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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Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset

Current Biology, Journal Year: 2023, Volume and Issue: 33(19), P. 4052 - 4068.e6

Published: Sept. 1, 2023

The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of are incompletely sampled often contain poorly supported branches. Here, we present complete Brassicaceae genus-level phylogenies to date (Brassicaceae Tree Life or BrassiToL) based on nuclear (1,081 genes, 319 349 genera; 57 58 tribes) plastome (60 265 all data. We found cytonuclear discordance between two, which likely result rampant hybridization among closely more distantly related lineages. To evaluate impact such phylogeny reconstruction, performed five different gene sampling routines, increasingly removed putatively paralog genes. Our cleaned subset 297 genes revealed high support for tribes, whereas main lineages (supertribes) was moderate. Calibration 20 clock-like suggests late Eocene Oligocene origin family. Finally, our results strongly recently published new classification, dividing into two subfamilies (one with supertribes), together representing tribes. This includes described re-established including Arabidopsideae, monogeneric tribe accommodating without any close relatives. With worldwide community thousands researchers working diverse members, will be an indispensable tool studies biodiversity biology.

Language: Английский

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A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

American Journal of Botany, Journal Year: 2021, Volume and Issue: 108(7), P. 1087 - 1111

Published: July 1, 2021

Premise To further advance the understanding of species‐rich, economically and ecologically important angiosperm order Myrtales in rosid clade, comprising nine families, approximately 400 genera almost 14,000 species occurring on all continents (except Antarctica), we tested Angiosperms353 probe kit. Methods We combined high‐throughput sequencing target enrichment with kit to evaluate a sample 485 across 305 (76% order). Results provide most comprehensive phylogenetic hypothesis for date. Relationships at ranks, such as relationship early‐diverging often reflect previous studies, but gene conflict is evident, relationships previously found be uncertain remain so. Technical considerations processing HTS data are also discussed. Conclusions High‐throughput powerful tools phylogenomic analysis, better genetic available required identify genes trees that account likely incomplete lineage sorting and/or hybridization events.

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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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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Phylogenomics and intergenomic conflict in a challenging orchid clade (Calypsoinae): monophyly of Corallorhiza, paraphyly of Oreorchis, and resurrection of Kitigorchis

Botanical Journal of the Linnean Society, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 17, 2025

Abstract Heterotrophic plants are among the most recalcitrant from a systematics perspective because of reduced morphological and genomic features, often extreme substitution rate heterogeneity. The orchid subtribe Calypsoinae exemplifies this, containing several lineages that have lost leaves photosynthesis. In particular, relationships leafy Asian Oreorchis leafless American Corallorhiza been contentious. Here we used nuclear sequence capture to resolve within addressed monophyly Oreorchis, for which previous studies highlighted conflicting patterns or paraphyly, depending on data analysed. Nuclear analyses provided strong support monophyletic paraphyletic latter with two strongly supported clades. As in studies, plastid recovered assemblages both genera. Topology tests using rejected constrained topologies, further revealing cytonuclear conflict. Network-based revealed lack evidence hybridization, suggesting incomplete lineage sorting associated biological historical factors driven intergenomic Additionally, found loci identified as putatively holomycotrophic species functionally enriched organellar functions. study provides case resurrection Kitigorchis sister Corallorhiza, species, erythrochrysea indica, highlights challenges phylogenetics mycoheterotrophs.

Language: Английский

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Exploring the potential of Angiosperms353 markers for species identification of Eastern Mediterranean orchids

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: unknown, P. 108360 - 108360

Published: April 1, 2025

Tuberous orchids are ecologically vulnerable species, threatened by a range of environmental pressures such as overharvesting, grazing and land use change. Conservation efforts require accurate species identification, but impeded limited phylogenetic resolution traditional genetic markers, which is exacerbated widespread taxonomic conflict regarding the classification orchids. Target enrichment holds promise to resolve both these challenges offering large set nuclear loci with increase evaluate competing models. Here, we effectiveness Angiosperms353 markers for distinguishing over 50 tuberous orchid native Greece explore possibility narrowing smaller that could function minimal probe set. Our methodology consists three-tiered approach: 1) generating species-level phylogeny using all sufficient target recovery, 2) evaluating models based on "splitter" "lumper" classifications through Bayes Factor delimitation, 3) ranking potential discriminate representatives lineages different divergence times their informativeness. While inferred multi-species coalescent had overall high support, delimitation revealed mixed outcomes, favouring splitting in Serapias, while basal clades lumping more recently diverged Ophrys. A molecular clock analysis Ophrys confirms rapid recent radiation marked uncertainty, suggesting need additional fully this genus. Finally, found 30 be highly phylogenetically informative across four epochs Orchidinae evolution; suggest promising candidates future marker development. findings enhance Plant Tree Life (PAFTOL) contributing phylogenomic data were previously underrepresented trees built shedding light ongoing "splitter"-vs-"lumper" debate new directions identification orchids, group distinct conservation challenges.

Language: Английский

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On the potential of Angiosperms353 for population genomic studies

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

Published: May 18, 2021

PREMISE The successful application of universal targeted sequencing markers, such as those developed for the Angiosperms353 probe set, within populations could reduce or eliminate need specific marker development, while retaining benefits full‐gene sequences in population‐level analyses. However, whether markers provide sufficient variation species to calculate demographic parameters is untested. METHODS Using herbarium specimens from a 50‐year‐old floristic survey Texas, we sequenced 95 samples 24 using set. Our data workflow calls variants and prepares population genetic analysis standard metrics. In our case study, gene recovery was affected by genomic library concentration only at low concentrations displayed limited phylogenetic bias. RESULTS We identified over 1000 segregating with zero missing 92% demonstrate that contain estimate pairwise nucleotide diversity (π)—typically between 0.002 0.010, most found flanking non‐coding regions. subset were filtered linkage, uncovered high heterozygosity many species, suggesting denser sampling should permit estimation flow dynamics. DISCUSSION benefit conservation studies providing repeatable data, haplotype information, permitting inclusion decades‐old specimens.

Language: Английский

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A Bird’s Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: July 14, 2022

Convolvulaceae is a family of c. 2,000 species, distributed across 60 currently recognized genera. It includes species high economic importance, such as the crop sweet potato (Ipomoea batatas L.), ornamental morning glories bindweeds (Convolvulus and dodders, parasitic vines (Cuscuta L.). Earlier phylogenetic studies, based predominantly on chloroplast markers or single nuclear region, have provided framework for systematic studies family, but uncertainty remains at level relationships among subfamilies, tribes, genera, hindering evolutionary inferences taxonomic advances. One enduring enigmas has been relationship Cuscuta to rest Convolvulaceae. Other examples unresolved issues include monophyly within Merremieae, "bifid-style" clade (Dicranostyloideae), well relative positions Erycibe Roxb. Cardiochlamyeae. In this study, we explore large dataset genes generated using Angiosperms353 kit, contribution resolving some these remaining uncertainties For first time, strongly supported backbone provided. confirmed belong "Merremieae," in their former tribal circumscription, are recovered non-monophyletic, with unexpected placement Distimake Raf. sister that contains Ipomoeeae Decalobanthus Ooststr., Convolvuleae nested "Merremieae." The Dicranostyloideae, including Jacquemontia Choisy, supported, albeit novel between genera hypothesized, challenging current delimitation. exact placements remain uncertain, requiring further investigation. Our study explores benefits limitations increasing sequence data higher-level Convolvulaceae, highlights need expanded sampling, facilitate much-needed revised classification family.

Language: Английский

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