Comparative chloroplast genomics provides insights into the phylogenetic relationships and evolutionary history for Actinidia species

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

Опубликована: Апрель 17, 2025

Actinidia species are fruit trees with various functions, such as providing edible fruit, serving ornamental plants, and having medicinal benefits. However, the taxonomy of is controversial due to widespread hybridization, history divergence polyploid speciation among also remains unclear. In this study, we conducted comparative analyses chloroplast genomes ploidy multiple species. The genes clpP, infA, ndhD, ndhK, rpl20 were absent from these genomes. ycf2 in under positive selection. Several regions (rps16-trnQ-UUG, trnS-GCU-trnR-UCU, ndhC-trnV-UAC, rbcL-accD, rps12-psbB, trnN-GUU-ndhF, ycf1-trnN-GUU, trnH-GUG-psbA) (ycf1, ycf2, accD, rpl20) exhibited high variability, which could potentially serve molecular markers delineation other phylogenetic studies. Through time estimation, genus originated 23 million years ago (Ma), experienced a tetraploidization event ~ 20 Ma. Subsequently, has undergone extensive diploidization. Our findings will provide valuable information identification, breeding programs, conservation efforts for

Язык: Английский

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The complete plastid genome of Citrus hystrix DC. 1813 (Rutaceae) and its phylogenetic analysis

Mitochondrial DNA Part B, Год журнала: 2025, Номер 10(1), С. 94 - 98

Опубликована: Янв. 2, 2025

The complete plastome size of Citrus hystrix DC. 1813 was 159,893 bp in length and has a typical quadripartite structure. 87,148-bp-long large single-copy the 18,763-bp-long small regions were separated by pair inverted repeats (each 26,991 bp). predicted to contain 132 genes, which 87 CDS, 37 tRNA, eight rRNA genes. A/T biassed, overall GC content 38.4%. Using maximum likelihood Bayesian inference methods, phylogenetic analysis sequence revealed close relationship between C. aurantiifolia, placing them under same clade as micrantha.

Язык: Английский

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Comparative genomics and phylogenetic analysis of chloroplast genomes of Asian Caryodaphnopsis taxa (Lauraceae)

Gene, Год журнала: 2024, Номер 907, С. 148259 - 148259

Опубликована: Фев. 10, 2024

Язык: Английский

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Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective

Genes, Год журнала: 2024, Номер 15(4), С. 444 - 444

Опубликована: Март 31, 2024

Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on between species, studies are scarce. Here, we sequenced from three species (Sedum alfredii, plumbizincicola, japonicum) to understand their evolutionary relationships plastome structural evolution. Our analyses revealed minimal size GC content variation across species. However, gene distribution at IR boundaries, repeat structures, codon usage patterns showed diversity both inter-specific intra-specific levels. Notably, an rps19 expansion a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving markers future studies. Phylogenetic confirmed non-monophyly divided Acre clade into two groups. Individuals same clustered together, with strong support S. tricarpum, plumbizincicola. Additionally, japonicum clearly affiliates clade. This study provides valuable insights intra-generic Sedum, well overall evolution within genus.

Язык: Английский

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Uncovering the first complete chloroplast genomics, comparative analysis, and phylogenetic relationships of the medicinal plants Rhamnus cathartica and Frangula alnus (Rhamnaceae)

Physiology and Molecular Biology of Plants, Год журнала: 2023, Номер 29(6), С. 855 - 869

Опубликована: Июнь 1, 2023

Язык: Английский

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A super-pangenome for cultivated citrus reveals evolutive features during the allopatric phase of their reticulate evolution

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Окт. 18, 2024

ABSTRACT Most of the rich genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa, C. medica , reticulata maxima and micrantha whose radiation occurred allopatry. In such an evolutive context, genome studies, GWAS analysis transcriptomic studies will be significantly enhanced through pangenome approaches. We report implementation super-pangenome for citrus, established with de novo assemblies pseudochromosomes (346 Mb), (332 Mb) (333 released first time alongside previously published chromosome-scale assembly . Gene annotation these revealed 28,090, 29,477, 29,258 30,101 genes, respectively, focus on pattern recognition receptors. Repetitive element that nearly half each consisted transposable elements or DNA-satellites. The 3 new display strong synteny collinearity, while significant discrepancies are assembly. Resequencing information (single nucleotide polymorphisms [SNPs], small indels gene presence-absence variation [PAV]) 55 accessions were used to explore intra- interspecific taxa their relationships main horticultural groups resulting evolution. Diagnostic SNPs all over genomes assemblies, introgressions several representative as well insights into origin phylogenomic structures modern groups. PAV absence presence was specific one (dPAV). Interestingly, diagnostic (dPAV) uncovered large chloroplastic introgression chromosome 4 inherited recent hybrids having this species male parent. Implementing combined identification orthologous genes across resequencing data. Significant inter- intraspecific variations highlighted, including 25,291 core, 2,431 soft-core 5,171 dispensable genes. functional enrichment species-specific adaptations distinct specializations. This highlights evolutionary paths have shaped species, contributing maintaining shared foundation essential biological processes. development is milestone genomics, providing comprehensive resource captures extensive citrus. Additionally, we dedicated Genome Hub, offering platform continuous genomic research allowing ongoing updates future inclusion additional species.

Язык: Английский

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Chemical Composition, Enantiomeric Distribution and Antimicrobial, Antioxidant and Antienzymatic Activities of Essential Oil from Leaves of Citrus x limonia

Molecules, Год журнала: 2025, Номер 30(4), С. 937 - 937

Опубликована: Фев. 18, 2025

Citrus x limonia is an aromatic species belonging to the Rutaceae family. In present study, chemical composition, enantiomeric distribution, and biological activity of essential oil isolated from leaves were determined. The was extracted through hydrodistillation. composition determined by gas chromatography (GC) coupled a flame ionization detector (GC-FID), mass spectrometer (GC-MS) using nonpolar column. distribution performed two enantioselective chromatographic columns. Antimicrobial broth microdilution method. antimicrobial tested against eight bacteria fungi. antioxidant ABTS DPPH methods. spectrophotometric method used determine anticholinesterase activity. oil, forty-three compounds identified. These represent 99.13% total composition. Monoterpene hydrocarbons most representative group in number (fourteen) terms relative abundance (65.67%). main constituent found be limonene (25.37 ± 0.80%), β-pinene (23.29 0.15%) sabinene (8.35 0.10%). Six pairs enantiomers identified fruits limonia. showed moderate antibacterial Gram-positive cocci Enterococcus faecalis, bacillus Lysteria monocytogenes with MIC 1000 μg/mL. exhibited strong antifungal fungi Aspergillus niger, yeasts Candida albicans 250 500 μg/mL, respectively. weak SC50 9.12 mg/mL. Additionally, presented IC50 71.02 1.02 µg/mL.

Язык: Английский

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Chemical and Biological Study of the Essential Oil Isolated from Fruits of Citrus x limonia

Plants, Год журнала: 2025, Номер 14(5), С. 705 - 705

Опубликована: Фев. 25, 2025

Citrus x limonia is an aromatic species, known locally in Ecuador as limón mandarina or chino. In the present study, chemical composition and biological activity of essential oil isolated from this species were determined. The was extracted through hydrodistillation. enantiomeric distribution determined by gas chromatography. Antimicrobial using broth microdilution method against tree Gram-positive cocci, a bacillus, four Gram-negative bacilli, fungus, yeast. antioxidant ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) DPPH (2,2-diphenyl-1-picrylhydrazyl) methods. spectrophotometric used to determine anticholinesterase activity. oil, thirty-nine compounds identified, which represented 99.35% total composition. Monoterpene hydrocarbons most representative group terms number (thirteen) relative abundance (91.39%). main constituents found be limonene (57.38 ± 1.09%), γ-terpinene (13.01 0.37%), β-pinene (12.04 0.63%). Five pairs enantiomers identified fruits limonia. presented minimum inhibitory concentration 4000 μg/mL Aspergillus niger. weak per method, with SC50 1.26 mg/mL. Additionally, exhibited moderate activity, IC50 203.9 1.03 µg/mL. This study provides first comprehensive analysis activities

Язык: Английский

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Comparative analysis of chloroplast genomes on Meliaceae species: insights into the evolution and species identification

Frontiers in Plant Science, Год журнала: 2025, Номер 16

Опубликована: Март 11, 2025

Introduction Meliaceae, a significant group in Sapindales, possesses material and medicinal value due to its applications timber bioactive compounds. However, the high morphological diversity of Meliaceae species lack comparative studies chloroplast (cp) genomes have led great challenges classification identification species. Methods In this study, we sequenced complete cp three Toona ( fargesii , ciliata sinensis ), conducted analyses these along with 29 previously published Meliaceae. Additionally, performed phylogenetic estimated divergence times Results The 32 ranged from 158,558 bp 160,978 length. Specifically, varied 159,242 159,617 These contained total 135 unique genes, comprising 90 protein-coding, 8 rRNA, 37 tRNA genes. Divergence time estimation revealed that family diverged into two subfamilies (Cedreloideae Melioideae) approximately 72.92 Ma (95% HPD: 60.62-87.01 Ma) Late Cretaceous. diversification Cedreloideae (47.86 Ma, 95% 47.42-48.22 occurred later than Melioideae (66.60 55.41-79.73 Ma). Furthermore, genomic analysis identified 52 116 simple sequence repeats (SSRs) twelve highly variable regions (HVRs) found among Discussion indicates most relatively recent origin, rapid occurring during Oligocene or Early Miocene epochs. Comparative exhibits relative conservation terms genome size, inverted-repeat (IR) boundary, structure, HVRs codon patterns. Although differences exist between subfamilies, overall similarity remains notably high. ycf 1, trn K- rps 16, ndh F- rpl exhibited highest nucleotide polymorphism within while 22 gene displayed genetic both subfamilies. As candidate molecular markers, may effectively distinguish findings not only provide insights evolution but also establish scientific foundation for future systematics

Язык: Английский

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Chloroplast Genome of Myristica fragrans : Assembly, Annotation, and Phylogenetic Relationships

Forest Science and Technology, Год журнала: 2025, Номер unknown, С. 1 - 8

Опубликована: Март 21, 2025

Myristica fragrans is a native and economically significant species in Indonesia. However, its complete chloroplast genome, particularly from Indonesia, has not been previously reported. In this study, we successfully sequenced assembled the genome of M. using next-generation sequencing technology. The total length 155,868 bp exhibits typical quadripartite structure, consisting large single-copy (LSC) region (87,062 bp), small (SSC) (20,664 pair inverted repeats (IRs) (24,071 each). Genome annotation identified 126 genes, including 83 protein-coding 8 ribosomal RNA 35 transfer genes. A 141 simple sequence (SSRs) were detected, with mononucleotide being most prevalent (90.07%). Phylogenetic analysis six genomes three outgroup confirmed that closely related to argentea, providing new insights into evolutionary relationships within Myristicaceae family.

Язык: Английский

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