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

---

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

---

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

---

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

---

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

---

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

---

Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(12)

Published: Dec. 1, 2022

Abstract The Angiosperms353 gene set (AGS) consists of a 353 universal low-copy nuclear genes that were selected by examining more than 600 angiosperm species. These can be used for phylogenetic studies and population genetics at multiple taxonomic scales. However, current pipelines are not able to recover efficiently accurately from high-throughput sequences. Here, we developed Easy353, reference-guided assembly tool the AGS sequencing (HTS) data (including genome skimming, RNA-seq, target enrichment). Easy353 is an open-source user-friendly assembler diverse types data. It has graphical user interface command-line compatible with all widely-used computer systems. Evaluations, based on both simulated empirical data, suggest yields low rates errors.

Language: Английский

---

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

---

Mitochondrial genomic data are effective at placing mycoheterotrophic lineages in plant phylogeny

New Phytologist, Journal Year: 2022, Volume and Issue: 236(5), P. 1908 - 1921

Published: June 22, 2022

Summary Fully mycoheterotrophic plants can be difficult to place in plant phylogeny due elevated substitution rates associated with photosynthesis loss. This potentially limits the effectiveness of downstream analyses mycoheterotrophy that depend on accurate phylogenetic inference. Although mitochondrial genomic data sets are rarely used phylogenetics, theory predicts they should resilient long‐branch artefacts, thanks their generally slow evolution, coupled limited rate elevation heterotrophs. We examined utility genomes for resolving contentious higher‐order placements lineages two test cases: monocots (focusing Dioscoreales) and Ericaceae. find Thismiaceae distantly related Burmanniaceae monocot order Dioscoreales, conflicting current classification schemes based few gene sets. confirm unusual Afrothismia is Taccaceae–Thismiaceae, a corresponding independent loss photosynthesis. In Ericaceae we recovered first well supported relationships among its five major lineages: not monophyletic, as pyroloids inferred sister core Ericaceae, monotropoids arbutoids. Genes from collectively resolved previously ambiguous mycoheterotroph relationships. propose considered standardised panels inferring overall phylogeny.

Language: Английский

---

The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data

Molecular Phylogenetics and Evolution, Journal Year: 2023, Volume and Issue: 182, P. 107702 - 107702

Published: Feb. 11, 2023

The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has obstructed the identification of major morphological biogeographic transitions within clade. We used target capture sequencing with Angiosperms353 probes, taxon-sampling encompassing all genera family, tree-based sequence curation, multiple approaches to investigate clades their relationship other Ericales. generated dated trees conducted broad-scale analyses as well stochastic character mapping growth habit. show that Ardisia, a pantropical genus largest in not monophyletic, at least 19 smaller nested it. Neotropical members Ardisia several form clade, an ancestor which arrived Neotropics began diversifying about 20 Ma. This clade most closely related Elingamita Tapeinosperma, are on islands Pacific. Both Androsace Primula non-monophyletic by inclusion genera. Ancestral state reconstructions revealed there have either been parallel herbaceous habit Primuloideae, Samolus, three lineages Myrsinoideae, or common was herbaceous. Our results provide robust estimate relationships across revised classification Myrsinoideae necessary render monophyletic.

Language: Английский

---