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

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: April 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.

Language: Английский

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

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: Jan. 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.

Language: Английский

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Phylogenomics and evolution of the Acer section Lithocarpa

Scientia Horticulturae, Journal Year: 2025, Volume and Issue: 341, P. 113988 - 113988

Published: Jan. 29, 2025

Language: Английский

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Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(4), P. 3606 - 3606

Published: Feb. 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

Language: Английский

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Historical climate change and vicariance events contributed to the intercontinental disjunct distribution pattern of ash species (Fraxinus, Oleaceae)

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: May 20, 2024

The Northern Hemisphere temperate forests exhibit a disjunct distributional pattern in Europe, North America, and East Asia. Here, to reveal the promoter of intercontinental distribution, Fraxinus was used as model organism integrate abundant fossil evidence with high-resolution phylogenies phytogeographic analysis. We constructed robust phylogenetic tree using genomic data, reconstructed geographic ancestral areas, evaluated effect incorporating information on biogeographic history. relationships were highly resolved divided into seven clades. originated western America during Eocene, six dispersal events five vicariance occured. Results suggest that climate change contributed distribution Fraxinus. Moreover, results highlight necessity integrating relationship improve reliability inferred our understanding processes underlying distributions.

Language: Английский

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Chloroplast Genomes Evolution and Phylogenetic Relationships of Caragana species

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(12), P. 6786 - 6786

Published: June 20, 2024

Caragana sensu lato (s.l.) includes approximately 100 species that are mainly distributed in arid and semi-arid regions. ecologically valuable for their roles windbreaking sand fixation. However, the taxonomy phylogenetic relationships of genus still unclear. In this study, we sequenced assembled chloroplast genomes representative reconstructed robust at section level. The genome has lost inverted repeat region wascategorized loss clade (IRLC). eight ranged from 128,458 bp to 135,401 contained 110 unique genes. All have a highly conserved structure gene order. number long repeats simple sequence (SSRs) showed significant variation among species, indicating heterogeneous evolution Caragana. Selective pressure analysis genes revealed most protein-coding evolved under purifying selection. analyses indicated each forms clade, except Spinosae, which was divided into two clades. This study elucidated within widely detailed information obtained can serve as resource understanding molecular dynamics

Language: Английский

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Phylogenomic insights into the historical biogeography, character-state evolution, and species diversification rates of Cypripedioideae (Orchidaceae)

Molecular Phylogenetics and Evolution, Journal Year: 2024, Volume and Issue: 199, P. 108138 - 108138

Published: July 6, 2024

Language: Английский

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Phylogenetic diversity and interspecies competition shaped species diversity in adaptive radiated Ligustrum (Oleaceae)

Journal of Systematics and Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 13, 2024

Abstract Speciation events often occur with adaptive radiation. The factors that promote these radiating species diversity patterns have intrigued biologists for more than a century. In the present study, we used radiated genus Ligustrum to evaluate relative contributions of environment, interactions, phylogenetic diversity, and diversification rates in generating extant patterns. Using complete chloroplast genome data, reconstructed highly supported dated backbone relationships . Biogeographic results indicated originated Southwest China during Oligocene spread suitable areas were warm humid via 18 dispersal events. For overlapping ranges pairs, smaller distance was detected high overlap low overlap, which is consistent no significant difference niche among different species. We found interspecies competition induced by insignificant divergence shaped global pattern diversity.

Language: Английский

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Genetic diversity and population divergence of Leonurus japonicus and its distribution dynamic changes from the last interglacial to the present in China

BMC Plant Biology, Journal Year: 2023, Volume and Issue: 23(1)

Published: May 25, 2023

Leonurus japonicus, a significant medicinal plant known for its therapeutic effects on gynecological and cardiovascular diseases, has genetic diversity that forms the basis germplasm preservation utilization in medicine. Despite economic value, limited research focused divergence.The avg. nucleotide of 59 accessions from China were 0.00029 hotspot regions petN-psbM rpl32-trnL(UAG) spacers, which can be used genotype discrimination. These divided into four clades with divergence. The subclades, split at approximately 7.36 Ma, likely influenced by Hengduan Mountains uplift global temperature drop. initial divergence gave rise to Clade D, crown age estimated 4.27 followed C, 3.39 Ma. not showed clear spatial distribution. Suitable climatic conditions species identified, including warmest quarter precipitation 433.20 mm ~ 1,524.07 mm, driest month > 12.06 coldest min temp -4.34 °C. high suitability distribution contraction LIG LGM, expansion LGM present. acted as glacial refuge during climate changes.Our findings reflected phylogenetic relationships within L. japonicus identified could facilitate time estimation suitable area simulation revealed evolution dynamics this may propose conservation suggestions exploitation approaches future.

Language: Английский

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Complete Chloroplast Genome of Hypericum perforatum and Dynamic Evolution in Hypericum (Hypericaceae)

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(22), P. 16130 - 16130

Published: Nov. 9, 2023

Hypericum perforatum (St. John's Wort) is a medicinal plant from the Hypericaceae family. Here, we sequenced whole chloroplast genome of H. and compared variation among five species to discover dynamic changes elucidate mechanisms that lead rearrangements in genomes. The 139,725 bp, exhibiting circular quadripartite structure with two copies inverted repeats (IRs) separating large single-copy region small region. encodes 106 unique genes, including 73 protein-coding 29 tRNAs, 4 rRNAs. genomes exhibit rearrangement significant variations species. size was remarkably associated expansion or contraction IR regions gene losses. Three genes-trnK-UUU, infA, rps16-were lost, three genes-rps7, rpl23, rpl32-were pseudogenized Hypericum. All lost introns clpP, intron rps12, second ycf3. contain many long repeat sequences, suggesting role facilitating rearrangements. Most according molecular evolution assessments, are under purifying selection.

Language: Английский

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