Phylogenomics and the rise of the angiosperms

Nature, Год журнала: 2024, Номер 629(8013), С. 843 - 850

Опубликована: Апрель 24, 2024

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods

Язык: Английский

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Toward a phylogenomic classification of magnoliids

American Journal of Botany, Год журнала: 2025, Номер unknown

Опубликована: Янв. 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

Язык: 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, Год журнала: 2023, Номер 14

Опубликована: Март 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.

Язык: Английский

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Phylogenomics Of Boraginaceae and Boraginales Using Lineage-Specific and Angiosperms353 Loci

Systematic Botany, Год журнала: 2025, Номер 49(4), С. 749 - 767

Опубликована: Янв. 6, 2025

Abstract— During the past 20 yr, phylogenetics of Boraginaceae has taken shape using plastid DNA regions and nuclear ribosomal internal transcribed spacer (ITS), but these only reflect a limited understanding evolutionary history family. Using hybridization-enrichment sequencing, 531 from lineage-specific Angiosperms353 loci were sequenced aligned for 49 species across Boraginaceae. Additionally, incorporated with broader dataset same 115 accessions Boraginales relatives. Based on multiple phylogenetic approaches datasets, resolved phylogenies quite similar to our current understanding, yet taxa recognized in different positions. These included: 1) Echiochiloideae as sister Cynoglossoideae instead rest entire family, 2) Moritzinae nested within Boragininae, 3) Lasiocaryeae Trichodesmeae not sisters. positions recovered, via methods, hundreds suggest that incomplete lineage sorting, hybridization, shifts substitution rates may have occurred during early origin In analyses Boraginales, Namaceae was non-monophyletic, providing evidence Hydrophyllaceae again be appropriate, Lennoaceae Ehretiaceae. While both sets allowed well-resolved well-supported phylogeny reconstructed, recovered some more intriguing relationships part because appear less conserved than those Angiosperms353. The two provide an interesting complement patterns evolution family order.

Язык: Английский

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Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Фев. 13, 2025

Abstract Chloroplasts are essential organelles in plants and eukaryotic algae, responsible for photosynthesis, fatty acid synthesis, amino production, stress responses. The genus Passiflora , known its species diversity dynamic chloroplast (cp) genome evolution, serves as an excellent model studying structural variations. This study investigates evolutionary relationships within by sequencing 11 new genomes, assessing selective pressures on cp genes, comparing plastid nuclear phylogenies. genomes showed significant variations size, gene content, structure, ranging from 132,736 to 163,292 base pairs, especially Decaloba . Structural rearrangements species-specific repeat patterns were identified. Selective pressure tests revealed adaptive evolution certain lineages, with several including clpP petL under positive selection. Phylogenetic analyses confirmed the monophyly of subgenera Astrophea while Deidamioides appeared polyphyletic. Nuclear phylogenetic analysis based 35S rDNA sequences supported but inconsistencies subgenus compared data. highlights complexity demonstrating evolution. findings underscore effectiveness phylogenomics resolving provide insights into mechanisms shaping angiosperms.

Язык: Английский

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Taxon‐specific or universal? Using target capture to study the evolutionary history of rapid radiations

Molecular Ecology Resources, Год журнала: 2021, Номер 22(3), С. 927 - 945

Опубликована: Окт. 6, 2021

Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon-specific probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales within rapidly radiating clades. We present here newly developed target set Bromeliaceae, large ecologically diverse plant family with highly variable diversification rates. The targets 1776 coding regions, including genes putatively involved key innovations, the aim empower testing of wide range evolutionary hypotheses. compare relative this set, Bromeliad1776, Angiosperms353 kit. results higher enrichment success across entire family; however, overall performance both trees is relatively comparable, highlighting vast potential resolving relationships. For more detailed or genetic analyses, example exploration gene tree concordance, nucleotide diversity structure, presents clear benefits. discuss lessons that comparative study provides future investigations, particular radiations.La captura selectiva de secuencias ADN ha surgido como una herramienta importante para la filogenética y genética poblaciones en taxones no-modelo. Mientras que el desarrollo sondas específicas cada taxón requiere un esfuerzo sostenido, las colecciones universales disponibles pueden tener potencia disminuida reconstrucción relaciones filogenéticas poco profundas o radiaciones rápidas. Presentamos aquí conjunto desarrollado recientemente familia plantas extensa, ecológicamente diversa con tasas diversificación muy variables. El se centra regiones codificación, incluyendo supuestamente implicados rasgos innovación clave, objetivo potenciar comprobación amplia gama hipótesis evolutivas. Comparamos relativa este diseñado específico, colección Angiosperms353. específico da lugar mayor éxito toda familia. Sin embargo, rendimiento global ambos reconstruir árboles filogenéticos es relativamente lo pone manifiesto gran potencial los resolver Para análisis más detallados, por ejemplo exploración congruencia genes, diversidad nucleótidos estructura población, Bromeliaceae presenta claras ventajas. Discutimos lecciones potenciales estudio comparativo proporciona futuras investigaciones poblaciones,

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Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations

Frontiers in Pharmacology, Год журнала: 2023, Номер 14

Опубликована: Май 3, 2023

Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality safety. New herbal products constantly being introduced to the market under varying regulatory frameworks, with no global consensus on definition or characterization. These biologically active mixtures sold through complex globalized value chains, which create around contamination profit-driven adulteration. Industry, academia, bodies must collaborate develop innovative strategies for identification authentication of botanicals ensure control. High-throughput sequencing (HTS) has significantly improved our understanding total species diversity within DNA mixtures. The standard concept barcoding evolved over last two decades encompass genomic data more broadly. Recent research metabarcoding focused developing methods quantifying product ingredients, yielding meaningful results a framework. Techniques, such as loop-mediated isothermal amplification (LAMP), barcode-based Recombinase Polymerase Amplification (BAR-RPA), coupled High-Resolution Melting (Bar-HRM), microfluidics-based methods, offer affordable tests detection target species. While capture genome skimming considerably increasing resolution challenging plant clades, ddPCR enables quantification samples could be detect intended unwanted ingredients medicines. Here, we explore latest advances emerging DNA-based technologies opportunities they provide taxa tools evaluating safety dietary supplements

Язык: Английский

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Phylogenomics of Puya (Bromeliaceae): Evolution in the Andean slopes and sky island ecosystems

Journal of Systematics and Evolution, Год журнала: 2024, Номер 62(2), С. 257 - 274

Опубликована: Март 1, 2024

Abstract Phylogenomics enhances our understanding of plant radiations in the biodiverse Andes. Our study focuses on Puya , primarily Andean and a part Bromeliaceae family. Using phylogenomic framework based Angiosperms353 probe set for 80 species, we explored ′s phenotypic evolution biogeography. Divergence time analyses ancestral area estimations suggested that originated Central Coastal Chile around 9 million years ago (Ma). Subsequently, it dispersed to dry valleys Andes Puna regions between 5–8 Ma, leading emergence major lineages. Key events last 2–4 include recolonization Chilean lowlands dispersal northern via Peru's Jalcas, facilitating passage through Huancabamba depression. This event gave rise high‐elevation Northern clade. phylogenetic comparative methods, tested hypothesis adaptation Andes' island‐like ecosystems was facilitated by unique leaf floral traits, life history, inflorescence morphology. findings suggest correlations axis compression, protective bract overlap, living, potentially preventing reproductive structure freezing. Semelparity evolved exclusively at high elevations, although its precise adaptive value remains uncertain. offers insights into evolution, highlighting lineages adapted can easily transition biomes. It also underscores how nature influences rates. Moreover, opens avenues explore genetic mechanisms underlying extreme mountain conditions.

Язык: Английский

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Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics

Applications in Plant Sciences, Год журнала: 2021, Номер 9(7)

Опубликована: Июль 1, 2021

Target enrichment represents a useful, cost-effective method for researchers working on the phylogenomics of non-model organisms (e.g., Cronn et al., 2012; Hale 2020). The ability to sequence customizable predefined genomic subset several dozens or even hundreds taxa allows in-depth analyses and testing phylogenetic hypotheses in ways that were not previously possible (reviewed McKain 2018). most popular methods targeted sequencing loci include (long-)amplicon (Rothfels 2017) hybridization capture (Mandel 2014; Weitemier 2014). Targeted amplicon is based single-fragment PCR amplification by using multiplexing such as microfluidic PCR-based multiple pre-selected regions Zhang Ozdemir, 2009; Ho 2014), which can then be pooled sequenced. Massively parallel was first used medical diagnostics (Turner 2009) later applied metazoan phylogenetics (Bybee 2011; O'Neill 2013). Microfluidic long-amplicon subsequently plant systematics (Uribe-Convers 2014, 2016; Gostel 2015). Amplicon-based time consuming they require careful optimization validation primers. These are also susceptible many common problems (such nonspecific products, inability amplify large their entirety, simply no products). Recently, approaches have been largely supplanted hybridization-based enrichment, relatively rapid probe design with reference few related transcriptomes genomes, simultaneous efficient recovery genes. via use customized universal probes (short nucleotide fragments between 80 120 bp length, called baits). This versatile powerful approach relies complementary sets targets from whole genome DNA cDNA samples solid-phase in-solution (Gnirke Mamanova 2010; 2012). To account frequent (ancient) duplication events, systematists identify consistently low-to-single-copy markers balance two issues: ensuring across broad range taxa, while containing sufficient informativeness. address specific research questions, including targeting genes metabolic pathway (Gardner Folk 2021) agronomic interest (Witek Soto Gomez 2019). often complete exonic sequences, but non-coding introns untranslated enriched. In-solution depends thermodynamics hybridization. process governed, part, complexity bait length. Longer tolerate more mismatches, making them suitable different species. Higher tiling density (the degree overlap, e.g., 75%) compensate failures hybridize low-quality input material, those stemming historical herbarium specimens, so-called herbariomic (Brewer While overlapping increase chance capturing target neighboring probes, there trade-off, higher tends reduce number examined per kit. nuclear overcomes potential drawbacks estimating phylogenies organelle data alone. single-locus behavior organellar DNAs means only single history provided: entire plastid expected function linkage group (Birky, 2001; see Organellar prone high rates genetic drift small population sizes, could lead less accurate estimate lineage differentiation, compared Wicke Schneeweiss, Although provide gene histories, analysis these requires bioinformatic approaches, assembly sequences without references detection local events violate assumptions orthology. In this regard, community has innovative addressing computational challenges, resulting wide adoption recent years. Angiosperms353 tool enabling phylogenomic-level any angiosperm at scale; associated (Johnson 2019) developed set low-copy infer phylogeny all green plants (One Thousand Plant Transcriptomes Initiative facilitate collection phylogenomic repeatable way. When considering Angiosperms353, it important distinguish orthologous found angiosperms 120-bp enrich libraries. selected copy (ideally, than 1400 available transcriptomes) contain useful signal deep scales. designed ~600 maximize similarity other angiosperms, minimizing design. Distinguishing when advantages, limitations, future directions systematics, discussed below. initial reports utility promising (Dodsworth 2019), key questions remain: (1) Can truly reliably recover groups flowering plants?; (2) Is an angiosperm-wide projects?; (3) What new bioinformatics tools needed apply intractable questions?; (4) Are variable enough within species extend studies? special issue its companion American Journal Botany (Baker 2021b), papers collected demonstrate employing will benefit studies. Applications Sciences focused variety methodological issues, comparisons taxon-specific sets, development lineages, lab technique libraries simultaneously, obtained Low-to-single-copy evolutionary studies Small 2004; Wu 2006; Duarte 2010). identification shared facilitated subsequent high-throughput issue, three application expansion loci. build existing resources lineage-specific (Eserman 2021; Ufimov 2021), generate performance (Siniscalchi investigate efficacy reaction (Hendriks 2021). Eserman al. (2021) describe Orchidaceae963, incorporates 254 loci, tested members subfamilies Orchidaceae. resource systematic work family conservation incorporation along custom marker becoming (Yardeni 2019; Jantzen 2020; Christe Ogutcen allow collaboration teams foster sharing Comparative naturally follow Larridon Shah For example, similar amount parsimony informative sites study Rosaceae subtribe Malinae. They showed allowed improved locus lower levels tree discordance (but Yardeni Siniscalchi Compositae1061 eight sunflower family. able average paralogy trees may simplify downstream latter versus former. Hendriks performed test case combining both (i.e., Brassicaceae) simultaneously 26 Brassicaceae included 16 tribe 10 reflecting broader sampling Their shows little extra cost sample. Taken together, highlight options choosing plants. ready low recovered orthologs taxa. feasibility during suggests additional flexibility. There designs per-sample costs focal group. However, far fewer design, allowing given probes. Whichever choice made, project, meta-analysis parallels single-gene past decades. into molecular genetics paralleled need analytical workflows. One active areas extensions data. specifically tie HybPiper 2016), flanking target-capture reads. A identified assembled Gaynor 2020), unclear whether lies poor DNA) tools). this, McLay files improve mapping frequency reads genes, result independently confirmed Slimp Lee (2021). workflow uses hidden Markov model choose clade-specific database sequences. results indicate divergence nucleic acid forgiving effect same analysis. struggling efficiency solution re-enrich file selecting appropriate Nauheimer HybPhaser, detecting hybrid assemblies. Using Nepenthes, employ two-step strategy representatives clades heterozygosity (and thus presumably hybrids). second step, putative hybrids mapped chosen clade representatives. Differential information phase placed multiply-labeled origins. HybPhaser promise phylogenetics: paralogous builds upon previous paralogs generalizable unsure about target-captured output, calculation within-species demographic parameters. adapts described workflows (Kates 2018) "supercontigs" (targeted coding regions) Within-species variants assessed jointly standard genomics programs (also Beck 2021 Wenzell further populations species, genome-scale estimation parameters now feasible develop methods. Since publication, substantial uptake questions. illustrate generated through extends beyond phylogenomics, applications genomics. Of course, adaptability comes requirement flexible analyze novel already emerging, we recognize some challenges improvements lie ahead. evaluate recovering vitro silico, reflected highlighting distinction them. presented here evidence diversity strong scales ranging level. Several innovations how recovered. Custom still resolution inclusion enable meta-analyses compare enhanced offers enriched illustrates newly complement original set. availability ever-increasing transcriptome massive should refinement better represent length extremely altered lifestyles affect rate evolution, heterotrophic Lam data, accessibility resources. Currently, central repository tailored access way taxon specific. Kew Tree Life Explorer (https://treeoflife.kew.org/) recently launched 2021a) make freely pre- post-publication thousands continued accessible store distribute accelerate progress made far. download repository, rather having filter publication-specific repositories, would significantly incorporate Similarly, centralized uploading annotated life facilitates standardization accessibility. streamlined identifying homologs building collection, much like MarkerMiner (Chamala 2015) provides starting generally cultivate growth methods, seen issue. As people opportunities positive developments further, create solutions paralogs, establishment databases likely addressed head-on embraced community. We thank authors reviewers valuable contributions Sciences. acknowledge tireless APPS publications team, especially Managing Editor Beth Parada Editor-in-Chief Theresa Culley.

Язык: Английский

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A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae

Genes, Год журнала: 2022, Номер 13(2), С. 350 - 350

Опубликована: Фев. 15, 2022

Relationships within the major clades of Cactaceae are relatively well known based on DNA sequence data mostly from chloroplast genome. Nevertheless, some nodes along backbone phylogeny, and especially generic species-level relationships, remain poorly resolved in need more informative genetic markers. In this study, we propose a new approach to solve relationships Cactaceae, applying targeted capture pipeline. We designed custom probe set for using MarkerMiner complemented it with Angiosperms353 set. then tested both sets against 36 different transcriptomes Hybpiper preferentially retaining phylogenetically loci reconstructed RAxML-NG Astral. Finally, each through sequencing 96 accessions, representing 88 species across Cactaceae. Our preliminary analyses recovered well-supported phylogeny near identical topology among clade as that plastome data. As expected, however, found incongruences when comparing our nuclear results datasets, at level. reveal great potential combination Cactaceae-specific Angiosperm353 application improve phylogenetic resolution other studies.

Язык: Английский

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