A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

Systematic Biology, Journal Year: 2021, Volume and Issue: 71(2), P. 301 - 319

Published: May 11, 2021

The tree of life is the fundamental biological roadmap for navigating evolution and properties on Earth, yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding evolutionary relationships. Here, we describe a comprehensive phylogenomic platform exploring angiosperm life, comprising set open tools based 353 nuclear genes targeted by universal Angiosperms353 sequence capture probes. primary goals this article (i) document methods, (ii) first release, (iii) present novel portal, Kew Tree Life Explorer (https://treeoflife.kew.org). We aim generate target all genera flowering plants, exploiting natural history collections such as herbarium specimens, augment it mined public data. Our described here, most extensive date, 3099 samples validated DNA barcode phylogenetic tests, representing 64 orders, 404 families (96$\%$) 2333 (17$\%$). A "first pass" was inferred from data, which totaled 824,878 sequences, 489,086,049 base pairs, 532,260 alignment columns, interactive presentation Explorer. This species generated using methods that were rigorous, tractable at scale operation. Despite limitations pertaining taxon gene sampling, recovery, models paralogy, strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders placing many time. set, intermediates openly accessible via will be updated further become available. major milestone toward complete plant opens doors highly integrated future phylogenomics through systematic standardized markers. approach has potential serve much-needed bridge between growing movement genomes Earth vast world's collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; phylogenomics; access; capture; life.].

Language: Английский

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What is the “modified” CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

Applications in Plant Sciences, Journal Year: 2023, Volume and Issue: 11(3)

Published: May 1, 2023

Cetyltrimethylammonium bromide (CTAB)-based methods are widely used to isolate DNA from plant tissues, but the unique chemical composition of secondary metabolites among species has necessitated optimization. Research articles often cite a "modified" CTAB protocol without explicitly stating how had been altered, creating non-reproducible studies. Furthermore, various modifications that have applied not rigorously reviewed and doing so could reveal optimization strategies across study systems. We surveyed literature for modified protocols isolation DNA. found every stage modified, we summarized those provide recommendations extraction Future genomic studies will rely on optimized protocols. Our review used, as well here, better standardize extractions, allowing repeatable transparent

Language: Английский

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Toward a phylogenomic classification of magnoliids

American Journal of Botany, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 14, 2025

Magnoliids are a strongly supported clade of angiosperms. Previous phylogenetic studies based primarily on analyses limited number mostly plastid markers have led to the current classification magnoliids into four orders and 18 families. However, uncertainty remains regarding placement several For first comprehensive phylogenomic analysis as whole, we sampled 235 species from 199 (74%) genera representing all families most subfamilies tribes. We analyzed newly generated data Angiosperms353 probe set using both coalescent concatenation testing impact multiple filtering alignment strategies. While our results generally provide further support for previously established relationships in whole large including Annonaceae Lauraceae, they also new evidence ambiguous relationships. In particular, found position Hydnoraceae sister remainder Piperales, though was conflicting, resolved backbone among Myristicaceae. Different analytical strategies tended rather small effects branch topology. Although some by low gene recovery taxa significant tree conflict relationships, this study represents step toward reconstructing evolutionary history major lineage Based these results, present an updated magnoliids, recognizing 21 families, summarizing tribes, describing tribes

Language: Английский

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Strategies for reducing per‐sample costs in target capture sequencing for phylogenomics and population genomics in plants

Applications in Plant Sciences, Journal Year: 2020, Volume and Issue: 8(4)

Published: April 1, 2020

The reduced cost of high‐throughput sequencing and the development gene sets with wide phylogenetic applicability has led to rise sequence capture methods as a plausible platform for both phylogenomics population genomics in plants. An important consideration large targeted projects is per‐sample cost, which can be inflated when using off‐the‐shelf kits or reagents not purchased bulk. Here, we discuss reduce costs projects. We review minimal equipment consumable requirements while comparing several alternatives bulk DNA extraction, library preparation, target enrichment, sequencing. consider how each workflow alterations may affected by quality (e.g., fresh vs. herbarium tissue), genome size, scale project. provide calculator researchers considering use designing projects, identify challenges future low‐cost non‐model plant systems.

Language: Английский

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A new classification of Cyperaceae (Poales) supported by phylogenomic data

Journal of Systematics and Evolution, Journal Year: 2021, Volume and Issue: 59(4), P. 852 - 895

Published: May 9, 2021

Abstract Cyperaceae (sedges) are the third largest monocot family and of considerable economic ecological importance. Sedges represent an ideal model to study evolutionary biology due their species richness, global distribution, large discrepancies in lineage diversity, broad range preferences, adaptations including multiple origins C 4 photosynthesis holocentric chromosomes. Goetghebeur′s seminal work on published 1998 provided most recent complete classification at tribal generic level, based a morphological inflorescence, spikelet, flower, embryo characters, plus anatomical other information. Since then, several family‐level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after last comprehensive family, we present first family‐wide phylogenomic targeted sequencing Angiosperms353 probe kit sampling 311 accessions. In addition, 62 accessions available from GenBank were mined for overlapping reads included analyses. Informed by this backbone phylogeny, new tribal, subtribal, levels is proposed. The majority previously recognized suprageneric groups supported, time, establish support tribe Cryptangieae as clade genus Koyamaea . We provide taxonomic treatment identification keys diagnoses 2 subfamilies, 24 tribes, 10 subtribes, basic information 95 genera. includes five subtribes Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae, Oreobolinae.

Language: Английский

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New targets acquired: Improving locus recovery from the Angiosperms353 probe set

Applications in Plant Sciences, Journal Year: 2021, Volume and Issue: 9(7)

Published: June 14, 2021

Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used capture loci throughout angiosperms, but default reference file includes sequence information from only 6-18 taxa per locus. Consequently, reads sequenced on-target DNA molecules may fail map references, resulting in fewer for assembly, and reducing locus recovery.

Language: Английский

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Phylogenomics of Gesneriaceae using targeted capture of nuclear genes

Molecular Phylogenetics and Evolution, Journal Year: 2021, Volume and Issue: 157, P. 107068 - 107068

Published: Jan. 9, 2021

Gesneriaceae (ca. 3400 species) is a pantropical plant family with wide range of growth form and floral morphology that are associated repeated adaptations to different environments pollinators. Although systematics has been largely improved by the use Sanger sequencing data, our understanding evolutionary history group still far from complete due limited number informative characters provided this type data. To overcome limitation, we developed here Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes Universal Angiosperms-353 kit. With an average 557,600 reads 87.8% recovery, target was successful across also other families Lamiales. From bait set, selected most 418 resolve phylogenetic relationships entire using maximum likelihood coalescent-based methods. Upon testing performance baits on 78 taxa representing 20 out 24 subtribes within family, showed data high support for among major lineages, were able provide resolution more recent radiations. Overall, molecular resources open new perspectives study phylogeny at taxonomical levels identification factors underlying diversification group.

Language: Английский

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Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

American Journal of Botany, Journal Year: 2022, Volume and Issue: 109(4), P. 580 - 601

Published: Feb. 16, 2022

Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree gene-tree discordance Solanum, one largest flowering plant genera includes cultivated potato, tomato, eggplant, as well 24 minor crop plants.A densely sampled species-level phylogeny Solanum is built using unpublished publicly available Sanger sequences comprising 60% all accepted species (742 spp.) nine regions (ITS, waxy, seven plastid markers). The robustness this topology tested by examining a full plastome dataset with 140 nuclear target-capture 39 (Angiosperms353 probe set).While taxonomic framework remained stable, tree conflicts generated from datasets were observed. latter correspond short internodal branches, network analysis polytomy tests suggest backbone composed three found at different evolutionary depths. strongest area discordance, near crown node could potentially represent hard polytomy.We argue incomplete lineage sorting due rapid diversification most likely cause for polytomies, embracing uncertainty underlies them crucial understand evolution large rapidly radiating lineages.

Language: Английский

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Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1059 - 1065

Published: July 1, 2021

Language: Английский

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Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: March 7, 2023

Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, 6570 species. However, family subfamily relationships in remain unclear, making reconstruction the order's spatio-temporal morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate most densely sampled phylogenetic trees date, with 448 samples 85% genera represented. The percentage paralogous loci allele divergence was characterized across phylogeny, which time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core clades subdivide order, first Kirkiaceae, Burseraceae, Anacardiaceae, second Simaroubaceae, Meliaceae, Rutaceae. Kirkiaceae sister Burseraceae and, contrary current understanding, Simaroubaceae Meliaceae Sapindaceae placed Nitrariaceae Biebersteiniaceae but between these likely due their rapid ancient diversification. emerged succession, coincident climatic change Mid-Cretaceous Hothouse event. Subfamily tribal within major need revision, particularly Sapindaceae, Rutaceae Meliaceae. Much difficulty reconstructing at level may be caused by prevalence loci, Rutaceae, that are indicative gene duplication events such hybridization polyploidization playing a role evolutionary history families. This study provides key insights into factors affect reconstructions multiple scales, state-of-the-art framework for further research.

Language: Английский

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