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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Phylogenomics and the rise of the angiosperms

Nature, Journal Year: 2024, Volume and Issue: 629(8013), P. 843 - 850

Published: April 24, 2024

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods

Language: Английский

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Green plant genomes: What we know in an era of rapidly expanding opportunities

Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(4)

Published: Jan. 18, 2022

Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land is essential. However, setting standards generation storage of complex set that characterize lineage life major challenge plant scientists. Such will need to accommodate immense variation genome size, transposable element content, structural complexity while enabling research into molecular evolutionary processes have resulted this enormous variation. Here we provide an overview assessment current state knowledge genomes. To date fewer than 300 complete chromosome-scale assemblies representing 900 been across estimated 450,000 500,000 clade. These range size from 12 Mb 27.6 Gb biased toward agricultural crops with large branches tree untouched genomic-scale sequencing. Locating suitable tissue samples most plants, especially those taxa extreme environments, remains one biggest hurdles our inventory. Furthermore, annotation at present undergoing intensive improvement. It hope fresh help development quality cohesive meaningful synthesis scale up future.

Language: Английский

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Phylogenomics and the flowering plant tree of life

Journal of Integrative Plant Biology, Journal Year: 2022, Volume and Issue: 65(2), P. 299 - 323

Published: Nov. 23, 2022

Abstract The advances accelerated by next‐generation sequencing and long‐read technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of studies adopting hundreds thousands genes across wealth clades have emerged ushered phylogenetics evolution into new era. meantime, roadmap researchers when making decisions different approaches their phylogenomic research design is imminent. This review focuses on utility genomic data (from organelle genomes, both reduced representation whole‐genome sequencing) in evolutionary investigations, describes baseline methodology experimental analytical procedures, summarizes recent progress flowering phylogenomics at ordinal, familial, tribal, lower levels. We also discuss challenges, such as adverse impact orthology inference reconstruction raised from systematic errors, underlying biological factors, duplication, hybridization/introgression, incomplete lineage sorting, together suggesting that bifurcating tree may not be best model life. Finally, we promising avenues future studies.

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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Genome‐scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets

Journal of Integrative Plant Biology, Journal Year: 2023, Volume and Issue: 65(6), P. 1479 - 1489

Published: Jan. 17, 2023

Angiosperms dominate the Earth's ecosystems and provide most of basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by APG IV classification. However, phylogenetic relationships angiosperms remain unclear, trees with different topologies have been reconstructed depending on sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data reconstruct phylogenies 366 species 241 genera belonging 97 families across 43 orders based orthologous nuclear, plastid, mitochondrial genomes same compatible datasets. were largely consistent previously constructed variations in each type. there inconsistencies five Mesangiospermae lineages when examined. We discuss ways address these inconsistencies, which could ultimately lead reconstruction a comprehensive tree presented here framework further updates comparisons. These can also be guides examine evolutionary trajectories among three types during lineage radiation.

Language: Английский

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The origin and speciation of orchids

New Phytologist, Journal Year: 2024, Volume and Issue: 242(2), P. 700 - 716

Published: Feb. 21, 2024

Orchids constitute one of the most spectacular radiations flowering plants. However, their origin, spread across globe, and hotspots speciation remain uncertain due to lack an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, c. 7% (1921) 29 524 accepted species, use it infer geographic range evolution, diversity, patterns by adding curated geographical distributions from World Checklist Vascular Plants. The orchids' recent common ancestor is inferred have lived in Late Cretaceous Laurasia. modern Apostasioideae, which comprises two genera with 16 species India northern Australia, interpreted as relictual, similar that numerous other groups went extinct at higher latitudes following global climate cooling during Oligocene. Despite ancient orchid diversity mainly originated over last 5 Ma, highest rates Panama Costa Rica. These results alter our understanding origin orchids, previously proposed Australian, pinpoint Central America region recent, explosive speciation.

Language: Английский

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Taxonomy in the light of incongruence: An updated classification of Malvales and Malvaceae based on phylogenomic data

Taxon, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

Abstract Malvales is a diverse order of flowering plants, economically and ecologically relevant, it known for its broad morphological variability. Recent phylogenomic studies have revealed complex evolutionary history the order, including localised phylogenetic discordances among nuclear loci. However, since late 1990s, classification has largely been neglected. This study aims to address this gap by revisiting Malvales, with focus on largest family, Malvaceae. By integrating datasets, our primary goals are provide an updated phylogeny map key traits supporting revised suprageneric classification, while accounting gene species tree conflicts. Our molecular dataset included 194 genera 309 genes, obtained through target sequence capture using Angiosperms353 probes. covers approximately half in representing all families subfamilies, as well nearly tribes, subtribes. A coalescent approach utilising trees was used infer relationships. matrix 50 characters relevant compiled, character‐state distributions selected were mapped against identify discuss diagnostic features clades. Phylogenetic relationships monophyly most groups aligned closely previous studies. Morphological that define clades varied significantly across differences observed growth habit, leaf structure, pollen type, floral features, fruit/seed morphology. In Malvaceae, we resolved uncertainties early Malvoideae lineages, describe new tribe, Pentaplareae tr. nov., which clarifies taxonomic placement previously uncertain genus. Additionally, propose recognition subfamily, Matisioideae subfam. elevated from former status positioned sister group Malvoideae. highlights how frameworks can be refined even face conflicting data, demonstrating importance evidence revising classifications.

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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Species tree branch length estimation despite incomplete lineage sorting, duplication, and loss

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 21, 2025

Abstract Phylogenetic branch lengths are essential for many analyses, such as estimating divergence times, analyzing rate changes, and studying adaptation. However, true gene tree heterogeneity due to incomplete lineage sorting (ILS), duplication loss (GDL), horizontal transfer (HGT) can complicate the estimation of species lengths. While several tools exist topology a addressing various causes discordance, much less attention has been paid length on multi-locus datasets. For single-copy trees, some methods available that summarize onto tree, including coalescent-based account ILS. no method exists multi-copy family trees have evolved with loss. To address this gap, we introduce CASTLES-Pro algorithm while accounting both GDL improves existing CASTLES by increasing its accuracy extends it handle ones. Our simulation studies show is generally more accurate than alternatives, eliminating systematic bias toward overestimating terminal often observed when using concatenation. Moreover, not theoretically designed HGT, maintains relatively high under rates random HGT. Code availability implemented inside software package ASTER, at https://github.com/chaoszhang/ASTER . Data The datasets scripts used in study https://github.com/ytabatabaee/CASTLES-Pro-paper

Language: Английский

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