The gradual establishment of complex coumarin biosynthetic pathway in Apiaceae

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Авг. 10, 2024

Complex coumarins (CCs) represent characteristic metabolites found in Apiaceae plants, possessing significant medical value. Their essential functional role is likely as protectants against pathogens and regulators responding to environmental stimuli. Utilizing genomes transcriptomes from 34 including our recently sequenced Peucedanum praeruptorum, we conduct comprehensive phylogenetic analyses reconstruct the detailed evolutionary process of CC biosynthetic pathway Apiaceae. Our results show that three key enzymes - p-coumaroyl CoA 2'-hydroxylase (C2'H), C-prenyltransferase (C-PT), cyclase originated successively at different nodes within through various means gene duplications: ectopic tandem duplications. Neofunctionalization endows these with novel functions necessary for biosynthesis, thus completing pathway. Candidate genes are cloned heterologous expression subjected vitro enzymatic assays test hypothesis regarding origins enzymes, precisely validate inferences. Among C-PTs primary determinant structural diversity CCs (linear/angular), due divergent activities evolved target positions (C-6 or C-8) umbelliferone. A amino acid variation (Ala161/Thr161) identified proven play a crucial alteration activity, possibly resulting distinct binding forms between substrates, thereby leading products. In conclusion, this study provides trajectory establishment evolution It explains why only portion, not all, plants can produce reveals mechanisms among plants.

Язык: Английский

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

BMC Plant Biology, Год журнала: 2024, Номер 24(1)

Опубликована: Янв. 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

Язык: Английский

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Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Фев. 3, 2025

Abstract Background Gene transfer between the organelles and nucleus plays a central role in shaping plant genome evolution. The identification analysis of nuclear DNA plastid (NUPTs) mitochondrial (NUMTs) origins are important for exploring extent intracellular genomes. Results We report complete genomes (plastome mitogenome) Cicuta virosa (Apiaceae) as well draft using high-fidelity (HiFi) PacBio sequencing technologies. C. plastome (154,449 bp) is highly conserved, with quadripartite structure, whereas mitogenome (406,112 exhibits two chromosomes (352,718 bp 53,394 bp). mitochondrial-encoded genes ( rpl2 , rps14 rps19 sdh3 ) were successfully transferred to genome. Our findings revealed extensive from nucleus, 6,686 NUPTs 6,237 NUMTs detected, covering nearly entire (99.93%) substantial portion (77.04%). These transfers exhibit range sequence identities (80–100%), suggesting multiple events over evolutionary timescales. Recent more frequent mitochondria than that plastids. Conclusions This study contributes understanding ongoing evolution underscores significance organelle-nuclear interplay species. provide valuable insights into processes shape organelle Apiaceae, implications broader

Язык: Английский

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The complete plastomes of seven Peucedanum plants: comparative and phylogenetic analyses for the Peucedanum genus

BMC Plant Biology, Год журнала: 2022, Номер 22(1)

Опубликована: Март 7, 2022

Abstract Background The Peucedanum genus is the backbone member of Apiaceae, with many economically and medically important plants. Although previous studies on provide us a good research basis, there are still unclear phylogenetic relationships taxonomic problems in , robust framework this has not been obtained, which severely hampers improvement revision system for genus. plastid genomes possessing more variable characters have potential reconstructing phylogeny Results In current study, we newly sequenced assembled seven genomes. Together five previously published performed comprehensively comparative analyses Twelve plastomes were similar terms genome structure, codon bias, RNA editing sites, SSRs, but varied size, gene content arrangement, border SC/IR. Fifteen mutation hotspot regions identified among that can serve as candidate DNA barcodes species identification . Our based generated high supports resolutions robustly supported non-monophyly Conclusion showed both conservation diversity. data efficient powerful improving complex summary, our study provides new sights into evolution, taxonomy, species.

Язык: Английский

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Easy353: A Tool to Get Angiosperms353 Genes for Phylogenomic Research

Molecular Biology and Evolution, Год журнала: 2022, Номер 39(12)

Опубликована: Дек. 1, 2022

Abstract The Angiosperms353 gene set (AGS) consists of a 353 universal low-copy nuclear genes that were selected by examining more than 600 angiosperm species. These can be used for phylogenetic studies and population genetics at multiple taxonomic scales. However, current pipelines are not able to recover efficiently accurately from high-throughput sequences. Here, we developed Easy353, reference-guided assembly tool the AGS sequencing (HTS) data (including genome skimming, RNA-seq, target enrichment). Easy353 is an open-source user-friendly assembler diverse types data. It has graphical user interface command-line compatible with all widely-used computer systems. Evaluations, based on both simulated empirical data, suggest yields low rates errors.

Язык: Английский

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A recent large-scale intraspecific IR expansion and evolutionary dynamics of the plastome of Peucedanum japonicum

Scientific Reports, Год журнала: 2025, Номер 15(1)

Опубликована: Янв. 2, 2025

Peucedanum japonicum (PJ), a member of the Apiaceae family, is widely distributed and cultivated in East Asian countries for edible functional foods. In this study, we compared plastid genomes (plastomes) 45S nuclear ribosomal DNA (45S nrDNA) simultaneously from 10 PJ collections. Plastome-based phylogenetic analysis showed that accessions were monophyletic within genus Peucedanum. However, ten plastomes classified into two different groups according to their length inverted repeat (IR) block, short-type (S-type) plastome group containing 18.6 kbp original IR long-type (L-type) 35.7 expanded by duplication 17.1 large single copy region. A total nine nucleotide polymorphisms eight insertions or deletions identified among five L-type plastomes, whereas variations S-type plastomes. Calculation synonymous substitution rates divergence time estimation suggested 17 expansion occurred recently. Molecular markers developed validated classify 55 germplasm types. Our study would be useful unraveling dynamic evolution family molecular breeding PJ.

Язык: Английский

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Prediction of the reaction mechanisms of sesquiterpene coumarin synthases supports a direct evolutionary link with triterpene biosynthesis

Phytochemistry Reviews, Год журнала: 2025, Номер unknown

Опубликована: Янв. 4, 2025

Язык: Английский

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

Frontiers in Plant Science, Год журнала: 2025, Номер 15

Опубликована: Янв. 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.

Язык: Английский

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Plastid phylogenomics of tribe Perseeae (Lauraceae) yields insights into the evolution of East Asian subtropical evergreen broad-leaved forests

BMC Plant Biology, Год журнала: 2022, Номер 22(1)

Опубликована: Янв. 13, 2022

Abstract Background The East Asian subtropical evergreen broad-leaved forests (EBLFs) harbor remarkable biodiversity. However, their historical assembly remains unclear. To gain new insights into the of this biome, we generated a molecular phylogeny one its essential plant groups, tribe Perseeae (Lauraceae). Results Our plastid tree topologies were robust to analyses based on different regions and strategies for data partitioning, nucleotide substitution saturation, gap handling. We found that comprised six major clades began colonize EBLFs Asia in early Miocene. diversification rates accelerated twice late Conclusions findings suggest intensified precipitation Miocene may have facilitated range expansions establishment within biome. By Miocene, species had become rapid.

Язык: 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, Год журнала: 2023, Номер 23(1)

Опубликована: Янв. 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 .

Язык: Английский

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