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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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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Precipitation is the main axis of tropical plant phylogenetic turnover across space and time

Science Advances, Journal Year: 2023, Volume and Issue: 9(7)

Published: Feb. 17, 2023

Early natural historians—Comte de Buffon, von Humboldt, and De Candolle—established environment geography as two principal axes determining the distribution of groups organisms, laying foundations for biogeography over subsequent 200 years, yet relative importance these remains unresolved. Leveraging phylogenomic global species data Mimosoid legumes, a pantropical plant clade c. 3500 species, we show that water availability gradient from deserts to rain forests dictates turnover lineages within continents across tropics. We demonstrate 95% speciation occurs precipitation niche, showing profound phylogenetic niche conservatism, lineage boundaries coincide with isohyets precipitation. reveal similar patterns on different continents, implying evolution dispersal follow universal processes.

Language: Английский

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Tackling Rapid Radiations With Targeted Sequencing

Frontiers in Plant Science, Journal Year: 2020, Volume and Issue: 10

Published: Jan. 9, 2020

In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount genomic data now available statistical tools analyze provide unprecedented power for inference. Targeted sequencing has emerged as a strong tool estimating species trees in the face rapid radiations, lineage sorting introgression. Evolutionary relationships Cyperaceae been studied mostly using Sanger until recently. Despite ample taxon sampling, many genera remain poorly understood, hampered diversification rates that outpace mutation loci used. C4 Cyperus Clade genus particularly difficult resolve. Previous based on limited set markers resolved among C3 photosynthetic pathway, but not taxa. We test ability two targeted kits Clade, universal Angiosperms-353 kit Cyperaceae-specific kit. Sequences were recovered from generated with both used investigate overlap between relative efficiency general custom approaches. shallow-level was tested summary tree method concatenated maximum likelihood approach. High resolution support are obtained approaches, high levels missing disproportionately impact latter. provides new insights into evolution morphology demonstrating example former segregate Alinula is polyphyletic its seeming morphological integrity. An unexpected result margaritaceus-Cyperus niveus complex comprises clade separate sister core Clade. Our results demonstrate family-specific do necessarily more than those kit, different can often be merged downstream analyses. Moreover, our study contributes growing consensus powerful resolving radiations.

Language: Английский

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A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project

Frontiers in Genetics, Journal Year: 2020, Volume and Issue: 10

Published: Feb. 21, 2020

High-throughput DNA sequencing techniques enable time- and cost-effective of large portions the genome. Instead annotating whole genomes, many phylogenetic studies focus effort on sets pre-selected loci, which further reduces costs bioinformatic challenges while increasing coverage. One common approach that enriches loci before is often referred to as target sequence capture. This technique has been shown be applicable greatly varying evolutionary depth. Moreover, it proven produce powerful, multi-locus datasets suitable for analyses. However, capture requires careful considerations, may affect success experiments. Here we provide a simple flowchart designing phylogenomic We discuss necessary decisions from identification final processing data. outline solutions related taxonomic scope, sample quality, available genomic resources projects. hope this review will serve useful roadmap carrying out successful studies.

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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