Pub Date : 2023-10-06 Yvonne Luong, Ariel Gasca-Herrera, Tracy M. Misiewicz, Benjamin E. Carter
There are relatively few studies of flower color at landscape scales that can address the relative importance of competing mechanisms (e.g., biotic: pollinators; abiotic: ultraviolet radiation, drought stress) at landscape scales.
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FieldPrism: A system for creating snapshot vouchers from field images using photogrammetric markers and QR codes Appl. Plant Sci. (IF 3.6) Pub Date : 2023-09-28 William N. Weaver, Stephen A. Smith
Field images are important sources of information for research in the natural sciences. However, images that lack photogrammetric scale bars, including most iNaturalist observations, cannot yield accurate trait measurements. We introduce FieldPrism, a novel system of photogrammetric markers, QR codes, and software to automate the curation of snapshot vouchers.
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A maceration technique for soft plant tissue without hazardous chemicals Appl. Plant Sci. (IF 3.6) Pub Date : 2023-09-18 Phillip C. Klahs, Elizabeth K. McMurchie, Jordan J. Nikkel, Lynn G. Clark
Current methods for maceration of plant tissue use hazardous chemicals. The new method described here improves the safety of dissection and maceration of soft plant tissues for microscopic imaging by using the harmless enzyme pectinase.
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Spatially resolved detection of small molecules from press-dried plant tissue using MALDI imaging Appl. Plant Sci. (IF 3.6) Pub Date : 2023-09-11 Zane G. Long, Jonathan V. Le, Benjamin B. Katz, Belen G. Lopez, Emily D. Tenenbaum, Bonnie Semmling, Ryan J. Schmidt, Felix Grün, Carter T. Butts, Rachel W. Martin
Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a chemical imaging method that can visualize spatial distributions of particular molecules. Plant tissue imaging has so far mostly used cryosectioning, which can be impractical for the preparation of large-area imaging samples, such as full flower petals. Imaging unsectioned plant tissue presents its own difficulties
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A comparison of methods for excluding light from stems to evaluate stem photosynthesis Appl. Plant Sci. (IF 3.6) Pub Date : 2023-09-04 Nadia A. Valverdi, Camilla Acosta, Gabriella R. Dauber, Gregory R. Goldsmith, Eleinis Ávila-Lovera
A comparison of methods using different materials to exclude light from stems to prevent stem CO2 exchange (i.e., photosynthesis), without affecting stem conductance to water vapor, surface temperature, and relative humidity, was conducted on stems of avocado trees in California.
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Correction to GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data Appl. Plant Sci. (IF 3.6) Pub Date : 2023-09-02
Sessa, E. B., R. R. Masalia, N. Arrigo, M. S. Barker, and J. A. Pelosi. 2023. GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data. Applications in Plant Sciences 11(4): e11536. In the Acknowledgments, a grant number was left out of the sentence “Funding was provided by the National Science Foundation (DEB #1844930 to E.B.S.).” This should have read “Funding
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RootBot: High-throughput root stress phenotyping robot Appl. Plant Sci. (IF 3.6) Pub Date : 2023-08-28 Mia Ruppel, Sven K. Nelson, Grace Sidberry, Madison Mitchell, Daniel Kick, Shawn K. Thomas, Katherine E. Guill, Melvin J. Oliver, Jacob D. Washburn
Higher temperatures across the globe are causing an increase in the frequency and severity of droughts. In agricultural crops, this results in reduced yields, financial losses, and increased food costs at the supermarket. Root growth maintenance in drying soils plays a major role in a plant's ability to survive and perform under drought, but phenotyping root growth is extremely difficult due to roots
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Correction to “A comparison of freezer-stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming” Appl. Plant Sci. (IF 3.6) Pub Date : 2023-08-19
McAssey, E. V., Downs, C., Yorkston, M., Morden, C., and Heyduk, K. 2023. A comparison of freezer-stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming. Applications in Plant Sciences 11(3): e11527 A statistical error was found after article publication. The relevant text from the Results section is provided below, with the corrected values shown in bold text. The error
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Using photogrammetry to create virtual permanent plots in rare and threatened plant communities Appl. Plant Sci. (IF 3.6) Pub Date : 2023-08-18 Andrea J. Tirrell, Aaron E. Putnam, Michael I. J. Cianchette, Jacquelyn L. Gill
Many plant communities across the world are undergoing changes due to climate change, human disturbance, and other threats. These community-level changes are often tracked with the use of permanent vegetative plots, but this approach is not always feasible. As an alternative, we propose using photogrammetry, specifically photograph-based digital surface models (DSMs) developed using structure-from-motion
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GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data Appl. Plant Sci. (IF 3.6) Pub Date : 2023-08-11 Emily B. Sessa, Rishi R. Masalia, Nils Arrigo, Michael S. Barker, Jessie A. Pelosi
The functional annotation of genes is a crucial component of genomic analyses. A common way to summarize functional annotations is with hierarchical gene ontologies, such as the Gene Ontology (GO) Resource. GO includes information about the cellular location, molecular function(s), and products/processes that genes produce or are involved in. For a set of genes, summarizing GO annotations using pre-defined
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Target capture and genome skimming for plant diversity studies Appl. Plant Sci. (IF 3.6) Pub Date : 2023-08-10 Flávia Fonseca Pezzini, Giada Ferrari, Laura L. Forrest, Michelle L. Hart, Kanae Nishii, Catherine A. Kidner
Recent technological advances in long-read high-throughput sequencing and assembly methods have facilitated the generation of annotated chromosome-scale whole-genome sequence data for evolutionary studies; however, generating such data can still be difficult for many plant species. For example, obtaining high-molecular-weight DNA is typically impossible for samples in historical herbarium collections
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Making sense of complexity: Advances in bioinformatics for plant biology Appl. Plant Sci. (IF 3.6) Pub Date : 2023-08-09 Katie Emelianova, Diego Mauricio Riaño-Pachón, Maria Fernanda Torres Jimenez
Coined by Dutch theoretical biologists in the 1970s, the term bioinformatics originally denoted a broad concept relating to the study of information processing in biological systems, such as ecosystem interaction, neuronal messaging, and transfer of genetic information (Hogeweg, 2011). Subsequently co-opted to describe the sequencing and analysis of molecules (from nucleic acids to proteins), bioinformatics
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Welcome to the big leaves: Best practices for improving genome annotation in non-model plant genomes Appl. Plant Sci. (IF 3.6) Pub Date : 2023-08-08 Vidya S. Vuruputoor, Daniel Monyak, Karl C. Fetter, Cynthia Webster, Akriti Bhattarai, Bikash Shrestha, Sumaira Zaman, Jeremy Bennett, Susan L. McEvoy, Madison Caballero, Jill L. Wegrzyn
Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements
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LoCoLotive: In silico mining for low-copy nuclear loci based on target capture probe sets and arbitrary reference genomes Appl. Plant Sci. (IF 3.6) Pub Date : 2023-07-28 Ulrich Lautenschlager, Agnes Scheunert
Universal target enrichment probe kits are used to circumvent the individual identification of loci suitable for phylogenetic studies in a given taxon. Under certain circumstances, however, target capture can be inefficient and costly, and lower numbers of marker loci may be sufficient. We therefore propose a computational pipeline that enables the easy identification of a subset of promising candidate
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hybpiper-nf and paragone-nf: Containerization and additional options for target capture assembly and paralog resolution Appl. Plant Sci. (IF 3.6) Pub Date : 2023-07-17 Chris Jackson, Todd McLay, Alexander N. Schmidt-Lebuhn
The HybPiper pipeline has become one of the most widely used tools for the assembly of target capture data for phylogenomic analysis. After the production of locus sequences and before phylogenetic analysis, the identification of paralogs is a critical step for ensuring the accurate inference of evolutionary relationships. Algorithmic approaches using gene tree topologies for the inference of ortholog
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Improved image processing for 3D virtual object construction from serial sections reveals tissue patterns in root tips of Zea mays Appl. Plant Sci. (IF 3.6) Pub Date : 2023-07-10 Yasushi Miki, Susumu Saito, Teruo Niki, Daniel K. Gladish
Previously we described methods for generating three-dimensional (3D) virtual reconstructions of plant tissues from transverse thin sections. Here, we report the applicability of longitudinal sections and improved image-processing steps that are simpler to perform and utilize free applications.
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Emerging methods in botanical DNA/RNA extraction Appl. Plant Sci. (IF 3.6) Pub Date : 2023-06-16 Nora Mitchell, Edward V. McAssey, Richard G. J. Hodel
Analyses of nucleic acids (DNA and RNA) have become a staple tool for botanists to answer questions across a wide variety of disciplines, ranging from population genetics to biogeography, ecology, development, microbiology, physiology, and phylogenetics. The rise of “next-generation” or “high-throughput” sequencing in particular has resulted in reduced sequencing costs and an explosion in the number
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A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring Appl. Plant Sci. (IF 3.6) Pub Date : 2023-06-14 Jonathan Selz, Nicolas R. Adam, Céline E. M. Magrini, Fulvia Malvido Montandon, Sven Buerki, Sebastian J. Maerkl
A novel protocol for rapid plant DNA extraction using microneedles is proposed, which supports botanic surveys, taxonomy, and systematics. This protocol can be conducted in the field with limited laboratory skills and equipment. The protocol is validated by sequencing and comparing the results with QIAGEN spin-column DNA extractions using BLAST analyses.
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Testing protocols to optimize DNA extraction from tough leaf tissue: A case study in Encephalartos Appl. Plant Sci. (IF 3.6) Pub Date : 2023-06-14 Maia M. Jones, Nathalie S. Nagalingum, Vanessa M. Handley
Plants with stiff, leathery leaves pose a challenge for standard DNA extraction protocols. These tissues are recalcitrant to mechanical disruption via TissueLyser (or analogous devices) and are often high in secondary metabolites. These compounding factors result in low yields, which may be sufficient for PCR amplification but are generally inadequate for genomic applications that require large quantities
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Modified CTAB protocols for high-molecular-weight DNA extractions from ferns Appl. Plant Sci. (IF 3.6) Pub Date : 2023-06-14 Pei-Jun Xie, Ya-Ting Ke, Li-Yaung Kuo
Efficient protocols for extracting high-molecular-weight (HMW) DNA from ferns facilitate the long-read sequencing of their large and complex genomes. Here, we perform two cetyltrimethylammonium bromide (CTAB)-based protocols to extract HMW DNA and evaluate their applicability in diverse fern taxa for the first time.
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High-molecular-weight DNA extraction for long-read sequencing of plant genomes: An optimization of standard methods Appl. Plant Sci. (IF 3.6) Pub Date : 2023-06-13 Myoungbo Kang, Andre Chanderbali, Seungyeon Lee, Douglas E. Soltis, Pamela S. Soltis, Sangtae Kim
Developing an effective and easy-to-use high-molecular-weight (HMW) DNA extraction method is essential for genomic research, especially in the era of third-generation sequencing. To efficiently use technologies capable of generating long-read sequences, it is important to maximize both the length and purity of the extracted DNA; however, this is frequently difficult to achieve with plant samples.
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A metabarcoding protocol targeting two DNA regions to analyze root-associated fungal communities in ferns and lycophytes Appl. Plant Sci. (IF 3.6) Pub Date : 2023-06-12 Thais Guillen-Otero, Soon-Jae Lee, Cheng-Wei Chen, Peter Szoevenyi, Michael Kessler
Detailed studies of the fungi associated with lycophytes and ferns provide crucial insights into the early evolution of land plants. However, most investigations to date have assessed fern–fungus interactions based only on visual root inspection. In the present research, we establish and evaluate a metabarcoding protocol to analyze the fungal communities associated with fern and lycophyte roots.
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Balancing read length and sequencing depth: Optimizing Nanopore long-read sequencing for monocots with an emphasis on the Liliales Appl. Plant Sci. (IF 3.6) Pub Date : 2023-06-06 Gisel Y. De La Cerda, Jacob B. Landis, Evan Eifler, Adriana I. Hernandez, Fay-Wei Li, Jing Zhang, Carrie M. Tribble, Nisa Karimi, Patricia Chan, Thomas Givnish, Susan R. Strickler, Chelsea D. Specht
We present approaches used to generate long-read Nanopore sequencing reads for the Liliales and demonstrate how modifications to standard protocols directly impact read length and total output. The goal is to help those interested in generating long-read sequencing data determine which steps may be necessary for optimizing output and results.
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A comparison of freezer-stored DNA and herbarium tissue samples for chloroplast assembly and genome skimming Appl. Plant Sci. (IF 3.6) Pub Date : 2023-06-05 Edward V. McAssey, Cassidy Downs, Mitsuko Yorkston, Clifford Morden, Karolina Heyduk
The use of DNA from herbarium specimens is an increasingly important source for evolutionary studies in plant biology, particularly in cases where species are rare or difficult to obtain. Here we compare the utility of DNA from herbarium tissues to their freezer-stored DNA counterparts via the Hawaiian Plant DNA Library.
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What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol Appl. Plant Sci. (IF 3.6) Pub Date : 2023-06-02 John J. Schenk, L. Ellie Becklund, S. James Carey, Paige P. Fabre
Cetyltrimethylammonium bromide (CTAB)–based methods are widely used to isolate DNA from plant tissues, but the unique chemical composition of secondary metabolites among plant species has necessitated optimization. Research articles often cite a “modified” CTAB protocol without explicitly stating how the protocol had been altered, creating non-reproducible studies. Furthermore, the various modifications
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Ethanol preservation and pretreatments facilitate quality DNA extractions in recalcitrant plant species Appl. Plant Sci. (IF 3.6) Pub Date : 2023-06-01 Gabriel Johnson, Steven W. J. Canty, Isaac H. Lichter-Marck, Warren Wagner, Jun Wen
The preservation of plant tissues in ethanol is conventionally viewed as problematic. Here, we show that leaf preservation in ethanol combined with proteinase digestion can provide high-quality DNA extracts. Additionally, as a pretreatment, ethanol can facilitate DNA extraction for recalcitrant samples.
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Optimizing the lysis step in CTAB DNA extractions of silica-dried and herbarium leaf tissues Appl. Plant Sci. (IF 3.6) Pub Date : 2023-05-27 S. James Carey, L. Ellie Becklund, Paige P. Fabre, John J. Schenk
The use of cetyltrimethylammonium bromide (CTAB) is an effective and inexpensive method of extracting DNA from plants. The CTAB protocol is frequently modified to optimize DNA extractions, but experimental approaches rarely perturb a single variable at a time to systematically infer their effect on DNA quantity and quality.
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Optimizing efficient PCR-amplifiable DNA extraction from herbarium specimens Appl. Plant Sci. (IF 3.6) Pub Date : 2023-05-21 Fred E. Gouker, Yonghong Guo, Harlan T. Svoboda, Margaret R. Pooler
The objective of this study was to optimize an existing DNA extraction protocol for recalcitrant plant taxa to obtain high-quality DNA from preserved herbarium tissue suitable for downstream PCR applications.
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Efficient homology-based annotation of transposable elements using minimizers Appl. Plant Sci. (IF 3.6) Pub Date : 2023-05-11 Laura Natalia Gonzalez-García, Daniela Lozano-Arce, Juan Pablo Londoño, Romain Guyot, Jorge Duitama
Transposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long-read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. Unfortunately, TE annotation currently represents
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An optimized RNA extraction method for diverse leaves of Hawaiian Metrosideros, a hypervariable tree species complex Appl. Plant Sci. (IF 3.6) Pub Date : 2023-04-27 Maryam Hadi, Elizabeth A. Stacy
The isolation of RNA from trees is challenging due to the interference of polyphenols and polysaccharides with downstream processes. Furthermore, many RNA extraction protocols are time consuming and involve hazardous chemicals. To address these issues, we aimed to develop a safe protocol for high-quality RNA extraction from diverse Metrosideros taxa representing a broad range of leaf toughness, pubescence
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Infrared spectroscopy for ploidy estimation: An example in two species of Veronica using fresh and herbarium specimens Appl. Plant Sci. (IF 3.6) Pub Date : 2023-04-03 Daniele Buono, Dirk C. Albach
Polyploidy has become a central factor in plant evolutionary biological research in recent decades. Methods such as flow cytometry have revealed the widespread occurrence of polyploidy; however, its inference relies on expensive lab equipment and is largely restricted to fresh or recently dried material.
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Does sorting by color using visible and high-energy violet light improve classification of taxa in honey bee pollen pellets? Appl. Plant Sci. (IF 3.6) Pub Date : 2023-03-28 Charlie P. Bailey, Carolyn A. Sonter, Jeremy L. Jones, Sabu Pandey, Simon Haberle, Karen C. B. S. Santos, Maria L. Absy, Romina Rader
Pollen collected by honey bees from different plant species often differs in color, and this has been used as a basis for plant identification. The objective of this study was to develop a new, low-cost protocol to sort pollen pellets by color using high-energy violet light and visible light to determine whether pollen pellet color is associated with variations in plant species identity.
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Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies Appl. Plant Sci. (IF 3.6) Pub Date : 2023-03-21 Christian S. Bowman, Ryan Traband, Xuesong Wang, Sara P. Knowles, Sassoum Lo, Zhenyu Jia, Nicholi Vorsa, Ira A. Herniter
The measurement of leaf morphometric parameters from digital images can be time-consuming or restrictive when using digital image analysis softwares. The Multiple Leaf Sample Extraction System (MuLES) is a new tool that enables high-throughput leaf shape analysis with minimal user input or prerequisites, such as coding knowledge or image modification.