Applications in Plant Sciences最新文献

{"title":"Making sense of complexity: Advances in bioinformatics for plant biology","authors":"Katie Emelianova,&nbsp;Diego Mauricio Riaño-Pachón,&nbsp;Maria Fernanda Torres Jimenez","doi":"10.1002/aps3.11538","DOIUrl":"10.1002/aps3.11538","url":null,"abstract":"<p>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, <span>2011</span>). Subsequently co-opted to describe the sequencing and analysis of molecules (from nucleic acids to proteins), bioinformatics has diverse applications including the analysis, visualization, storage, and generation of data relating to living organisms and the molecular information they carry. Plant biology has reaped dividends from the development and maturation of bioinformatics; it has not only extended our understanding of model plant species such as <i>Arabidopsis thaliana</i> (Cantó-Pastor et al., <span>2021</span>) but also driven innovative solutions to characterize non-model species (Nevado et al., <span>2014</span>). Both avenues of discovery contribute to key objectives in improving food security, conservation, and biotechnology.</p><p>The size and complexity of many plant genomes has historically made their analysis financially and computationally difficult. Frequent polyploidy and repeat element expansion make the elucidation of plant genome sequences challenging (Soltis et al., <span>2015</span>). Furthermore, high heterozygosity in wild populations, pervasive hybridization, and a lack of inbred lines present roadblocks to analyses such as read mapping and assembly (Kajitani et al., <span>2019</span>). Long-read technologies have become ever more accessible in recent years, and algorithmic advances have accommodated sequential updates to error models, read lengths, and library types (Michael and VanBuren, <span>2020</span>). Moreover, novel methods to scaffold contigs and obtain long-range interaction information have driven impressive improvements in genome assembly quality, making telomere-to-telomere genome sequencing projects an achievable goal for many labs (Kress et al., <span>2022</span>).</p><p>Long-read technologies paired with novel mapping algorithms have fueled discovery of new transposable element (TE) dynamics, and there has been an associated resurgence of interest in their role in adaptive trait evolution and phenotypic variation (Schrader and Schmitz, <span>2019</span>; Pimpinelli and Piacentini, <span>2020</span>). Bioinformatics developments in this field have led to vast improvements in our ability to detect complex TE mobilization patterns such as nested insertions and structural variants (Bree et al., <span>2022</span>; Lemay et al., <span>2022</span>). Despite these advancements, characterization and annotation of genomic features such as genes and repetitive elements remain challenging due to species-specific genomic configurations, taxonomically patchy reference databases, and a lack of robust benchmarking and quality control. While structural and functional annotation methods still have significant obstacles to ov","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11538","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44733584","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}

{"title":"Welcome to the big leaves: Best practices for improving genome annotation in non-model plant genomes","authors":"Vidya S. Vuruputoor,&nbsp;Daniel Monyak,&nbsp;Karl C. Fetter,&nbsp;Cynthia Webster,&nbsp;Akriti Bhattarai,&nbsp;Bikash Shrestha,&nbsp;Sumaira Zaman,&nbsp;Jeremy Bennett,&nbsp;Susan L. McEvoy,&nbsp;Madison Caballero,&nbsp;Jill L. Wegrzyn","doi":"10.1002/aps3.11533","DOIUrl":"10.1002/aps3.11533","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>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, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein-coding gene predictions.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The impact of repeat masking, long-read and short-read inputs, and de novo and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The annotations were benchmarked for structural traits and sequence similarity.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Benchmarks that reflect gene structures, reciprocal similarity search alignments, and mono-exonic/multi-exonic gene counts provide a more complete view of annotation accuracy. Transcripts derived from RNA-read alignments alone are not sufficient for genome annotation. Gene prediction workflows that combine evidence-based and ab initio approaches are recommended, and a combination of short and long reads can improve genome annotation. Adding protein evidence from de novo assemblies, genome-guided transcriptome assemblies, or full-length proteins from OrthoDB generates more putative false positives as implemented in the current workflows. Post-processing with functional and structural filters is highly recommended.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>While the annotation of non-model plant genomes remains complex, this study provides recommendations for inputs and methodological approaches. We discuss a set of best practices to generate an optimal plant genome annotation and present a more robust set of metrics to evaluate the resulting predictions.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11533","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10050062","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}

{"title":"LoCoLotive: In silico mining for low-copy nuclear loci based on target capture probe sets and arbitrary reference genomes","authors":"Ulrich Lautenschlager,&nbsp;Agnes Scheunert","doi":"10.1002/aps3.11535","DOIUrl":"10.1002/aps3.11535","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>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 loci for a taxon of interest.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Target sequences used for probe design are filtered based on an assembled reference genome, resulting in presumably intron-containing single-copy loci as present in the reference taxon. The applicability of the proposed approach is demonstrated based on two probe kits (universal and family-specific) in combination with several publicly available reference genomes.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Guided by commercial probe kits, LoCoLotive enables fast and cost-efficient marker mining. Its accuracy mainly depends on the quality of the reference genome and its relatedness to the taxa under study.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11535","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46096480","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}

{"title":"hybpiper-nf and paragone-nf: Containerization and additional options for target capture assembly and paralog resolution","authors":"Chris Jackson,&nbsp;Todd McLay,&nbsp;Alexander N. Schmidt-Lebuhn","doi":"10.1002/aps3.11532","DOIUrl":"10.1002/aps3.11532","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>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 groups are computationally efficient and broadly applicable to non-model organisms, especially in the absence of a known species tree.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We containerized and expanded the functionality of both HybPiper and a pipeline for the inference of ortholog groups, providing novel options for the treatment of target capture sequence data, and allowing seamless use of the outputs of the former as inputs for the latter. The Singularity container presented here includes all dependencies, and the corresponding pipelines (hybpiper-nf and paragone-nf, respectively) are implemented via two Nextflow scripts for easier deployment and to vastly reduce the number of commands required for their use.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The hybpiper-nf and paragone-nf pipelines are easily installed and provide a user-friendly experience and robust results to the phylogenetic community. They are used by the Australian Angiosperm Tree of Life project. The pipelines are available at https://github.com/chrisjackson-pellicle/hybpiper-nf and https://github.com/chrisjackson-pellicle/paragone-nf.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f4/1c/APS3-11-e11532.PMC10439820.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10046655","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}

{"title":"Improved image processing for 3D virtual object construction from serial sections reveals tissue patterns in root tips of Zea mays","authors":"Yasushi Miki,&nbsp;Susumu Saito,&nbsp;Teruo Niki,&nbsp;Daniel K. Gladish","doi":"10.1002/aps3.11531","DOIUrl":"10.1002/aps3.11531","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>In order to obtain improved digital images and a virtual 3D object (cuboid), GIMP 2.10 and ImageJ 2.3.0 running on a laptop computer were used. Sectional views of the cuboid and 3D visualization were realized with use of the plug-ins “Volume Viewer” and “3D Viewer” in ImageJ.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>A 3D object was constructed and sectional views along several cutting planes were generated. The 3D object consisted of selected tissues inside the cuboid that were extracted and visualized from the original section data, and an animated video of the 3D construct was also produced.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Virtual cuboids can be constructed by stacking longitudinal images along the transverse depth direction or stacking transverse images vertically along the organ axis, with both generating similar 3D objects. Which to use depends on the purpose of the investigation: if the vertical cell structures need close examination, the former method may be better, but for more general spatial evaluations or for evaluation of organs over longer tissue distances than can be accommodated with longitudinal sectioning, the latter method should be chosen.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11531","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43230397","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}

{"title":"Emerging methods in botanical DNA/RNA extraction","authors":"Nora Mitchell,&nbsp;Edward V. McAssey,&nbsp;Richard G. J. Hodel","doi":"10.1002/aps3.11530","DOIUrl":"10.1002/aps3.11530","url":null,"abstract":"<p>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 of botanical studies using DNA or RNA data (Egan et al., <span>2012</span>). Yet, the crucial step of extracting these nucleic acids from plant tissues can be extremely difficult and is often overlooked or under-emphasized. Although there are many options for nucleic acid kits and nearly countless papers (over 22,000 at the time of this special issue) referencing a “modified” version of the Doyle and Doyle (<span>1987</span>) cetyltrimethylammonium bromide (CTAB) extraction protocol, taxon-specific difficulties render many of these methods ineffective. Troubleshooting the extraction step remains a major sink of researchers' time and energy, potentially acting as a barrier to downstream analyses and answering fundamental botanical questions.</p><p>Difficulties in nucleic acid extraction arise due to factors such as the diversity and volume of secondary metabolites expressed by plants (Varma et al., <span>2007</span>), degradation during storage (Pyle and Adams, <span>1989</span>), contamination from DNA of organisms in the plant microbiome (Trivedi et al., <span>2022</span>), and the need for high-molecular-weight nucleic acids for downstream analyses (Pollard et al., <span>2018</span>). Addressing these issues requires knowledge of both the underlying chemistry involved during each step of the extraction process and the requirements of the isolated product. The 12 papers in this special issue, “Emerging Methods in Botanical DNA/RNA Extraction,” highlight the current state of knowledge in nucleic acid extractions, including both the key challenges and creative innovations that have been developed to circumvent these difficulties to address a variety of exciting botanical questions.</p><p>N.M. prepared the first draft of the manuscript. All authors provided select article summaries and reviewing and editing assistance and approved the final version of the manuscript.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11530","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49607037","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}

{"title":"A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring","authors":"Jonathan Selz,&nbsp;Nicolas R. Adam,&nbsp;Céline E. M. Magrini,&nbsp;Fulvia Malvido Montandon,&nbsp;Sven Buerki,&nbsp;Sebastian J. Maerkl","doi":"10.1002/aps3.11529","DOIUrl":"10.1002/aps3.11529","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Two sets of DNA extractions were conducted on 13 species spanning various leaf anatomies and phylogenetic lineages: (i) fresh leaves were punched with custom polymeric microneedle patches to recover genomic DNA, or (ii) QIAGEN DNA extractions. Three plastid (<i>matK</i>, <i>rbcL</i>, and <i>trnH-psbA</i>) and one nuclear ribosomal (ITS) DNA regions were amplified and sequenced using Sanger or nanopore technology. The proposed method reduced the extraction time to 1 min and yielded the same DNA sequences as the QIAGEN extractions.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our drastically faster and simpler method is compatible with nanopore sequencing and is suitable for multiple applications, including high-throughput DNA-based species identifications and monitoring.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11529","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9764040","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}

{"title":"Modified CTAB protocols for high-molecular-weight DNA extractions from ferns","authors":"Pei-Jun Xie,&nbsp;Ya-Ting Ke,&nbsp;Li-Yaung Kuo","doi":"10.1002/aps3.11526","DOIUrl":"10.1002/aps3.11526","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We describe two modified CTAB protocols, with key adjustments to minimize mechanical disruption during lysis to prevent DNA shearing. One of these protocols uses a small amount of fresh tissue but yields a considerable quantity of HMW DNA with high efficiency. The other accommodates a large amount of input tissue, adopts an initial step of nuclei isolation, and thus ensures a high yield in a short period of time. Both methods were proven to be robust and effective in obtaining HMW DNA from diverse fern lineages, including 33 species in 19 families. The DNA extractions mostly had high DNA integrity, with mean sizes larger than 50 kbp, as well as high purity (A₂₆₀/A₂₃₀ and A₂₆₀/A₂₈₀ &gt; 1.8).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This study provides HMW DNA extraction protocols for ferns in the hope of facilitating further attempts to sequence their genomes, which will bridge our genomic understanding of land plant diversity.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/32/c2/APS3-11-e11526.PMC10278929.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9709978","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}

{"title":"Testing protocols to optimize DNA extraction from tough leaf tissue: A case study in Encephalartos","authors":"Maia M. Jones,&nbsp;Nathalie S. Nagalingum,&nbsp;Vanessa M. Handley","doi":"10.1002/aps3.11525","DOIUrl":"https://doi.org/10.1002/aps3.11525","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>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 of high-quality DNA. Cycads in the genus <i>Encephalartos</i> exemplify these challenges, as this group of plants is fortified for life in harsh, dry habitats with notoriously thick and rigid leaves.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>Using a DNA extraction kit, we tested three methods of mechanical disruption and examined the differences between stored vs. freshly collected samples and mature vs. senescing leaflets. We found that the manual method of pulverizing tissue yields the highest concentrations of DNA, and that both senescing leaflets and leaflet tissue that has been stored for extended periods yield sufficient DNA for genomic analyses.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>These findings shed light on the feasibility of using senescing leaves and/or tissue that has been stored on silica for long periods of time when attempting to extract large amounts of DNA. We provide here an optimized DNA extraction protocol that can be applied to cycads and other plant groups with tough or rigid leaves.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11525","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50150733","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}

{"title":"High-molecular-weight DNA extraction for long-read sequencing of plant genomes: An optimization of standard methods","authors":"Myoungbo Kang,&nbsp;Andre Chanderbali,&nbsp;Seungyeon Lee,&nbsp;Douglas E. Soltis,&nbsp;Pamela S. Soltis,&nbsp;Sangtae Kim","doi":"10.1002/aps3.11528","DOIUrl":"10.1002/aps3.11528","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>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.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We present a HMW DNA extraction method that combines (1) a nuclei extraction method followed by (2) a traditional cetyltrimethylammonium bromide (CTAB) DNA extraction method for plants with optimized extraction conditions that influence HMW DNA recovery. Our protocol produced DNA fragments (percentage of fragments &gt;20 kbp) that were, on average, ca. five times longer than those obtained using a commercial kit, and contaminants were removed more effectively.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This effective HMW DNA extraction protocol can be used as a standard protocol for a diverse array of taxa, which will enhance plant genomic research.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":null,"pages":null},"PeriodicalIF":3.6,"publicationDate":"2023-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://bsapubs.onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.11528","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9764041","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}