Chloroplast Genome Sequencing and Comparative Analysis of Six Medicinal Plants of Polygonatum

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 1, 2025

ABSTRACT The genus Polygonatum boasts abundant germplasm resources and comprises numerous species. Among these, medicinal plants of this genus, which have a long history, garnered attention scholars. This study sequenced analyzed the chloroplast genomes six species ( P. zanlanscianense , kingianum sibiricum cyrtonema filipes odoratum respectively) to explore their interspecific relationships. sequence length (154, 578–155, 807 bp) genome structure were conserved among species, with typical tetrad structure. 127–131 genes contained in genomes, 84–85 are protein‐coding genes, 37–38 transfer RNA 6–8 ribosomal genes. 64–76 simple repeats (SSRs) 36–62 repetitive sequences. Codon bias patterns tended use codons ending A/T. In 30 types RSCU > 1, 93.3% ended A/T Twenty‐one highly variable plastid regions identified plants. Furthermore, phylogenetic analysis encompassing these 53 other revealed that clustered together on one clade, whereas formed separate clades. Notably, emerged as standalone our tree reinforces classification forming monophyly. provides novel basis for intragenus taxonomy DNA barcoding molecular identification within

Language: Английский

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Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

BMC Plant Biology, Journal Year: 2024, Volume and Issue: 24(1)

Published: Jan. 24, 2024

Abstract Background The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on provided us with good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, evolutionary history of this also remains inadequately understood. plastid genomes possessing highly conserved structure limited rate proved be an effective tool studying plant phylogeny evolution. Results In current study, we newly sequenced assembled fifteen complete plastomes. Combined two previously reported plastomes, performed comprehensively phylogenomics analyses gain novel insights into genus. comparative results indicated seventeen plastomes exhibited high degree conservation similarity in terms their structure, size, GC content, gene order, IR borders, codon bias patterns SSRs profiles. Such as all them displayed typical quadripartite including large single copy region (LSC: 85,074–86,197 bp), small (SSC: 17,047–17,132 bp) separated by pair inverted repeat regions (IRs: 26,176–26,334 bp). And had similar boundaries adjacent genes were identical. rps 19 was located at junction LSC/IRa, IRa/SSC between trn N ndh F gene, ycf 1 appeared SSC/IRb IRb/LSC boundary rpl 12 H gene. Twelve specific mutation hotspots ( atp F, cem A, acc D, 22, rbc L, mat K, 1, -psb 4 -cem L -acc E -trn T G R) identified can serve potential DNA barcodes species identification within . Furthermore, data Internal Transcribed Spacer (ITS) sequences reconstruct Sanicula. tree topologies incongruent, both strong evidence supporting monophyly Saniculoideae Apioideae. addition, sister groups Apioideae strongly suggested. involved study clustered clade, Eryngium together. However, it clearly observed sections respectively recovered monophyletic group. Molecular dating analysis explored origin occurred during late Eocene period, approximately 37.84 Ma (95% HPD: 20.33–52.21 Ma) years ago diversification early Miocene 18.38 10.68–25.28 Ma). Conclusion plastome-based ITS-based generated incongruences, which may attributed event hybridization/introgression, incomplete lineage sorting (ILS) chloroplast capture. Our highlighted power plastome significantly improve phylogenetic supports resolutions, efficiently explore Miocene, largely influenced prevalence East Asian monsoon uplift Hengduan Mountains (HDM). summary, our provides evolution, relationships, framework evolution

Language: Английский

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Morphology, phylogeography, phylogeny, and taxonomy of Cyclorhiza (Apiaceae)

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 8, 2025

The genus Cyclorhiza is endemic to China and belongs the Apiaceae family, which widely distributed in Himalaya-Hengduan Mountains (HHM) region. However, its morphology, phylogeny, phylogeography, taxonomy, evolutionary history were not investigated due insufficient sampling lack of population plastome data. Additionally, we found that Seseli purpureovaginatum was similar members but resembled species indicating taxonomic position S. needs be re-evaluated. First, observed morphology genus. Second, newly sequenced four plastomes conducted comparative analyses. Third, used internal transcribed spacer (ITS) chloroplast DNA (cpDNA) (matK, trnQ-rps16, trnD-trnT) from 27 populations totaling 244 individuals explore genetic diversity structure. Finally, performed phylogenetic analyses based on three datasets (plastome data, ITS sequences, haplotypes) estimated origin divergence time plants highly similar, their structure features conserved. possessed high significant lineage geographic structure, may associated with long-term history, complex terrain habitat, sexual reproduction mode. originated late Eocene (36.03 Ma), closely related early uplift Qinghai-Tibetan Plateau (QTP) Hengduan (HDM). diversification occurred Oligocene (25.43 largely influenced by colonization available climate terrain. results showed clustered into a separate clade nested within Cyclorhiza. waltonii sister peucedanifolia, puana purpureovaginatum. Thus, analyses, evidence, should transferred All these evidences further supported monophyly after including clarified generic limits provided classification key index for In conclusion, study comprehensively evolution first time.

Language: Английский

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The plastid genome of twenty-two species from Ferula, Talassia, and Soranthus: comparative analysis, phylogenetic implications, and adaptive evolution

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

Published: Jan. 5, 2023

Abstract Background The Ferula genus encompasses 180–185 species and is one of the largest genera in Apiaceae, with many possessing important medical value. previous studies provided more information for , but its infrageneric relationships are still confusing. In addition, genetic basis adaptive evolution remains poorly understood. Plastid genomes variable sites have potential to reconstruct robust phylogeny plants investigate plants. Although chloroplast been reported within genus, few conducted using genomes, especially endemic China. Results Comprehensively comparative analyses 22 newly sequenced assembled plastomes indicated that these had highly conserved genome structure, gene number, codon usage, repeats type distribution, varied size, GC content, SC/IR boundaries. Thirteen mutation hotspot regions were detected they would serve as promising DNA barcodes candidates identification related genera. Phylogenomic high supports resolutions showed Talassia transiliensis Soranthus meyeri nested thus should be transferred into genus. Our phylogenies also monophyly subgenera Sinoferula Narthex Twelve genes significant posterior probabilities identified positively selective analysis, their function may relate photosystem II, ATP subunit, NADH dehydrogenase. Most them might play an role help adapt high-temperatures, strong-light, drought habitats. Conclusion Plastome data powerful efficient improve support resolution complicated phylogeny. helpful harsh environment. Overall, our study supplies a new perspective comprehending .

Language: Английский

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Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 13

Published: Jan. 6, 2023

Background Phyllanthus urinaria L. is extensively used as ethnopharmacological material in China. In the local marketplace, this medicine can be accidentally contaminated, deliberately substituted, or mixed with other related species. The contaminants herbal products are a threat to consumer safety. Due scarcity of genetic information on plants, more molecular markers needed avoid misidentification. Methods study, complete chloroplast genome nine species genus was de novo assembled and characterized. Results This study revealed that all these exhibited conserved quadripartite structure, which includes large single copy (LSC) region small (SSC) region, two copies inverted repeat regions (IRa IRb), separate LSC SSC regions. And codon usage, sequences were highly showed similarities among Three variable ( trnS-GCU-trnG-UCC , trnT-UGU-trnL-UAA petA-psbJ ) might helpful potential for identifying P. its contaminants. addition, clock analysis results divergence time occur at ~ 48.72 Ma. Conclusion provides valuable further identification, evolution, phylogenetic research .

Language: Английский

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Backbone phylogeny and adaptive evolution of Pleurospermum s. l.: New insights from phylogenomic analyses of complete plastome data

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: March 30, 2023

Pleurospermum is a taxonomically challenging taxon of Apiaceae, as its circumscription and composition remain controversial for morphological similarities with several related genera, leading to dispute between in the broad sense strict sense. While evidence from previous molecular studies recognized plural branching lineages within s. l., it did not support latest delimitation str. by only two closely northern species. So far, no proper has come up, many taxa l. unresolved, which may be due poor phylogenetic resolution yielded barely ITS sequences. Herein, we newly assembled 40 complete plastomes 36 species 34 were first reported generated well-resolved backbone phylogeny framework subfamily Apioideae. From greatly improved resolution, total six well-supported monophyletic falling different major clades Combining characteristics inference, suggested re-delimit introducing nine mainly Himalayan regions proposed boundary features; remaining excluded incorporate into their more being revealed. On this basis, plastome comparison revealed high conservatism but also mild differences among structure gene evolution. Overall, our study provided essential further difficult

Language: Английский

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Genome skimming provides evidence to accept two new genera (Apiaceae) separated from the Peucedanum s.l.

Frontiers in Plant Science, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 20, 2025

Background The Peucedanum s.l. genus, the backbone member of subfamily Apioideae, includes many medically and economically important plants. Although previous studies have proved that genus was not a natural taxonomic unit taxonomists also conducted several revisions for taxa this classifications numerous still been satisfactorily resolved, especially those endemic to China. Therefore, we comprehensive revision within polyphyletic in study. Methods We used two molecular datasets (103 plastomes 43 nrDNA sequences) generated by genome skimming reconstructed reliable phylogenetic framework with high support resolution. In addition, investigated divergence time core clade taxa. Results Discussion Both analyses failed recover as monophyletic group robustly supported P. morisonii , representative s.s., distantly related other members, which implied these were “truly plants”. Among plastid-based phylogenies recognized clades, A (four species) B (10 taxa). Meanwhile, obvious features morphology, plastome, chromosome number each detected: dorsally compressed glabrous mericarps filiform dorsal ribs, winged lateral vittae commissure furrow, IRa/LSC border falling into rpl 23 gene, an overall plastome size 152,288-154,686 bp, numbers 2n=20 found A; whereas pubescent ycf 2 146,718-147,592 2n=22 discovered B. established new genera ( Shanopeucedanum gen. nov. Sinopeucedanum nov.) respectively accommodate clades Furthermore, dating analysis showed diversification occurred early Pleistocene late Pliocene, respectively, may driven complex geological climate shifts periods. summary, our study impelled members improved system Apiaceae family.

Language: Английский

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Phenylpropanoid-rich Essential Oils of Peucedanum longifolium Waldst. & Kit. from Montenegro and Their Antioxidant Properties

Natural Product Communications, Journal Year: 2025, Volume and Issue: 20(4)

Published: April 1, 2025

Objective: To examine the impact of prolonged and fractionated extraction on yield, chemical composition, bioactivity essential oils (EOs) from Peucedanum longifolium Waldst. & Kit. (PL). Methods: A 24-h hydrodistillation method was applied to flower fruit plant material collected two localities in Montenegro (Lovćen Rumija). total 24 EOs were obtained analysed for composition using Gass Chromatography-Mass Spectrometry related antioxidant activity, assessed by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging Ferric-Reducing Antioxidant Power (FRAP) assays. Results: significant difference yield observed: PL Lovćen gave up 3 times more than that originating Rumija. 66 compounds identified, with myristicin as main constituent (up 72.9%), accompanied its structural analogues elemicin 18.8%) isoelemicin 47%), amount which varied depending reproductive organ locality. Most showed weak activity IC 50 value 0.61-2.54 mg/mL (assessed DPPH), while FRAP 3.48-11.56 mmol Fe 2+ /g indicating moderate reducing power. Conclusion: phenylpropanoid-rich chemotype, previously unreported either or other species, distinguished. This study also reports first time properties PL.

Language: Английский

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Comparative Analysis of the Complete Chloroplast Genomes in Allium Section Bromatorrhiza Species (Amaryllidaceae): Phylogenetic Relationship and Adaptive Evolution

Genes, Journal Year: 2022, Volume and Issue: 13(7), P. 1279 - 1279

Published: July 19, 2022

With the development of molecular sequencing approaches, many taxonomic and phylogenetic problems genus Allium L. have been solved; however, relationships some subgenera or sections, such as section Bromatorrhiza, remain unresolved, which has greatly impeded our full understanding species among major clades Allium. In this study, complete chloroplast (cp) genomes nine in sect. Bromatorrhiza were determined using Illumina paired-end sequencing, NOVOPlasty de novo assembly strategy, PGA annotation method. The results showed that cp genome exhibited high conservation revealed a typical circular tetrad structure. Among species, gene content, SSRs, codon usage, RNA editing site similar. structure IR regions’ fluctuation investigated while genes, CDSs, non-coding regions extracted for phylogeny reconstruction. Evolutionary rates (Ka/Ks values) calculated, positive selection analysis was further performed branch-site model. Five hypervariable identified candidate markers authentication. A clear relationship detected based on concatenated genes respectively, suggested is monophyly. addition, there three with higher Ka/Ks values (rps2, ycf1, ycf2), four (rpoC2, atpF, atpI, rpl14) to own selected sites. These provide new insights into plastome component, phylogeny, evolution species.

Language: Английский

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Plastome evolution and phylogenomics of Impatiens (Balsaminaceae)

Planta, Journal Year: 2023, Volume and Issue: 257(2)

Published: Jan. 25, 2023

Language: Английский

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