Applications in Plant Sciences最新文献

{"title":"Detecting introgression from phylogenetic invariant site patterns using machine learning","authors":"Patrick F. McKenzie,&nbsp;Deren A. R. Eaton","doi":"10.1002/aps3.70061","DOIUrl":"https://doi.org/10.1002/aps3.70061","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Detecting historical introgression among populations or species from genomic data is a common goal in evolutionary genetics. Most current methods fall into two major categories: network inference and admixture inference. Network inference (e.g., SNaQ) is computationally challenging and typically requires first reducing large genomic datasets into a less informative collection of inferred gene trees. In contrast, admixture inference (e.g., ABBA-BABA tests) can accommodate enormous single-nucleotide polymorphism (SNP) datasets but is restricted to examining subsets of four to five samples at a time. Here, we demonstrate a new approach to evaluate SNP frequencies among quartet samples under a phylogenetic hypothesis (similar to ABBA-BABA tests), while examining all quartet information simultaneously (similar to the network inference methods).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>To do this, our method simcat trains a neural network machine learning model on coalescent simulations to discriminate between introgression scenarios based on learned SNP frequency patterns. We demonstrate the accuracy of simcat to classify introgression events from simulations, evaluate its sensitivity to variation in species tree parameters, and demonstrate its application to an empirical dataset of oak trees (<i>Quercus</i> ser. <i>Virentes</i>).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Our approach represents a first step towards leveraging machine learning to expand phylogenetic invariants–based methods beyond the scale of quartets to a larger phylogenetic context.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 3","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70061","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300057","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":"Leveraging target enrichment and genome skimming (Hyb-Seq) of herbarium collections to unlock timber DNA barcoding","authors":"Sidonie Bellot,&nbsp;Dyana Ndiade Bourobou,&nbsp;Camila Quintero-Berns,&nbsp;Laszlo Csiba,&nbsp;Peter Gasson,&nbsp;Barrett McBride,&nbsp;Bhely Angoboy Ilondea,&nbsp;Gaël U. D. Bouka,&nbsp;Emmanuel Ebanyenle,&nbsp;Cynel Gwenael Moundounga,&nbsp;Martin Ricker,&nbsp;Philomena Yarwoah,&nbsp;Guy Herman Zanguim Tchoutezou,&nbsp;Janvier Lisingo,&nbsp;Victor Deklerck","doi":"10.1002/aps3.70063","DOIUrl":"https://doi.org/10.1002/aps3.70063","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>DNA barcoding for timber species identification requires comprehensive reference datasets, informative DNA barcodes, and cost-effective protocols. We developed a workflow leveraging Hyb-Seq (target capture sequencing and genome skimming) to address these challenges, and we tested it on four genera from the mahogany family (Meliaceae).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We sequenced up to 350 nuclear and 177 plastid loci from 132 herbarium specimens representing leaf samples of 22 species. We determined the DNA barcoding potential of each locus by looking at species recovery and monophyly in gene trees. We then selected 13 short regions (candidate barcodes) within high-potential loci and tested their PCR amplification and Sanger sequencing on wood DNA.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Three candidate barcodes emerged as the most reliably sequenced from wood DNA and as providing the most accurate species-level identifications, with species monophyly rates above 80%. Failure to obtain sequences from some wood DNA extracts was more often associated with potential DNA impurity (as inferred from DNA color) than with DNA degradation.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our reference data and candidate barcodes provide a foundation to support the DNA barcoding of mahogany and its relatives. Our workflow illustrates how the wealth of Hyb-Seq data currently generated from global herbaria may be leveraged to monitor plant diversity.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 3","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70063","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300038","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":"Branching out: Resolving plant evolution through phylogenetic networks","authors":"George P. Tiley,&nbsp;Claudia Solís-Lemus","doi":"10.1002/aps3.70065","DOIUrl":"https://doi.org/10.1002/aps3.70065","url":null,"abstract":"&lt;p&gt;The diversity of life is shaped by the interplay of multiple evolutionary processes. Some of these processes, like speciation, are well represented by a bifurcating tree. Others, like gene flow, hybridization, and introgression, are more appropriately described by networks. In plants, there are other common processes, such as polyploidy, reproductive mechanisms, and rapid shifts in life history characters, that can blur lineage boundaries and complicate evolutionary histories. As high-quality genomic data have become increasingly accessible, it has become evident that some of the most persistent challenges in resolving relationships in the plant tree of life do not arise from insufficient data, but from the need to model these reticulate processes explicitly.&lt;/p&gt;&lt;p&gt;To better detect patterns of reticulate evolution in plants and infer the mechanisms underlying those patterns, new method development and increased accessibility of bioinformatic tools that especially consider plant biology are needed. However, methodological progress has not kept pace with the increasing amounts of genomic data and its now routine application to basic research in plant evolutionary biology. Inferring phylogenetic networks remains considerably more difficult than estimating trees, both statistically and computationally. Models that accommodate reticulation must also account for other sources of discordance, such as incomplete lineage sorting, leading to a rapid increase in complexity even for modest datasets. Moreover, the evolution of a hybridizing complex or even a single species can involve multiple overlapping events, producing network structures that are challenging to estimate and interpret. Practical limitations, such as computational scalability to large numbers of taxa, sensitivity to noise and missing data, and limited incorporation of biologically relevant processes, further constrain current approaches. As a result, there remains a substantial methodological gap to detect the signatures of reticulate evolution in modern plant phylogenomic datasets.&lt;/p&gt;&lt;p&gt;This special issue presents a collection of papers that showcase the breadth of current work on phylogenetic networks and related approaches for studying reticulate evolution in plants. The contributions include new tools for network visualization (Schliep et al., &lt;span&gt;2026&lt;/span&gt;), streamlined hybrid enrichment (Hyb-Seq) phylogenomic workflows (Liu et al., &lt;span&gt;2026&lt;/span&gt;), haplotype assembly from long-read amplicon data (Fakoya et al., &lt;span&gt;2026&lt;/span&gt;), detection of introgression from site-frequency patterns with machine learning (McKenzie and Eaton, &lt;span&gt;2026&lt;/span&gt;), and statistical detection of ghost lineage introgression (Forsythe et al., &lt;span&gt;2026&lt;/span&gt;). These methodological advances are complemented by empirical studies that creatively harness the information within genomic data: repurposing population genomic datasets to characterize plant-associated microbiomes (Gonzalez-Ramirez et al","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 3","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70065","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300049","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":"Ancient hybridization and phylogenetic discordance: Exploring evolutionary complexity in Asteraceae","authors":"Paige A. Ellestad,&nbsp;Erika R. Moore-Pollard,&nbsp;Carolina M. Siniscalchi,&nbsp;Ramhari Thapa,&nbsp;Linda E. Watson,&nbsp;J. Mauricio Bonifacino,&nbsp;Jennifer R. Mandel","doi":"10.1002/aps3.70058","DOIUrl":"https://doi.org/10.1002/aps3.70058","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Conflicting phylogenetic signals are common in plant phylogenomics and often reflect evolutionary histories shaped by processes like hybridization, incomplete lineage sorting, and whole-genome duplication (WGD). We aimed to identify and assess these complex processes in the hyper-diverse family Asteraceae to offer insight into the underlying causes of phylogenetic discordance.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We used new and existing Hyb-Seq and transcriptome data to explore phylogenetic discordance by testing for nuclear/plastid incongruences, WGD, and reticulation. We present a tutorial detailing the execution of complex bioinformatic analyses to increase transparency, facilitate reproducibility, and support advancements in the field of plant evolution (https://github.com/erika-r-moore/Ellestad_etal_2025_APPS_Hybridizations).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>We uncovered extensive discordance among nuclear gene trees and deep reticulation events, particularly among South American lineages. Signals of WGD were found across the family but were often difficult to interpret, likely due to variation in data completeness, the complexity of the events, and their ancient origins.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our study and tutorial, along with a growing body of phylogenomic research, emphasize the role of reticulation and WGD in the evolution of large, diverse clades, while also underscoring the challenges. We anticipate continued advancements in theoretical approaches that will further enhance empirical studies in reticulate evolution.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 3","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70058","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300030","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":"tanggle: An R package for the visualization of phylogenetic networks","authors":"Klaus Schliep,&nbsp;Marta Vidal-García,&nbsp;Leann Biancani,&nbsp;L. Francisco Henao-Díaz,&nbsp;Eren Ada,&nbsp;Joshua Justison,&nbsp;Claudia Solís-Lemus","doi":"10.1002/aps3.70060","DOIUrl":"https://doi.org/10.1002/aps3.70060","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Phylogenetic trees depict evolutionary relationships among taxa. However, they are strictly bifurcating structures that do not take into account several types of evolutionary events such as horizontal gene transfer, hybridization, or introgression. Although the development of new methods in phylogenetic networks has recently increased, limited visualization software is available to plot the phylogenetic networks.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and results</h3>\u0000 \u0000 <p>Here, we present the R package tanggle, a visualization package for phylogenetic networks. Our package extends the widely used visualization package ggtree and allows a variety of input data from DNA sequences to extended Newick format; it also builds on the flexibility of ggplot2 to manipulate colors and other plot characteristics. In addition, our package allows for the inclusion of images and mapped morphological and geographical characteristics on the network.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>In response to growing demands for reproducible, open-source research, tanggle facilitates the production of script-based, publication-quality figures rather than graphics manually created with design software. By embedding figure code and metadata directly within analysis pipelines, tanggle improves transparency, traceability, and version control; enables automated regeneration of figures as data or methods change; and simplifies sharing and reuse of visualizations.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 3","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70060","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300102","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":"HybSuite: An integrated pipeline for hybrid capture phylogenomics from reads to trees","authors":"Yu-Xuan Liu,&nbsp;Zi-Jia Lu,&nbsp;Wyckliffe Omondi Omollo,&nbsp;Meng-Meng Wang,&nbsp;Li-Guo Zhang,&nbsp;Tao Xiong,&nbsp;Xue-Qin Wang,&nbsp;Yi-Ying Wang,&nbsp;Miao Sun","doi":"10.1002/aps3.70059","DOIUrl":"https://doi.org/10.1002/aps3.70059","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Hybrid capture sequencing (Hyb-Seq) is a widely used approach in phylogenomics, providing efficient access to targeted genomic regions. However, deriving high-quality phylogenetic trees from raw sequencing reads requires extensive bioinformatics processing, which increases complexity, the risk of errors, and challenges in file management, especially for users unfamiliar with bioinformatics workflows.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods and Results</h3>\u0000 \u0000 <p>We developed HybSuite, a streamlined Bash-based bioinformatics pipeline built upon mainstream tools such as HybPiper 2, designed to simplify the Hyb-Seq phylogenomic analysis from raw reads to species trees. Compared to existing tools (e.g., HybPiper 2, CAPTUS), it offers a modular yet integrated workflow covering all key steps from downloading from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), adapter removal, data assembly, and paralog handling to species tree inference and extensive in-depth analysis. We validated HybSuite by reconstructing a robust phylogeny for the Elaeagnaceae family, using the Angiosperms353 probe set and a dataset of 100 single-copy nuclear loci from <i>Arabidopsis</i>.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>HybSuite provides a flexible and user-friendly pipeline for Hyb-Seq phylogenomic analyses, and its high accuracy and efficiency were demonstrated through benchmarking with two empirical datasets. HybSuite is freely available at https://github.com/Yuxuanliu-HZAU/HybSuite. The pipeline is compatible with both the Linux and MacOS platforms.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 3","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70059","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300103","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":"HapAsmbl: A reference-aided pipeline for assembling haplotypes in Nanopore amplicon sequence data of polymorphic populations","authors":"Ayodele Oluwaseyi Fakoya,&nbsp;Augustine Chen,&nbsp;Rowan Paul Herridge,&nbsp;Richard Colin Macknight,&nbsp;Lynette Ruth Brownfield","doi":"10.1002/aps3.70062","DOIUrl":"https://doi.org/10.1002/aps3.70062","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Advances in long-read sequencing offer new possibilities to investigate haplotype diversity across multiple genes in plants and other taxa through multi-locus, long-read amplicon sequencing (multi-locus LRAS). Despite this progress, there is a notable absence of dedicated bioinformatics pipelines for assembling diploid haplotypes of heterozygous individuals from such multi-locus LRAS datasets, which is required for highly polymorphic populations.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We first evaluated various de novo and reference-based assembly methods, culminating in a custom pipeline (HapAsmbl) to assemble haplotypes from Oxford Nanopore Technologies (ONT) LRAS data of five flowering genes (<i>FT3</i>, <i>FTL9</i>, <i>VRN1</i>, <i>VRN2A</i>, and <i>VRN2B</i>) generated from perennial ryegrass, a highly heterozygous species. After verifying the efficacy using a simulated heterozygous dataset, the HapAsmbl pipeline was used to explore haplotype diversity of <i>CO</i>, <i>FT3</i>, and <i>VRN1</i> across multiple ryegrass populations.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>HapAsmbl outperformed existing tools by reliably reconstructing diploid haplotypes across multiple loci, enabling efficient haplotype characterization and novel allele discovery in genetically diverse populations.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>HapAsmbl simplifies haplotype resolution from complex LRAS datasets from heterozygous individuals, allowing routine use of ONT long-read sequencing for scalable haplotype analysis. HapAsmbl will enable researchers to uncover novel alleles and relate these to phenotype, supporting plant-breeding efforts in non-model crops.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 3","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/aps3.70062","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300037","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148024218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating nitrogen uptake: Methods and applications for plant research","authors":"Emilia Pierce,&nbsp;Amanda Rasmussen,&nbsp;Alexandra Huddell,&nbsp;Erin E. Sparks","doi":"10.1002/aps3.70050","DOIUrl":"10.1002/aps3.70050","url":null,"abstract":"<p>Nitrogen is an essential nutrient for the growth and development of plants, aiding many physiological and biological functions. Due to the high demand for the nutrient, it is common for agricultural production systems to fertilize crop fields with large quantities of nitrogen. However, excessive fertilization can be harmful economically and environmentally. Understanding the mechanism by which plants take up nitrogen from their environment is critical to optimize plant growth and agricultural productions. Over the past several decades, researchers have used a variety of methods to quantify nitrogen uptake, including using nitrogen isotopes, measuring uptake through depletion of a solution over time, using compartmented chambers or agarose blocks to target specific root regions, and more recent small-scale approaches such as nanoscale secondary ion mass spectrometry (nanoSIMS), microdialysis, and biomarkers. Several of these studies have been conducted in maize due to its high nitrogen demand and significance in global food and feed production; however, these techniques can be applied to any plant system. This review will examine the application of these methods, highlighting their advantages and limitations. By exploring existing methods, we aim to provide insights into advancing nitrogen uptake studies, ultimately supporting sustainable nitrogen management and improving crop production efficiency.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147759783","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":"Creation of a Pseudotsuga menziesii nucellus cell suspension culture system to produce proteins involved in reproduction","authors":"Andrea Coulter,&nbsp;YuQi Li,&nbsp;Julia Lakhani,&nbsp;Natalie Prior,&nbsp;Patrick von Aderkas","doi":"10.1002/aps3.70048","DOIUrl":"10.1002/aps3.70048","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Cell suspension cultures of Douglas-fir (<i>Pseudotsuga menziesii</i>) nucellus were created to overcome phenological limitations to the in situ study of bioactive proteins within and secreted by nucellar cells.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Proteins isolated from the cell suspension culture medium were analyzed using mass spectrometry, as were Douglas-fir post-pollination prefertilization drops and nucellus tissue excised from the ovule at the time of drop production.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>A total of 280 proteins ranging in size from 5 to 224 kDa were found in the three sample types. Identical proteins were found in the post-pollination prefertilization drop and in the nucellar suspension culture medium or the nucellus. Secretory proteins isolated from the culture medium were either carbohydrate metabolism-related or defense proteins, consistent with previous proteomic studies of pollination drops. Intracellular proteins were found in all three sample types and were consistent with previous proteomic studies of pollination drops, implying similar metabolic processes are at work in the gymnosperm nucellus at the time of drop production.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Cell suspension cultures of Douglas-fir nucellus are able to produce secretory proteins that are biologically relevant during pollination. This is potentially a tractable system that can overcome barriers to in situ studies presented by gymnosperm reproductive phenology.</p>\u0000 </section>\u0000 </div>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":"14 2","pages":""},"PeriodicalIF":2.4,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13103538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147759848","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}