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1.
Genes (Basel) ; 15(3)2024 02 28.
Artigo em Inglês | MEDLINE | ID: mdl-38540379

RESUMO

Toona ciliata is a deciduous or semi-deciduous tree species and belongs to the Toona genus of the Meliaceae family. Owing to low natural regeneration and over-exploitation, the species is listed as an endangered species at level II in China and its conservation has received increasing concern. Here, we sampled 447 individuals from 29 populations across the range-wide distribution of the T. ciliata complex in China and assessed their genetic variation using two chloroplast DNA markers. The results showed that the overall haplotype diversity and nucleotide diversity per site were high at h = 0.9767 and π = 0.0303 for the psbA-trnH fragment and h= 0.8999 and π = 0.0189 for the trnL-trnL fragment. Phylogenetic analysis supported the division of the natural distribution of T. ciliata complex into western and eastern regions. The genetic diversity was higher in the western region than in the eastern region, showing significant phylogeographic structure. Genetic differentiation among populations was moderate (Φst=42.87%), and the effects of isolation by distance (IBD) were significant. A neutrality test and mismatch distribution analysis indicated that the distribution of the T. ciliata complex generally did not expand, although a few local populations could likely expand after bottleneck effects. The overall results were complementary to and consolidated previous studies using mitochondrial and nuclear DNA markers. We finally discussed strategies for the genetic conservation of the T. ciliata complex.


Assuntos
Meliaceae , Humanos , Meliaceae/genética , Toona/genética , DNA de Cloroplastos/genética , Variação Genética/genética , Filogenia , Marcadores Genéticos
2.
Plants (Basel) ; 13(3)2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-38337968

RESUMO

Forest genetic conservation is typically species-specific and does not integrate interspecific interaction and community structure. It mainly focuses on the theories of population and quantitative genetics. This approach depicts the intraspecific patterns of population genetic structure derived from genetic markers and the genetic differentiation of adaptive quantitative traits in provenance trials. However, it neglects possible interspecific interaction in natural forests and overlooks natural hybridization or subspeciation. We propose that the genetic diversity of a given species in a forest community is shaped by both intraspecific population and interspecific community evolutionary processes, and expand the traditional forest genetic conservation concept under the community ecology framework. We show that a community-specific phylogeny derived from molecular markers would allow us to explore the genetic mechanisms of a tree species interacting with other resident species. It would also facilitate the exploration of a species' ecological role in forest community assembly and the taxonomic relationship of the species with other species specific to its resident forest community. Phylogenetic ß-diversity would assess the similarities and differences of a tree species across communities regarding ecological function, the strength of selection pressure, and the nature and extent of its interaction with other species. Our forest genetic conservation proposal that integrates intraspecific population and interspecific community genetic variations is suitable for conserving a taxonomic species complex and maintaining its evolutionary potential in natural forests. This provides complementary information to conventional population and quantitative genetics-based conservation strategies.

3.
Ecol Evol ; 13(12): e10828, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38094154

RESUMO

Toona ciliata is an endangered species due to over-cutting and low natural regeneration in China. Its genetic conservation is of an increasing concern. However, several varieties are recognized according to the leaf and flower traits, which complicates genetic conservation of T. ciliata. Here, we sequenced the whole chloroplast genome sequences of three samples for each of four varieties (T. ciliata var. ciliata, T. ciliata var. yunnanensis, T. ciliata var. pubescens, and T. ciliata var. henryi) in sympatry and assessed their phylogenetic relationship at a fine spatial scale. The four varieties had genome sizes ranged from 159,546 to 159,617 bp and had small variations in genome structure. Phylogenomic analysis indicated that the four varieties were genetically well-mixed in branch groups. Genetic diversity from the whole chloroplast genome sequences of 12 samples was low among varieties (average π = 0.0003). Besides, we investigated genetic variation of 58 samples of the four varieties in sympatry using two markers (psaA and trnL-trnF) and showed that genetic differentiation was generally insignificant among varieties (Ф st = 0%-5%). Purifying selection occurred in all protein-coding genes except for the ycf2 gene that was under weak positive selection. Most amino acid sites in all protein-coding genes were under purifying selection except for a few sites that were under positive selection. The chloroplast genome-based phylogeny did not support the morphology-based classification. The overall results implicated that a conservation strategy based on the T. ciliata complex rather than on intraspecific taxon was more appropriate.

4.
Genome Biol Evol ; 15(8)2023 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-37561000

RESUMO

Alternation of generations in plant life cycle provides a biological basis for natural selection occurring in either the gametophyte or the sporophyte phase or in both. Divergent biphasic selection could yield distinct evolutionary rates for phase-specific or pleiotropic genes. Here, we analyze models that deal with antagonistic and synergistic selection between alternative generations in terms of the ratio of nonsynonymous to synonymous divergence (Ka/Ks). Effects of biphasic selection are opposite under antagonistic selection but cumulative under synergistic selection for pleiotropic genes. Under the additive and comparable strengths of biphasic allelic selection, the absolute Ka/Ks for the gametophyte gene is equal to in outcrossing but smaller than, in a mixed mating system, that for the sporophyte gene under antagonistic selection. The same pattern is predicted for Ka/Ks under synergistic selection. Selfing reduces efficacy of gametophytic selection. Other processes, including pollen and seed flow and genetic drift, reduce selection efficacy. The polymorphism (πa) at a nonsynonymous site is affected by the joint effects of selfing with gametophytic or sporophytic selection. Likewise, the ratio of nonsynonymous to synonymous polymorphism (πa/πs) is also affected by the same joint effects. Gene flow and genetic drift have opposite effects on πa or πa/πs in interacting with gametophytic and sporophytic selection. We discuss implications of this theory for detecting natural selection in terms of Ka/Ks and for interpreting the evolutionary divergence among gametophyte-specific, sporophyte-specific, and pleiotropic genes.


Assuntos
Células Germinativas Vegetais , Pólen , Pólen/genética , Polimorfismo Genético , Plantas , Evolução Biológica , Seleção Genética
5.
Genes (Basel) ; 14(4)2023 03 31.
Artigo em Inglês | MEDLINE | ID: mdl-37107613

RESUMO

Neolamarckia cadamba (Roxb.) Bosser is a fast-growing deciduous tree species and belongs to the Neolamarckia genus of the Rubiaceae family. This species has great economic and medical values in addition to being an important timber species for multiple industrial purposes. However, few studies have examined the genetic diversity and population structure in the natural distribution of this species in China. Here, we applied both the haploid nrDNA ITS (619 bp for aligned sequences) and mtDNA (2 polymorphic loci) markers to investigate 10 natural populations (239 individuals in total) that covered most of the distribution of the species in China. The results showed that the nucleotide diversity was π = 0.1185 ± 0.0242 for the nrDNA ITS markers and π = 0.00038 ± 0.00052 for the mtDNA markers. The haplotype diversity for the mtDNA markers was h = 0.1952 ± 0.2532. The population genetic differentiation was small (Fstn = 0.0294) for the nrDNA ITS markers but large (Fstm = 0.6765) for the mtDNA markers. There were no significant effects of isolation by distance (IBD), by elevation, and by two climatic factors (annual average precipitation and tem perature). A geographic structure among populations (Nst

Assuntos
Variação Genética , Rubiaceae , Humanos , Variação Genética/genética , Filogenia , Melhoramento Vegetal , DNA Mitocondrial/genética , Rubiaceae/genética
6.
Genes (Basel) ; 13(10)2022 10 05.
Artigo em Inglês | MEDLINE | ID: mdl-36292684

RESUMO

Toona ciliata and Toona sinensis belong to the Toona genus of the Meliaceae family and are important timber species in China. T. ciliata is an endangered species at level II due to overcutting and a low rate of natural regeneration. T. sinensis was cultivated as an economic and nutritious tree for more than 2000 years. The two species differ in flower and leaf morphological traits, reproductive systems, and range size of natural distribution. To reveal the potential molecular basis of these divergences, we examined the similarities and differences in their whole genome sequences. Results indicate that T. ciliata had a higher number of expanded gene families than T. sinensis. The whole genome duplication (WGD) occurred before their speciation. The long-terminal repeats (LTRs) insertion was earlier in the T. ciliata genome (3.2985 ± 2.5007 Mya) than in the T. sinensis genome (3.1516 ± 2.2097 Mya). Twenty-five gene families in the T. ciliata genome were detected to be under positive selection compared with background branches of ten different land species. The T. ciliata genome was highly collinear with the T. sinensis genome, but had low collinearity with the genomes of more distant species. These genomic and evolutionary divergences are potentially associated with the differences between T. ciliata and T. sinensis in terms of their reproductive systems and ecological adaptation.


Assuntos
Meliaceae , Toona , Animais , Meliaceae/genética , Folhas de Planta , Espécies em Perigo de Extinção , Árvores
7.
Genes (Basel) ; 14(1)2022 12 31.
Artigo em Inglês | MEDLINE | ID: mdl-36672857

RESUMO

Toona ciliata is an important timber species but is recognized as an endangered species at level II in China. Its genetic conservation is of increasing concern. Provenance trials and other breeding programs were conducted to develop seed transfer rules and multiplications. Here, we investigated twenty-nine populations sampled across the natural distribution of the T. ciliata complex using mtDNA and nrDNA ITS (ribosomal internal transcribed spacer) markers. Haplotype diversity was h = 0.190 ± 0.202 and nucleotide diversity was π = 0.000383 ± 0.000536 for mtDNA marker. Nucleotide diversity for ITS sequences was 0.00837 ± 0.000783. Haplotypes exhibited phylogeographic structure in spatial distribution. The extent of genetic differentiation was significant (Fst = 0.6994 ± 0.0079 for ITS and 0.8870 ± 0.0077 for mtDNA marker). Isolation by distance (IBD) and by elevation (IBE) occurred among populations. Phylogenetic relationships from mtDNA marker indicated three genetically distinct regions, each without IBD effects. Compared with pollen flow, seed flow was strongly impeded in the western region, but extensive in the central region, and less impeded in the eastern region. Most populations did not exhibit expansion, with only a few populations showing expansion after bottleneck effects. We discussed a strategy of region-based genetic conservation and proposed to conserve multiple populations in the western and eastern regions and a few populations in the central region.


Assuntos
Meliaceae , Filogeografia , Meliaceae/genética , Toona/genética , Variação Genética/genética , Filogenia , Melhoramento Vegetal , China , DNA Mitocondrial/genética , Nucleotídeos
8.
Chem Pharm Bull (Tokyo) ; 66(1): 55-60, 2018 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-29118308

RESUMO

A series of novel quinolone derivatives (8a-j) were synthesized, and their anticancer activities were tested in human cancer cell lines, human lung carcinoma cell (A549), human promyelocytic leukemia cell (HL-60), and human cervical cancer cell (Hela). Compound 8i was found to be 5-times more potent in cell-killing activity for cell lines A549, HL-60, and Hela than the positive control irinotecan or cisplatin, with IC50 of 0.009, 0.008 and 0.010 µM, respectively. The docking study revealed that compound 8i might have strong interactions with the active site of DNA-topoisomerase I.


Assuntos
Antineoplásicos/farmacologia , DNA Topoisomerases Tipo I/metabolismo , Simulação de Acoplamento Molecular , Quinolonas/farmacologia , Inibidores da Topoisomerase I/farmacologia , Antineoplásicos/síntese química , Antineoplásicos/química , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Relação Dose-Resposta a Droga , Ensaios de Seleção de Medicamentos Antitumorais , Humanos , Estrutura Molecular , Quinolonas/síntese química , Quinolonas/química , Relação Estrutura-Atividade , Inibidores da Topoisomerase I/síntese química , Inibidores da Topoisomerase I/química
9.
Chem Pharm Bull (Tokyo) ; 61(6): 631-6, 2013.
Artigo em Inglês | MEDLINE | ID: mdl-23558565

RESUMO

A novel series of quinolone derivatives (6a-n) were designed and synthesized, and their biological activities were evaluated as potential antitumor topoisomerase I (Top I) inhibitors. Among these compounds, 6j exhibited the most potent antitumor activities against multiple cancer cell lines. Docking simulation was performed to insert compound 6j into the crystal structure of DNA-Top I to determine the probable binding model.


Assuntos
Antineoplásicos/síntese química , DNA Topoisomerases Tipo I/química , Desenho de Fármacos , Quinolonas/química , Inibidores da Topoisomerase I/síntese química , Antineoplásicos/química , Antineoplásicos/toxicidade , Sítios de Ligação , Linhagem Celular Tumoral , Sobrevivência Celular/efeitos dos fármacos , DNA Topoisomerases Tipo I/metabolismo , Avaliação Pré-Clínica de Medicamentos , Ensaios de Seleção de Medicamentos Antitumorais , Células HeLa , Humanos , Ligação de Hidrogênio , Simulação de Acoplamento Molecular , Estrutura Terciária de Proteína , Quinolonas/síntese química , Quinolonas/toxicidade , Inibidores da Topoisomerase I/química , Inibidores da Topoisomerase I/toxicidade
10.
Molecules ; 16(3): 2293-303, 2011 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-21389907

RESUMO

A method for the analysis of flavonoids in Astragali Radix by high-performance liquid chromatography (HPLC) combined with photodiode-array detection (DAD) and an electrospray ionization (ESI)--mass spectrometry (MS) was developed. After the samples were extracted with ethanol, the optimum separation conditions for these analytes were achieved using a gradient elution system and a 2.0 x 150 mm Shimadzu VP-ODS column. Eight flavonoids were identified to exist in Astragali Radix based on their characteristic UV data and mass spectra. The concentrations of three major components in this herb--ononin, calycosin and formononetin--were determined by LC/ESI-MS in positive selective ion monitoring (SIM) mode. The calibration curves were linear in the range of 0.9~180.0 µg·mL⁻¹ for ononin, 1.8~360.0 µg·mL⁻¹ for calycosin and 1.4~280 µg·mL⁻¹ for formononetin, respectively. The limits of quantification (LOQ) and detection (LOD) were 0.9 µg· mL⁻¹ and 0.2 µg mL⁻¹ for ononin, 1.8 µg mL⁻¹ and 0.5 µg·mL-1 for calycosin, 1.4 µg mL⁻¹ and 0.5 µg·mL⁻¹ for formononetin, respectively. The standard recoveries were between 95.4~104.7%. The developed method was proven to be useful for the quantitative and qualitative analysis of flavonoid constituents in various resources of Astragali Radix.


Assuntos
Astrágalo/química , Cromatografia Líquida de Alta Pressão/métodos , Flavonoides/análise , Extratos Vegetais/análise , Espectrometria de Massas por Ionização por Electrospray/métodos , Cromatografia Líquida
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