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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Atmospheric CO2 decline and the timing of CAM plant evolution

Annals of Botany, Journal Year: 2023, Volume and Issue: 132(4), P. 753 - 770

Published: Aug. 29, 2023

Abstract Background and Aims CAM photosynthesis is hypothesized to have evolved in atmospheres of low CO2 concentration recent geological time because its ability concentrate around Rubisco boost water use efficiency relative C3 photosynthesis. We assess this hypothesis by compiling estimates when clades arose using phylogenetic chronograms for 73 clades. further consider evidence how atmospheric affects Results Where origins can be inferred, strong estimated appeared the past 30 million years 46 48 examined clades, after had declined from high (near 800 ppm) lower (<450 values. In turn, 21 25 containing species (but where are less certain) also years. these probably younger than clade origin. found repeated weak evolution during higher conditions before ago, possible Crassulaceae Cretaceous period prior decline. Most CAM-specific 15 years, a similar pattern observed C4 Conclusions The indicates repeatedly reduced Weaker pre-date and, Crassulaceae, may arisen water-limited microsites under relatively CO2. Experimental extant demonstrates that elevated reduces importance nocturnal fixation increasing contribution daily carbon gain. Thus, advantage would CO2, such appears likely restricted more extreme environments

Language: Английский

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Twelve newly assembled jasmine chloroplast genomes: unveiling genomic diversity, phylogenetic relationships and evolutionary patterns among Oleaceae and Jasminum species

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

Published: April 25, 2024

Abstract Background Jasmine ( Jasminum ), renowned for its ornamental value and captivating fragrance, has given rise to numerous species accessions. However, limited knowledge exists regarding the evolutionary relationships among various species. Results In present study, we sequenced seven distinct species, resulting in assembly of twelve high-quality complete chloroplast (cp) genomes. Our findings revealed that size 12 cp genomes ranged from 159 165 kb encoded 134–135 genes, including 86–88 protein-coding 38–40 tRNA 8 rRNA genes. J. nudiflorum exhibited a larger genome compared other mainly attributed elevated number forward repeats (FRs). Despite typically conservative nature chloroplasts, variations presence or absence acc D have been observed within sambac . The calculation nucleotide diversity Pi ) values 19 indicated potential mutation hotspots were more likely be located LSC regions than regions, particularly genes ycf 2, rbc L, atp E, ndh K, C > 0.2). Ka/Ks strong selection pressure on rps A, rpo C1, rpl 33 when comparing with three most closely related auriculatum , multiflorum dichotomum ). Additionally, SNP identification, along results Structure, PCA, phylogenetic tree analyses, divided into six groups. Notably, polyanthum showed gene flow signals both G5 group G3 tortuosum fluminense Phylogenetic analysis reflected same genus clustered together robust support Oleaceae, strongly supporting monophyletic Conclusion Overall, this study provides comprehensive insights genomic composition, variation, These enhance our understanding genetic history

Language: Английский

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Comparative Plastome Analysis of Apocynaceae with de novo Sequencing of Thevetia peruviana: Insights into Evolution and Phylogeny

Tropical Plant Biology, Journal Year: 2025, Volume and Issue: 18(1)

Published: May 13, 2025

Language: Английский

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Ultraconserved Elements Reveal the Relationship Between Facultative Keratinophagy and Synanthropic Evolution in Clothes Moths

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: May 16, 2025

ABSTRACT Synanthropic species live in close association with, or benefit from, humans. Despite their potential impacts to human health, little is known about the mechanisms driving synanthropic life‐history evolution, evolutionary forces shaping diet among synanthropes, how these combined factors affect population dynamics and/or speciation. The Tineidae moth family contains several species, including globally distributed pest Tineola bissellellia , that contribute ~$1 billion worth of damage caused annually by keratinophagous synanthropes. Synanthropy associated with a wide range dietary strategies. While most tineids display obligate detritivory, are typically either facultatively obligately keratinophagous. However, relationships within Tineidae, hampering efforts investigate relationship between synanthropy and evolution. Here, address this challenge, we extracted DNA from 39 tineid samples two outgroups, closely related Tinea genera, generated genome‐wide sequence data for thousands ultraconserved elements (UCEs). Our phylogenetic analyses, using concatenated maximum‐likelihood‐based approach, resulted well‐supported, fully resolved phylogeny demonstrates has evolved multiple times consistently facultative keratinophagy. Bayesian divergence time estimation indicates Cretaceous deep‐branching lineages, an ancestral origin keratinophagy, recent economically important pest, bissellellia, genus . Taken together, our results suggest shift keratinophagy was key innovation fuelled repeated evolution life histories deep‐diverging family.

Language: Английский

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Chromosome-scale genome analysis of Apocynum venetum sheds light on Apocynum phylogenetics, bast fiber development, and flavonoid synthesis

Industrial Crops and Products, Journal Year: 2024, Volume and Issue: 212, P. 118325 - 118325

Published: March 2, 2024

Language: Английский

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Asclepiadoideae subfamily (Apocynaceae): ethnopharmacology, biological activities and chemophenetics based on pregnane glycosides

Phytochemistry Reviews, Journal Year: 2024, Volume and Issue: 23(4), P. 1027 - 1063

Published: March 22, 2024

Language: Английский

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Comparative analysis of Artemisia plastomes and insights into the infra-generic phylogenetic relationships of the genus

Published: July 16, 2024

Background The genus Artemisia is a taxonomically difficult group comprising 400–500 species mainly distributed in northern hemisphere. Only limited number of plastomes are currently available. Their structure has not been comparatively analyzed, and the phylogenetic backbone based on plastome-scale data reported with dense taxon sampling. This situation greatly hindered our understanding plastome variation patterns infra-generic relationships genus. With advancement next generation sequencing technologies, it becoming easier to obtain analyze plastome, use construct phylogeny. Results In this study, we newly sequenced 34 representing 30 three varieties. Combing 38 previously published plastomes, total 72 complete were analyzed. results indicated that conserved terms structure, GC content, gene order. All have typical quadripartite 87 protein coding, 37 tRNA, 8 rRNA genes. IR regions similar length among compared generic more than intergenic spacer regions. sequence divergence higher LSC SSC Three protein-coding genes four non-coding regions, i.e., accD, petG, ycf1, rpoC1-rpoC2, rpoC2-rps2, trnG(UCC)-trnfM(CAU), ndhG-ndhI, found be highly diverse, could chosen as candidates DNA barcode. Phylogenetic constructed using coding divided into several clades did match previous divisions Artemisia, subgenera monophyletic. Furthermore, they also inconsistent those nuclear markers. And position A. stracheyi still controversial. Conslusions study reveals conservative, especially CDS further confirmed natural. lay foundation for future evolutionary studies Artemisia.

Language: Английский

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Full-length chloroplast genome of Vincetoxicum atratum and phylogeny of the genus Vincetoxicum

Genetic Resources and Crop Evolution, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 30, 2024

Language: Английский

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Analysis of the RNA Editing Sites and Orthologous Gene Function of Transcriptome and Chloroplast Genomes in the Evolution of Five Deutzia Species

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(16), P. 12954 - 12954

Published: Aug. 19, 2023

In this study, the chloroplast genomes and transcriptomes of five Deutzia genus species were sequenced, characterized, combined, analyzed. A phylogenetic tree was constructed, including 32 other genome sequences Hydrangeoideae species. The results showed that typical circular 156,860-157,025 bp in length, with 37.58-37.6% GC content. Repeat analysis had 41-45 scattered repeats 199-201 simple sequence repeats. Comparative genomic pi analyses indicated are conservative gene structures stable. According to tree, appear be closely related Kirengeshoma palmata Philadelphus. By combining transcriptomic analyses, 29-31 RNA editing events 163-194 orthologous genes identified. ndh, rpo, rps, atp most sites, all C-to-U type. Most annotated chloroplast, mitochondria, nucleus, functions energy production conversion, translation, protein transport. Genes biosynthesis monoterpenoids flavonoids also identified from transcriptome spp. Our will contribute further studies information potential uses

Language: Английский

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