Phylogenomic approaches untangle early divergences and complex diversifications of the olive plant family

BMC Biology, Год журнала: 2022, Номер 20(1)

Опубликована: Апрель 25, 2022

Abstract Background Deep-branching phylogenetic relationships are often difficult to resolve because signals obscured by the long history and complexity of evolutionary processes, such as ancient introgression/hybridization, polyploidization, incomplete lineage sorting (ILS). Phylogenomics has been effective in providing information for resolving both deep- shallow-scale across all branches tree life. The olive family (Oleaceae) is composed 25 genera classified into five tribes with tribe Oleeae consisting four subtribes. Previous analyses showed that ILS and/or hybridization led incongruence family. It was essential distinguish signal conflicts, explore mechanisms uncertainties concerning family, especially at deep-branching nodes. Results We used whole plastid genome nuclear single nucleotide polymorphism (SNP) data infer assess variation rates among main clades also 2608 1865 orthologous genes Oleaceae subtribes Oleeae, respectively. Concatenated coalescence trees based on genome, SNPs multiple suggest events introgression during diversification Oleaceae. Additionally, there extreme heterogeneity substitution tribes. Furthermore, our results supported rather than ILS, factor discordance have originated via polyploidy, its most likely parentages ancestral Jasmineae or sister group, which a “ghost lineage,” Forsythieae. However, mainly responsible Oleeae. Conclusions This study showcases using sequence datasets (plastid genomes, thousands genes) diverse phylogenomic methods partition, heterogeneous models, quantifying branch lengths (QuIBL) analysis, species network analysis can facilitate untangling complex processes introgression, paleopolyploidization, ILS.

Язык: Английский

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Insights into the phylogeny and chloroplast genome evolution of Eriocaulon (Eriocaulaceae)

BMC Plant Biology, Год журнала: 2023, Номер 23(1)

Опубликована: Янв. 14, 2023

Eriocaulon is a wetland plant genus with important ecological value, and one of the famous taxonomically challenging groups among angiosperms, mainly due to high intraspecific diversity low interspecific variation in morphological characters species within this genus. In study, 22 samples representing 15 from China, were sequenced combined published test phylogenetic resolution using complete chloroplast genome. Furthermore, comparative analyses genomes performed investigate genome evolution Eriocaulon.The nine proved highly similar size, gene content, order. The exhibited typical quadripartite structures lengths 150,222 bp 151,584 bp. Comparative revealed that four mutation hotspot regions (psbK-trnS, trnE-trnT, ndhF-rpl32, ycf1) could serve as effective molecular markers for further identification species. Phylogenetic results supported monophyletic group. identified relationships taxonomic treatment section Heterochiton Leucantherae, was first divergent tree divided into five clades. divergence times indicated all sections diverged later Miocene most extant Quaternary. phylogeny rapid radiation occurred history Eriocaulon.Our study mostly at level China demonstrated power whole sequences. developed can help us better identify understand evolutionary future.

Язык: Английский

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Phylogenomics and evolution of the Acer section Lithocarpa

Scientia Horticulturae, Год журнала: 2025, Номер 341, С. 113988 - 113988

Опубликована: Янв. 29, 2025

Язык: Английский

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Phylogenomics and morphological evolution of the mega-diverse genus Artemisia (Asteraceae: Anthemideae): implications for its circumscription and infrageneric taxonomy

Annals of Botany, Год журнала: 2023, Номер 131(5), С. 867 - 883

Опубликована: Март 28, 2023

Abstract Background and Aims Artemisia is a mega-diverse genus consisting of ~400 species. Despite its medicinal importance ecological significance, well-resolved phylogeny for global Artemisia, natural generic delimitation infrageneric taxonomy remain missing, owing to the obstructions from limited taxon sampling insufficient information on DNA markers. Its morphological characters, such as capitulum, life form leaf, show marked variations are widely used in taxonomy. However, their evolution within poorly understood. Here, we aimed reconstruct via phylogenomic approach, infer evolutionary patterns key characters update circumscription Methods We sampled 228 species (258 samples) allies both fresh herbarium collections, covering all subgenera main geographical areas, conducted analysis based nuclear single nucleotide polymorphisms (SNPs) obtained genome skimming data. Based phylogenetic framework, inferred possible six previous Key Results The Kaschgaria was revealed be nested with strong support. A eight highly supported clades recovered, two which were identified first time. Most previously recognized not monophyletic. Evolutionary inferences showed that different states these originated independently more than once. Conclusions enlarged include Kaschgaria. traditionally do match new tree. They experienced complex history thought. propose revised newly circumscribed accommodate results.

Язык: Английский

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Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars

International Journal of Molecular Sciences, Год журнала: 2023, Номер 24(4), С. 3606 - 3606

Опубликована: Фев. 10, 2023

Lagerstroemia indica L. is a well-known ornamental plant with large pyramidal racemes, long flower duration, and diverse colors cultivars. It has been cultivated for nearly 1600 years essential investigating the germplasm assessing genetic variation to support international cultivar identification breeding programs. In this study, 20 common cultivars from different varietal groups morphologies, as well multiple wild relative species, were analyzed investigate maternal donor of discover relationships among based on plastome nuclear ribosomal DNA (nrDNA) sequences. A total 47 single nucleotide polymorphisms (SNPs) 24 insertion/deletions (indels) identified in cultivars' 25 SNPs nrDNA. Phylogenetic analysis sequences showed that all formed clade species indica, indicating was Population structure PCA analyses supported two clades cultivars, which exhibited significant differences according dataset. The results nrDNA divided into three most had at least backgrounds higher gene flow. Our suggest can be used molecular markers

Язык: Английский

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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Journal of Integrative Plant Biology, Год журнала: 2024, Номер 66(3), С. 546 - 578

Опубликована: Янв. 30, 2024

Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of angiosperms in fossil record was referred to Darwin as "abominable mystery," hence contributing heightened interest angiosperm evolution. display wide ranges morphological, physiological, and ecological characters, some which have probably influenced their species richness. evolutionary analyses these characteristics help address questions diversification require well resolved phylogeny. Following great successes phylogenetic using plastid sequences, dozens thousands nuclear genes from next-generation sequencing been used phylogenomic analyses, providing phylogenies new insights into evolution angiosperms. In this review we focus on recent large clades, orders, families, subdivisions families provide a summarized Nuclear Phylogenetic Tree Angiosperm Families. newly established relationships highlighted compared previous results. sequenced genomes Amborella, Nymphaea, Chloranthus, Ceratophyllum, monocots, Magnoliids, basal eudicots, facilitated phylogenomics among five major clades. All but one 64 orders were included except placements several orders. Most robust highly supported placements, especially for within important families. Additionally, examine divergence time estimation biogeographic basis frameworks discuss differences analyses. Furthermore, implications ancestral reconstruction characters groups, limitations current studies, taxa that future attention.

Язык: Английский

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Phylogenomics and biogeography of Catalpa (Bignoniaceae) reveal incomplete lineage sorting and three dispersal events

Molecular Phylogenetics and Evolution, Год журнала: 2021, Номер 166, С. 107330 - 107330

Опубликована: Окт. 22, 2021

Язык: Английский

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Chloroplast Genome Evolution and Species Identification of Styrax (Styracaceae)

BioMed Research International, Год журнала: 2022, Номер 2022, С. 1 - 13

Опубликована: Фев. 24, 2022

The genus Styrax L. consists of approximately 130 species distributed in the Americas, eastern Asia, and Mediterranean region. phylogeny evolutionary history this are not clear. Knowledge phylogenetic relationships method for identification will be critical evolution genus. In study, we sequenced chloroplast genome 17 samples added additional sequences from GenBank. data were used to investigate evolution, infer relationships, access rate within Styrax. contains typical quadripartite structures, ranging 157,641 bp 159,333 bp. 114 unique genes. P distance among ranged 0.0003 0.00611. Seventeen small inversions SSR sites discovered genome. By comparing with sequences, six mutation hotspots identified, markers ycf1b trnT-trnL identified as best Styrax-specific DNA barcodes. specific barcodes superbarcode exhibited higher discriminatory power than universal Chloroplast phylogenomic results improved resolution compared previous analyses.

Язык: Английский

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Species discrimination in Schima (Theaceae): Next‐generation super‐barcodes meet evolutionary complexity

Molecular Ecology Resources, Год журнала: 2022, Номер 22(8), С. 3161 - 3175

Опубликована: Июль 5, 2022

Plastid genome and nuclear ribosomal DNA (nrDNA) arrays, proposed recently as "super-barcodes," might provide additional discriminatory power overcome the limitations of traditional barcoding loci, yet super-barcodes need to be tested for their effectiveness in more plant groups. Morphological homoplasy among Schima species makes genus a model testing efficacy super-barcodes. In this study, we generated multiple data sets comprising standard barcodes (matK, rbcL, trnH-psbA, nrITS) (plastid genome, nrDNA arrays) across 58 individuals from 12 out 13 China. No samples were correctly assigned using while only 27.27% with accessions distinguished plastid its partitioned sets-the lowest estimated rate super-barcode success literature so far. For other taxa similarly divergence low levels genetic variation, incomplete lineage sorting, hybridization or taxonomic oversplitting are all possible causes failure. Taken together, our study suggests that by no means immune challenges imposed evolutionary complexity. We therefore call developing multilocus markers discrimination

Язык: Английский

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Phylogenomics of Aralia sect. Aralia (Araliaceae): Signals of hybridization and insights into its species delimitations and intercontinental biogeography

Molecular Phylogenetics and Evolution, Год журнала: 2023, Номер 181, С. 107727 - 107727

Опубликована: Фев. 7, 2023

Язык: Английский

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