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The complete chloroplast genome of Phyla nodiflora (Linnaeus) Greene (1899) from the Verbenaceae family and its phylogenetic analysis.

ABSTRACT: Phyla nodiflora (Linnaeus) Greene (1899) is a perennial creeping herb belonging to the family Verbenaceae. It has numerous pharmacological properties, including anti-dandruff, anti-inflammatory, anti-oxidant, anti-melanogenesis, anti-hypertensive, and anti-hyperuricemic properties. We generated the complete chloroplast genome sequence of P. nodiflora using Illumina paired-end sequencing data. The P. nodiflora chloroplast genome is 154,341 bp in length, containing a large single copy (LSC) region of 85,185 bp and a small single copy (SSC) region of 17,222 bp, separated by a pair of inverted repeats (IRs) of 25,967 bp. The genome contained 128 genes, including 86 protein-coding, 34 tRNA, and eight rRNA genes. Six genes had one intron, one gene had two introns, and the others did not have an intron. Overall GC content of the chloroplast genome was 39%, while those of LSC, SSC, and IR regions were 38.2%, 33.7%, and 44%, respectively. Phylogenetic analysis of the chloroplast genome revealed that P. nodiflora is closely related to the other species from Verbenaceae.

SUBMITTER: Sharmishtha R

PROVIDER: S-EPMC10588534 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Phyla nodiflora (Linnaeus) Greene (1899) from the Verbenaceae family and its phylogenetic analysis.

Sharmishtha Ray R Tanuja Tanuja T Balaji Raju R Parani Madasamy M

Mitochondrial DNA. Part B, Resources 20231018 10

Phyla nodiflora (Linnaeus) Greene (1899) is a perennial creeping herb belonging to the family Verbenaceae. It has numerous pharmacological properties, including anti-dandruff, anti-inflammatory, anti-oxidant, anti-melanogenesis, anti-hypertensive, and anti-hyperuricemic properties. We generated the complete chloroplast genome sequence of P. nodiflora using Illumina paired-end sequencing data. The P. nodiflora chloroplast genome is 154,341 bp in length, containing a large sin ...[more]

PMID: 37869568

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Project description:PurposeThe enzyme Cyclooxygenases (COX-1 and COX-2) catalyze the formation of prostaglandin, a mediator of the inflammatory pathway. Inflammation related pathological conditions may be alleviated by targeting the Cox enzymes.COX-2 inhibitors that are currently available in the market causes undesirable side effects. Our present study focuses on the in-silico inhibition of COX -2 enzyme by the phytocompounds from Albizia amara and Phyla nodiflora.MethodsThe phytochemicals present in Albizia amara and Phyla nodiflora were analyzed for their COX-2 inhibition potential. Eight compounds from Albizia amara and eleven compounds from Phyla nodiflora obtained from GC-MS analysis was used for the current study. Molecular docking was performed using AutoDock vina. The crystal structure of COX-2 (PDB ID: 5IKR) was obtained from Protein data bank. PyMol was used to remove any solvent, organic and inorganic molecules. Energy minimization of the protein was carried out using SPDBV software. Geometrical optimizations of the ligands were performed using Avogadro software. Celecoxib was used as the positive control. ADMET properties of the compounds were analyzed using SwissADME and ProtoxII online servers. Molecular mechanics/generalized born surface area (MM/GBSA) calculations were performed to evaluate the binding efficiency. Molecular dynamics of the protein and protein-ligand complex was studied for about 100 ns using Desmond package of Schrodinger suite.ResultsAmong the eighteen compounds, Squalene present in both the plants showed a better binding energy of -7.7 kcal/mol, when compare to other phytocompounds present in the extract. The control celecoxib showed a binding energy of about - 9.4 kcal/mol. The toxicity and ADMET properties of squalene indicated that it is non-toxic and followed Lipinski's rule. Molecular Dynamics (MD) analysis showed that the binding of squalene to the enzyme was stable.ConclusionSqualene could potentially inhibit COX2 and o wing to its properties, squalene can be formulated in gels/creams and could be possibly used for external edema and inflammation.

Project description:IntroductionPhyla nodiflora L. is a perennial herbaceous plant belonging to the Verbenaceae family. It is widely used as an herbal drink to treat many diseases. It has antioxidant, antifungal and anti-inflammatory properties. In traditional medicine, it is used to treat skin infections. However, there is little information on the chemical composition of organic plant extracts. Therefore, the aim of this study was to determine the chemical composition of organic extracts of P. nodiflora L.MethodsIn this study, organic extracts were prepared using a continuous Soxhlet extractor and four different solvents with increasing polarity from nonpolar to polar solvents (petroleum ether, chloroform, ethyl acetate, and isopropanol) to ensure the possibility of extracting a wide range of compounds. GC‒MS analysis was performed to determine the chemical constituents of the organic extracts.ResultsNineteen compounds were identified in the petroleum ether (Et) extract, 14 in the chloroform (Ch) extract, 18 in the ethyl acetate (Ea) extract and 15 in the isopropanol (Is) extract. The most important compounds in the Et extract were 1,1-diethoxyethane (33.9 %) and nonadecane (19.9 %). The most important compound in the Ch extract was octacosane (37.4 %). The most important compounds in the Ea extract were 3-hydroxy-dodecanoic acid (17.7 %) and geranyl isovalerate (15.5 %). The most important compound in the Is extract was behenic acid alcohol (18.6 %). The chemical structures of the major compounds were confirmed by mass spectrometry by studying their fragmentation mechanism and comparing the molecular weights of the resulting fragments with the molecular weights of the peaks present in each mass spectrum.ConclusionsThe results of this study show that the dominant compounds in nonpolar extracts (petroleum ether and chloroform) are hydrocarbons, ethers, epoxides, and silicon compounds, while the dominant compounds in moderately polar extracts (ethyl acetate and isopropanol) are alcohols, carbonyl compounds, and oxygenated terpenes.

Dataset Information

The complete chloroplast genome of Phyla nodiflora (Linnaeus) Greene (1899) from the Verbenaceae family and its phylogenetic analysis.

Publications

The complete chloroplast genome of <i>Phyla nodiflora</i> (Linnaeus) Greene (1899) from the Verbenaceae family and its phylogenetic analysis.

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