Applications in Plant Sciences最新文献

{"title":"Molecular methods for differentiating <i>Phragmites australis</i> subspecies and identification of hybrid stands in the Upper Midwestern United States.","authors":"Nicholas P Tippery, Daniel J Larkin, Julia Bohnen, Douglas L Wendell, Neil O Anderson, Susan M Galatowitsch, Marie Abbey, Alan G Smith, Andrzej K Noyszewski","doi":"10.1002/aps3.70073","DOIUrl":"10.1002/aps3.70073","url":null,"abstract":"<p><strong>Premise: </strong>In North America, <i>Phragmites australis</i> (common reed) has drawn a great deal of research attention. Non-native <i>P. australis</i> subsp. <i>australis</i> is a noxious weed that has locally displaced native <i>P. australis</i> subsp. <i>americanus</i> in some areas. Although morphological features can distinguish the two subspecies, molecular tools often are required to confirm identifications. Additionally, the existence of natural intrasubspecific hybrids presents novel management challenges. Hybrid <i>Phragmites</i> is difficult to detect, and it has become standard practice to apply molecular tools to survey for hybrids.</p><p><strong>Methods: </strong>We applied several molecular techniques-microsatellite, DArTseq (a type of genotyping-by-sequencing), restriction fragment length polymorphism (PCR-RFLP), and next-generation sequencing-to characterize <i>P. australis</i> at the landscape scale in Minnesota and Wisconsin and to search for hybrids.</p><p><strong>Results: </strong>We obtained molecular data for <i>Phragmites</i> plants sampled from 341 stands, ultimately characterizing 98 stands as native and 236 as non-native. Plants from two adjacent stands in Washington County, Minnesota, were confirmed to be hybrids.</p><p><strong>Discussion: </strong>These are the first confirmed hybrids from the Upper Midwest/western Great Lakes region. We also discuss the relative cost and effectiveness of the various molecular methods and offer recommendations for future studies.</p>","PeriodicalId":8022,"journal":{"name":"Applications in Plant Sciences","volume":" ","pages":"e70073"},"PeriodicalIF":3.5,"publicationDate":"2026-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13435300/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148672896","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":"Off-target metagenomics: Leveraging whole genome sequencing to study the bacteriome of the liverwort Calasterella californica","authors":"Ixchel S. González-Ramírez,&nbsp;Michael J. Song,&nbsp;Elijah C. Mehlferber,&nbsp;Brent D. Mishler","doi":"10.1002/aps3.70064","DOIUrl":"https://doi.org/10.1002/aps3.70064","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>The recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility and the development of new marker-based pipelines enable the use of short reads to study bacterial communities associated with organisms.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>We utilized population genomic data of the liverwort <i>Calasterella californica</i> obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The bacterial communities associated with <i>C. californica</i> were dominated by the methanotroph <i>Methylobacterium</i> and other Hyphomicrobiales, a group that includes well-known plant symbionts. While diversity metrics of bacteria composition were similar across localities, we found significant differences in the relative abundance of a few taxa across California regions, likely driven by differences in precipitation and temperature seasonality.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our results support previous observations that liverwort bacterial communities are not randomly assembled, suggesting a potential role of the plant in determining community composition, an emerging pattern that deserves more attention. The novel off-target metagenomics approach can be applied to any population-level resequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using repurposed data from landscape genomics.</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/aps3.70064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300034","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":"Detecting cryptic ghost lineage introgression in four-taxon genomic datasets","authors":"Evan S. Forsythe,&nbsp;Blaine S. Pappa,&nbsp;Darren A. Clavette,&nbsp;Devin Y. Mendoza","doi":"10.1002/aps3.70045","DOIUrl":"https://doi.org/10.1002/aps3.70045","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Premise</h3>\u0000 \u0000 <p>Hybridization and introgression are pervasive evolutionary forces that have played fundamental roles in shaping the diversity of wild and domesticated plants. Four-taxon tests for introgression provide a reliable framework for detecting signatures of ancient introgression from genomic data, which have played an important role in revealing the reticulate nature of plant evolution; however, there is emerging evidence that a cryptic process known as ghost lineage introgression has the potential to dramatically skew interpretations of four-taxon introgression statistics, particularly our ability to determine the lineages involved in introgression. This ambiguity limits our ability to resolve the mechanisms and functional implications of introgression because it means we can determine neither the donor nor the recipient of introgressed alleles with confidence.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Here, we develop ghostbuster, a statistical test designed to detect ghost lineage introgression in genomic data based on patterns of sequence divergence. We employ coalescent simulations to test our method and ascertain the conditions under which it accurately identifies ingroup versus ghost lineage introgression. Finally, to demonstrate the utility of ghostbuster, we apply it to a previously identified introgression event in the plant family Brassicaceae.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our simulations reveal that ghostbuster accurately distinguishes ghost lineage introgression from ingroup introgression across a range of introgression scenarios, with errors arising only when divergence events are closely spaced or when ancestral population sizes are unbalanced. Our analysis of empirical plant data reveals that the previously identified introgression likely constitutes ghost lineage introgression and, thus, was previously misinterpreted.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Discussion</h3>\u0000 \u0000 <p>Our analyses of simulated and empirical data demonstrate that ghostbuster will be a helpful tool in resolving reticulate evolution in plants and other taxa. We demonstrate the biological insights that ghostbuster provides by presenting an updated model of ghost lineage introgression in Brassicaceae, impacting our understanding of the molecular evolution of crop and model species in this important plant lineage. Ghostbuster code is freely available at: https://github.com/EvanForsythe/Ghost_introgression.</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/aps3.70045","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300033","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":"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}