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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Plastome structure and phylogenetic relationships of genus Hydrocotyle (apiales): provide insights into the plastome evolution of Hydrocotyle

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

Published: Aug. 15, 2024

The genus Hydrocotyle Tourn. ex L. is a key group for further study on the evolution of Apiales, comprising around 170 species globally. Previous studies mainly focused separate sections and provided much information about this genus, but its infrageneric relationships are still confusing. In addition, genetic basis adaptive remains poorly understood. To investigate phylogeny we selected ten representative covering two three diversity distribution centers exhibiting rich morphology diversity. Comparative plastome analysis was conducted to clarify structural character plastomes. Positive selection analyses were implemented assess genus. Phylogenetic inferences with protein-coding sequences (CDS) 17 related also performed. Plastomes within generally conservative in structure, gene order, size. A total 14 regions (rps16-trnK, trnQ-rps16, atpI-atpH, trnC-petN-psbM, ycf3-trnS, accD-psaI-ycf4, petA-psbJ, rps12-rpl20, rpl16 intron, rps3-rpl16 rps9-rpl22, ndhF-rpl32, ndhA ycf1a) recognized as hotspot which suggested be promising DNA barcodes global phylogenetic Hydrocotyle. ycf15 species, it could used barcode identify analysis, monophyletic clades (Clade I, II, III) identified evidence rapid radiation speciation Clade I. selective pressure detected that six CDS genes (ycf1b, matK, atpF, accD, rps14, psbB) under positive selection. Within last four conservative, suggesting relation unique Apiales. Seven (atpE, psbH, ycf1a, ycf1b, rpoA, ycf2) some degree different taxa Hydrocotyle, indicating their role species. Our offers new insights into significantly enhance resolution provide genomic resources potential markers useful future

Language: Английский

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Comparative and phylogenomic plastome analysis of the Physalideae tribe (Solanaceae)

Plant Systematics and Evolution, Journal Year: 2025, Volume and Issue: 311(2)

Published: March 29, 2025

Language: Английский

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Encapsulation of Ferula-derived bioactive compounds in nanoparticles: A promising therapeutic route for cancers and infectious diseases

International Immunopharmacology, Journal Year: 2025, Volume and Issue: 157, P. 114705 - 114705

Published: April 29, 2025

Language: Английский

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Plastid phylogenomics contributes to the taxonomic revision of taxa within the genus Sanicula L. and acceptance of two new members of the genus

Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 15

Published: June 10, 2024

The genus

Language: Английский

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Phylogenomics and adaptive evolution of hydrophytic umbellifers (tribe Oenantheae, Apioideae) revealed from chloroplast genomes

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

Published: Nov. 28, 2024

Tribe Oenantheae consists mainly of aquatic species within the Apioideae. The unique morphology and habitat distinguish this group from other Apioideae groups. However, genomic information these has not been widely developed, molecular mechanisms adaptive evolution remain unclear. We provide comparative analyses on 30 chloroplast genomes tribe representing five genera to explore variation response plant adaptations. presented typical quadripartite structures, with sizes ranging 153,024 bp 155,006 bp. Gene content order were highly conserved no significant expansion or contraction observed. Seven regions (rps16 intron–trnK, rpoB–trnC, trnE–trnT–psbD, petA–psbJ, ndhF–rpl32–trnL, ycf1a–rps15, ycf1a gene) identified as remarkable candidate DNA markers for future studies identification, biogeography, phylogeny Oenantheae. Our study elucidated relationships among subdivided Sium Oenanthe. Oenanthe I clade be further clarified. Eight positively selected genes (accD, rbcL, rps8, ycf1a, ycf1b, ycf2, ndhF, ndhK) persuasively detected under site models tests, might have played roles in adaptation environments. results sufficient subsequent Oenantheae, promote understanding

Language: Английский

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Comparative Analysis and Phylogeny of the Complete Chloroplast Genomes of Nine Cynanchum (Apocynaceae) Species

Genes, Journal Year: 2024, Volume and Issue: 15(7), P. 884 - 884

Published: July 5, 2024

Cynanchum belongs to the Apocynaceae family and is a morphologically diverse genus that includes around 200 shrub or perennial herb species. Despite utilization of CPGs, few molecular phylogenetic studies have endeavored elucidate infrafamilial relationships within through extensive taxon sampling. In this research, we constructed phylogeny estimated divergence time based on chloroplast genomes (CPGs) nine We sequenced annotated (CP) in study. The comparative analysis these from species revealed typical quadripartite structure, with total sequence length ranging 158,283 161,241 base pairs (bp). CP genome (CPG) was highly conserved moderately differentiated. Through annotation, identified 129–132 genes. Analysis boundaries inverted repeat (IR) regions showed consistent positioning: rps19 gene located IRb region, varying 46 50 bp. IRb/SSC junctions were between trnN ndhF did not detect major expansions contractions IR region rearrangements insertions CPGs results SSR variation number SSRs, 112 150. five types largest mononucleotide repeats, smallest hexanucleotide repeats. long repeats cp 35 80. Cynanchum, GC3s values ranged 26.80% 27.00%, indicating strong bias towards A/U-ending codons. Comparative analyses four hotspot CPG, ndhA-ndhH, trnI-GAU-rrn16, psbI-trnS-GCU, rps7-ndhB, which could potentially serve as markers. addition, tree construction CPG indicated formed monophyletic group. Molecular dating suggested diverged its sister approximately 18.87 million years ago (Mya) diversification primarily occurred during recent Miocene epoch. estimation presented study will facilitate future research aid differentiation, investigations into economically ecologically important genus.

Language: Английский

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Chloroplast genomes of Simarouba Aubl., molecular evolution and comparative analyses within Sapindales

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Sept. 12, 2024

Language: Английский

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Sesquiterpenes and Sesquiterpene Derivatives from Ferula: Their Chemical Structures, Biosynthetic Pathways, and Biological Properties

Antioxidants, Journal Year: 2023, Volume and Issue: 13(1), P. 7 - 7

Published: Dec. 19, 2023

Ferula is a genus of flowering plants known for its edible and medicinal properties. Since ancient times, many species have been used in traditional medicine to treat various health issues across countries, such as digestive disorders, respiratory problems, even remedy headaches toothaches. In addition, they are also flavoring agent cuisines. As the main active ingredients Ferula, sesquiterpenes their derivatives, especially sesquiterpene coumarins, phenylpropanoids, chromones, attracted attention scientists due diversity chemical structures, well extensive promising biological properties, antioxidative, anti-inflammatory, antibacterial However, there has not comprehensive review derivatives from this plant. This aims provide an overview biosynthetic pathways, properties which may help guide future research directions possible application methods valuable

Language: Английский

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