Nephelium lappaceum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA669909 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12904123_1.fastq.gz | Fastqsanger.gz | |||
| SRR12904123_2.fastq.gz | Fastqsanger.gz |
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Project description:Whole Genome and Transcriptome Sequencings of Nephelium lappaceum
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Project description:Nephelium lappaceum (Rambutan), is one of tropical fruit in which - cultivated widely in Indonesia and has good taste and aroma. However, the transcriptomic study of rambutan has limited. In this study, we performed transcriptome assembly using paired-end Illumina technology. The assembled transcriptome was constructed using Trinity and after filtering and removal sequences redundancy produced 36,303 contigs. The contig ranged 201-11,770 bp and N50 has 1327 bp. The contig was annotated with several databases such as SwissProt, TrEMBL, and nr/nt of NCBI databases. The raw reads are deposited in the DDBJ with DRA accession number, DRA007359: https://www.ncbi.nlm.nih.gov/sra/?term=DRA007359. The assembled contigs of transcriptome are deposited in the DDBJ TSA repository with accession number IADQ01000001-IADQ01036303: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/tsa/IADQ.gz and also can be accessed at http://rujakbase.id.
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Project description:Nephelium lappaceum is a popular tropical fruit belonging to the Sapindaceae family. The plant originated in Malaysia and Indonesia and is commonly called rambutan. Because of its refreshing flavor and exotic appearance, rambutan is widely accepted in the World. Due to its significant medicinal properties, the fruit has also been employed in traditional medicine for centuries. The chloroplast genome of rambutan was sequenced, assembled, and annotated in the present study. The chloroplast genome length was 161,356 bp and contained 132 genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. It possessed the typical quadripartite circle structure with a large single-copy region (86,009 bp), a small single-copy region (18,153 bp), and two inverted repeat regions (28,597 bp). A total of 35 SSR markers were found in the chloroplast genome of Nephelium lappaceum, of which 33 were monomer, 1 was dimer and 1 was tetramer. Phylogenetic analysis based on the complete chloroplast genome sequences of 21 plant species showed that rambutan was closely related to Pometia tomentosa. These results provide a foundation for further phylogenetic and evolutionary studies of the Sapindaceae family.
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Project description:The emergence and spread of antimicrobial resistance have been of serious concern to human health and the management of bacterial infectious diseases. Effective treatment of these diseases requires the development of novel therapeutics, preferably free of side effects. In this regard, natural products are frequently conceived to be potential alternative sources for novel antibacterial compounds. Herein, we have evaluated the antibacterial activity of the epicarp extracts of the Malaysian cultivar of yellow rambutan fruit (Nephelium lappaceum L.) against six pathogens namely, Bacillus subtilis, methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pyogenes, Pseudomonas aeruginosa, Klebsiella pneumoniae and Salmonella enterica. Among a series of solvent extracts, fractions of ethyl acetate and acetone have revealed significant activity towards all tested strains. Chemical profiling of these fractions, via HPLC, LC-MS and GC-MS, has generated a library of potentially bioactive compounds. Downstream virtual screening, pharmacological prediction, and receptor-ligand molecular dynamics simulation have eventually unveiled novel potential antibacterial compounds, which can be extracted for medicinal use. We report compounds like catechin, eplerenone and oritin-4-beta-ol to be computationally inhibiting the ATP-binding domain of the chaperone, DnaK of P. aeruginosa and MRSA. Thus, our work follows the objective to propose new antimicrobials capable of perforating the barrier of resistance posed by both the gram positives and the negatives.
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Project description:Thailand is one of the leading exporting countries of rambutan and rambutan peels are considered as a biological waste. In this study, rambutan (Nephelium lappaceum L. cv. Rong Rian) peel extracts (RPE) obtained by water extraction were analyzed for their phytochemical composition, antibacterial and antioxidant activities, and cytotoxicity. The bioactive compounds in RPE identified by GC-MS were mome inositol (35.99 mg/g), catechol (29.37 mg/g), 5-hydroxymethylfurfural (5.69 mg/g), 2-pentenal, (E)-(5.22 mg/g), acetic acid (3.69 mg/g), 1,2,3-propanetriol (3.67 mg/g), 2-furan-carboxaldehyde (2.66 mg/g), and other compounds. FT-IR analysis confirmed the presence of alcohol and phenol in the extract. Antibacterial activities of RPE against food pathogenic and spoilage bacteria showed that RPE could inhibited Bacillus subtilis, B. cereus, Staphylococcus aureus, Vibrio cholerae, V. parahaemolyticus, Pseudomonas aeruginosa, and P. fluorescens, with MIC values ranging between 1024 and 8192 µg/mL. The extract also showed antioxidant properties, as determined by DPPH and ABTS assays. The cytotoxicity analysis after 72 h of treatment showed the IC50 values at 194.97 ± 4.87, 205.92 ± 2.55, and 94.11 ± 1.33 µg/mL for L929, Vero, and MCF-7 cell lines, respectively. Therefore, this study provided a basis of knowledge of rambutan peels as an excellent source of natural bioactive compounds for various applications.
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