Plastid phylogenomic insights into relationships of all flowering plant families

BMC Biology, Journal Year: 2021, Volume and Issue: 19(1)

Published: Oct. 28, 2021

Abstract Background Flowering plants (angiosperms) are dominant components of global terrestrial ecosystems, but phylogenetic relationships at the familial level and above remain only partially resolved, greatly impeding our full understanding their evolution early diversification. The plastome, typically mapped as a circular genome, has been most important molecular data source for plant phylogeny reconstruction decades. Results Here, we assembled by far largest plastid dataset angiosperms, composed 80 genes from 4792 plastomes 4660 species in 2024 genera representing all currently recognized families. Our tree (PPA II) is essentially congruent with those previous phylogenomic analyses generally provides greater clade support. In PPA II tree, 75% nodes or ordinal 78% were resolved high bootstrap support (BP ≥ 90). We obtained strong many interordinal interfamilial that poorly previously within core eudicots, such Dilleniales, Saxifragales, Vitales being successive sisters to remaining rosids, Santalales, Berberidopsidales, Caryophyllales asterids. However, placement magnoliids, although sister other Mesangiospermae , not well supported disagrees topologies inferred nuclear data. Relationships among five major clades intractable despite increased sampling, probably due an ancient rapid radiation. Conclusions provide comprehensive date well-resolved which together foundation future evolutionary studies flowering plants.

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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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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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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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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Highly Resolved Papilionoid Legume Phylogeny Based on Plastid Phylogenomics

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

Published: Feb. 23, 2022

Comprising 501 genera and around 14,000 species, Papilionoideae is not only the largest subfamily of Fabaceae (Leguminosae; legumes), but also one most extraordinarily diverse clades among angiosperms. Papilionoids are a major source food forage, ecologically successful in all biomes, display dramatic variation both floral architecture plastid genome (plastome) structure. Plastid DNA-based phylogenetic analyses have greatly improved our understanding relationships groups Papilionoideae, yet backbone phylogeny remains unresolved. In this study, we sequenced assembled 39 new plastomes that covering key representing morphological diversity subfamily. From 244 total taxa, produced eight datasets for maximum likelihood (ML) based on entire and/or concatenated sequences 77 protein-coding (CDS) two multispecies coalescent (MSC) individual gene trees. We additionally combined nucleotide dataset comprising CDS plus matK only, which papilionoid were sampled. A ML tree plastome maximally supported deep recent divergences papilionoids (223 out 236 nodes). The Swartzieae, ADA (Angylocalyceae, Dipterygeae, Amburaneae), Cladrastis, Andira, Exostyleae formed grade to remainder concordant with nine MSC Phylogenetic remaining five lineages (Vataireoid, Dermatophyllum, Genistoid s.l., Dalbergioid Baphieae + Non-Protein Amino Acid Accumulating or NPAAA clade) remained uncertain, because insufficient support conflicting Our study fully resolved nodes however, some require further exploration. More genome-scale data rigorous needed disentangle lineages.

Language: Английский

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Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments

Molecular Biology and Evolution, Journal Year: 2022, Volume and Issue: 39(5)

Published: April 14, 2022

Land plants first evolved from freshwater algae, and flowering returned to water as early the Cretaceous multiple times subsequently. Alismatales is largest clade of aquatic angiosperms including all marine angiosperms, well terrestrial plants. We used explore plant adaptations environments by analyzing a data set that included 95 samples (89 species) covering four genomes 91 transcriptomes (59 generated in this study). To provide basis for investigating adaptations, we assessed phylogenetic conflict whole-genome duplication (WGD) events Alismatales. recovered relationship three main clades (Tofieldiaceae, Araceae) + core Alismatids. also found among was best explained incomplete lineage sorting introgression. Overall, identified 18 putative WGD across One them occurred at most recent common ancestor Alismatids, seagrass lineages. life-form were both important different evolutionary patterns genes related adaptation. For example, several light- or ethylene-related lost Zosteraceae, but are present other seagrasses species. Stomata-related submersed species seagrasses. Nicotianamine synthase genes, which iron intake, expanded Our results advance understanding adaptation WGDs using phylogenomics.

Language: Английский

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A plastid phylogenomic framework for the palm family (Arecaceae)

BMC Biology, Journal Year: 2023, Volume and Issue: 21(1)

Published: March 8, 2023

Abstract Background Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies large families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, a family ca. 181 genera and 2600 important components tropical rainforests bearing great cultural economic significance. Taxonomy phylogeny have been extensively investigated by series molecular phylogenetic in last two decades. Nevertheless, some relationships within not yet well-resolved, especially at tribal generic levels, consequent impacts for downstream research. Results Plastomes 182 palm representing 111 were newly sequenced. Combining these previously published plastid DNA data, we able to sample 98% conduct investigation family. Maximum likelihood analyses yielded robustly supported hypothesis. Phylogenetic among all five subfamilies 28 tribes most inter-generic also resolved strong support. Conclusions inclusion nearly generic-level coupled genomes strengthened understanding plastid-based palms. This comprehensive genome dataset complements growing body nuclear genomic data. Together, datasets form novel baseline palms an increasingly robust framework future comparative biological this exceptionally plant

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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The first mitogenome of Lauraceae (Cinnamomum chekiangense)

Plant Diversity, Journal Year: 2023, Volume and Issue: 46(1), P. 144 - 148

Published: Nov. 18, 2023

• The first reported mitochondrial genome ( Cinnamomum chekiangense ) of the Lauraceae family. mitogenome C. retains almost all ancestral protein-coding genes and has highest RNA editing number in angiosperms to date. Both plastid phylogenetic trees support magnoliids as a sister group clade comprising monocots eudicots.

Language: Английский

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