Nephelium lappaceum
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ABSTRACT:
PROVIDER: PRJNA669936 | ENA |
REPOSITORIES: ENA
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Project description:Whole Genome and Transcriptome Sequencings of Nephelium lappaceum
| PRJDB7348 | ENA
Project description:Nephelium lappaceum cultivar:BR7 Raw sequence reads
| PRJNA744585 | ENA
Project description:Nephelium lappaceum cultivar:R-162 Genome sequencing and assembly
| PRJNA766632 | ENA
Project description:Rambutan genome revealed gene networks for spine formation and aril development
| PRJNA728838 | ENA
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.
| S-EPMC6321968 | biostudies-literature
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.
| S-EPMC7889156 | biostudies-literature
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.
| S-EPMC8257635 | biostudies-literature
Project description:The trend of microsatellite marker discovery and development revolved as a result of the advancement of next generation sequencing (NGS) technology as it has developed numerous microsatellites within a short period of time at a low cost. This study generated microsatellite markers using RAD sequencing technologies for the understudied Nephelium lappaceum. A total of 1403 microsatellite markers were successfully designed, which consisted of 853 di-, 525 tri-, 17 tetra-, 5 penta-, and 3 hexanucleotide microsatellite markers. Subsequently, selection of 39 microsatellites was made for the evaluation of genetic diversity of the selected 22 rambutan varieties. Twelve microsatellites, which exhibited high call rates across the samples, were used to assess the diversity of the aforementioned rambutan varieties. The analysis of 12 microsatellites revealed the presence of 72 alleles and six alleles per locus in average. Furthermore, the polymorphic information content (PIC) value ranged from 0.326 (NlaSSR20) to 0.832 (NlaSSR32), which included an average of 0.629 per locus, while the generated Neighbour Joining dendrogram showed two major clusters. The pairwise genetic distance of shared alleles exhibited a range of values from 0.046 (R134↔R170) to 0.818 (R5↔R170), which suggested highest dissimilarity detected between R5 and R170. Notably, these research findings would useful for varietal identification, proper management and conservation of the genetic resources, and exploitation and utilization in future breeding programs.
| S-EPMC7527576 | biostudies-literature
Project description:Nephelium lappaceum (rambutan) is an edible tropical fruit that is widely grown in Southeast Asia. In general, the seeds contain high nutrients, but rambutan seeds are thrown out during processing. In this study, the anti-aging activity of rambutan seeds was evaluated with a new approach through the selective inhibition of the senescence-associated secretory phenotype (senomorphics). Luciferase promoter assays using p16INK4A and SA-?-gal promoters for rambutan showed that its seeds possessed strong senomorphic activity. Molecular networking using ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-qTOF-MS) with a tandem database (UPLC-qTOF-MS/MS) was applied to determine the chemical composition of rambutan. Based on the activity results, nine compounds, one new (7) and eight known kaempferol type compounds, were isolated from the seeds. Compounds 2, 4 and 9 significantly reduced the mRNA expression levels of senescence markers, such as p16INK4A, p21CIP1, p53 and SA-?-gal. These compounds also significantly increased the level of SIRT1, a longevity modulator. Compounds 2, 4 and 9 decreased the mRNA expression levels of senescence-associated secretory phenotypes (SASPs) and subsequently decreased the number of SA-?-gal-positive cells. Thus, rambutan seeds and its constituents might be able to protect against age-related problems.
| S-EPMC7284571 | biostudies-literature