Chloroplast genomic insights into adaptive evolution and rapid radiation in the genus Passiflora (Passifloraceae)

BMC Plant Biology, Journal Year: 2025, Volume and Issue: 25(1)

Published: Feb. 13, 2025

Abstract Chloroplasts are essential organelles in plants and eukaryotic algae, responsible for photosynthesis, fatty acid synthesis, amino production, stress responses. The genus Passiflora , known its species diversity dynamic chloroplast (cp) genome evolution, serves as an excellent model studying structural variations. This study investigates evolutionary relationships within by sequencing 11 new genomes, assessing selective pressures on cp genes, comparing plastid nuclear phylogenies. genomes showed significant variations size, gene content, structure, ranging from 132,736 to 163,292 base pairs, especially Decaloba . Structural rearrangements species-specific repeat patterns were identified. Selective pressure tests revealed adaptive evolution certain lineages, with several including clpP petL under positive selection. Phylogenetic analyses confirmed the monophyly of subgenera Astrophea while Deidamioides appeared polyphyletic. Nuclear phylogenetic analysis based 35S rDNA sequences supported but inconsistencies subgenus compared data. highlights complexity demonstrating evolution. findings underscore effectiveness phylogenomics resolving provide insights into mechanisms shaping angiosperms.

Language: Английский

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Literature-based screening and bibliometric analysis of the chemical composition, antioxidant and antimicrobial potential of essential oils isolated from Allium genus: 23 years of investigation

Pharmacological Research - Modern Chinese Medicine, Journal Year: 2024, Volume and Issue: 10, P. 100354 - 100354

Published: Jan. 4, 2024

Various medicinal and aromatic plants possess bioactive components that exhibit therapeutic, cosmetic pharmaceutical properties. Allium species comprise a subgroup of these which offers potential advantages. The natural volatile oils derived from have broad range functions owing to their richness in components. Therefore, the interest presents study is provide an updated quantified information regarding therapeutical commercial products, chemical composition, biological applications, such as antioxidant antimicrobial activity genus essential This work designed using mixed methodology; extensive data search was conducted for period 2000 2023 (July). keywords "Essential oil", "Allium genus", "Bioactive components", "Antimicrobial activity", "Antioxidant potential", were utilised extract data. literature review obtained PubMed database, while SCOPUS online database used bibliometric analysis. A total 294 entries found PubMed, out only 42 studies selected comprehensive based on experimental approach, including vivo (1) vitro (41) studies. Apart this, 244 articles subjected analysis VOSviewer Bibliometrix software. one most representative genera Amaryllidaceae family, whose therapeutic benefits are properly consolidated wide variety ailments. Traditionally, been consumed China spices vegetables. Although, modern Chinese medicine system several over years address applications commercially available products containing Allium. In this sense, concise provides overview composition (antioxidant antimicrobial) species-derived oils. results published works also illustrate effective microbial can be exploited multi-potent drug against various ailments with advanced safety efficacy. integration past knowledge current research underscores enduring significance Furthermore, it highlights patterns future trends domain, providing valuable insights researchers explore domain further.

Language: Английский

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On the Edge of Dispensability, the Chloroplast ndh Genes

International Journal of Molecular Sciences, Journal Year: 2021, Volume and Issue: 22(22), P. 12505 - 12505

Published: Nov. 19, 2021

The polypeptides encoded by the chloroplast ndh genes and some nuclear form thylakoid NADH dehydrogenase (Ndh) complex, homologous to mitochondrial complex I. Except for Charophyceae (algae related higher plants) a few Prasinophyceae, all eukaryotic algae lack genes. Among vascular plants, are absent in epiphytic species scattered among different genera, families, orders. recent identification of many plants lacking plastid allows comparison on phylogenetic trees functional investigations protect Angiosperms under various terrestrial stresses, maintaining efficient photosynthesis. On edge dispensability, provide test natural selection photosynthesis-related evolution. Variable evolutionary environments place without at risk extinction and, probably, most extant ones may have lost recently. Therefore, they endpoints trees. low number sequenced DNA long lifespan Gymnosperms challenge models about role protecting against stress promoting leaf senescence. Additional sequencing into molecular mechanisms their response will unified model consequences

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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Comparative chloroplast genomics reveals the phylogeny and the adaptive evolution of Begonia in China

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: Oct. 27, 2023

The Begonia species are common shade plants that mostly found in southwest China. They have not been well studied despite their medicinal and decorative uses because gene penetration, decreased adaptability, restricted availability all caused by frequent interspecific hybridization.To understand the patterns of mutation chloroplast genomes different Begonia, as evolutionary relationships, we collected seven China sequenced genomes. exhibit a quadripartite structure (157,634 - 169,694 bp), consisting two pairs inverted repeats (IR: 26,529 37,674 large single copy (LSC: 75,477 86,500 small (SSC: 17,861 18,367 bp). 128-143 genes (comprising 82-93 protein-coding genes, 8 ribosomal RNAs, 36-43 transfer RNAs) Based on comparative analyses, this taxon has relatively similar genome structure. A total six substantially divergent DNA regions (trnT-UGU-trnL-UAA, atpF-atpH, ycf4-cemA, psbC-trnS-UGA, rpl32-trnL-UAG, ccsA-ndhD) seventeen These suitable for identification phylogeographic analysis. Phylogenetic analysis shows were suited to comparable environments grouped clade formed one big phylogenetic tree, supporting genus' monophyly. In addition, positive selection sites discovered eight (rpoC1, rpoB, psbE, psbK, petA, rps12, rpl2, rpl22), majority which involved protein production photosynthesis.Using these resources, can resolve deep-level relationships between families, leading better understanding processes. addition enhancing resolution, results demonstrate utility complete phylogenetically taxonomically challenging plant groupings.

Language: Английский

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Signatures of selection in Mulinia lateralis underpinning its rapid adaptation to laboratory conditions

Evolutionary Applications, Journal Year: 2024, Volume and Issue: 17(2)

Published: Feb. 1, 2024

The dwarf surf clam,

Language: Английский

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Extensive reorganization of the chloroplast genome of Corydalis platycarpa: A comparative analysis of their organization and evolution with other Corydalis plastomes

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 13

Published: Dec. 9, 2022

The chloroplast (cp) is an autonomous plant organelle with individual genome that encodes essential cellular functions. architecture and gene content of the cp highly conserved in angiosperms. plastome Corydalis belongs to Papaveraceae family, comprised unusual rearrangements content. Thus far, no extensive comparative studies have been carried out understand evolution genomes.Therefore, platycarpa was sequenced, wide-scale were conducted using publicly available twenty plastomes.Comparative analyses showed rearrangement IR expansion occurred, these events evolved independently species. By contrast, plastomes its closely related subfamily Papaveroideae other Ranunculales taxa are conserved. On hand, synapomorphy characteristics both accD ndh loss happened common ancestor sub-clade lineage, respectively. Corydalis-sub clade species (ndh lost) distributed predominantly Qinghai-Tibetan plateau (QTP) region. phylogenetic analysis divergence time estimation also employed for species.The (44.31 - 15.71 mya) coincides very well uplift Qinghai-Tibet Plateau Oligocene Miocene periods, maybe during this period, it has probably triggered radiation species.To best authors' knowledge, first large-scale study their evolution. present may provide insights into molecular

Language: Английский

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Complete chloroplast genomes and phylogenetic relationships of Pedicularis chinensis and Pedicularis kansuensis

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

Published: June 21, 2024

The complete cp genomes of Pedicularis chinensis (GenBank accession number: OQ587614) and kansuensis OQ587613) were sequenced, assembled, annotated. Their chloroplast (cp) genome lengths 146,452 bp, 146,852 respectively; 120 116 genes identified, comprising 75 72 protein-coding (PCGs), 37 36 transfer RNA (tRNA) genes, 8 ribosomal (rRNA) for P. kansuensis, respectively. A simple sequence repeat (SSR) analysis revealed that the repetitive sequences mainly composed mononucleotide repeats (A/T motif) dinucleotide (AT/TA motif). Comparative genomics identified several variant (rpl22, rps19, rpl12, ycf1, trnH, psbA, ndhH) regions (trnS-GGA, trnV-UAC, ndhJ-trnV, ycf4-cemA, ndhE-nhdG, rpl32-trnL) with a high Pi, indicating potential to serve as deoxyribo nucleic acid (DNA) barcodes species identification. results show same those other plants in Pedicularis, different degrees AT preference codons. Large differences number SSRs expansion inverted (IR) region showed strong variability interspecific differentiation between these two represented genus Pedicularis. phylogenetic had closest relationship oliveriana, aschistorhyncha. These will facilitate study classification evolution plants.

Language: Английский

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Evolutionary history and population dynamics of a rare and endangered medicinal plant Bergenia scopulosa (Saxifragaceae): Evidences from chloroplast genomes and ecological niche analysis

Global Ecology and Conservation, Journal Year: 2024, Volume and Issue: 54, P. e03097 - e03097

Published: July 16, 2024

Geological and climatic events have long been considered to profoundly affect population evolution demographic history of species, but the evolutionary rare endangered herbaceous plants in East Asia remains less well understood. In this study, chloroplast genomes, environmental variables geographical distribution information were integrated determine dynamics Bergenia scopulosa T.P.Wang, an medicinal herb endemic central China (Qinling Mountains). Population genomic analysis based on genomes indicated a significant degree intraspecific differentiation within B. scopulosa, where two separate genetic lineages identified eastern western groups Qinling Mountains, respectively. The found low level nucleotide diversity. Meanwhile, ecological niche revealed that had obvious divergence. Species modeling illustrated experienced prominent contraction from interglacial periods present, while suitable habitat was predicted shift higher elevations response global warming future scenarios. These findings suggested geological factors together affected divergence Mountains Asia. particular, geographic isolation appeared play greater role scopulosa. Therefore, conservation units should be correspondingly established for

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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