Project description:Oryctes rhinoceros nudivirus (OrNV) is a dsDNA virus which has been used as a biocontrol agent to suppress Coconut Rhinoceros Beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. Recently a new wave of O. rhinoceros incursions in Oceania is thought to be related to the presence of low virulence isolates of OrNV or virus tolerant haplotypes of beetles. Here, chronically infected beetles were collected from the Philippines, Fiji, PNG and the Solomon Islands (SI). RNAseq was performed to investigate the global viral gene expression profiles and comparative genomic analysis of structural variations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the SI and the Philippines are closely related to while OrNV strains from PNG and Fiji formed a distinct adjacent clade. We detected several polymorphic sites with a frequency higher than 35% in 892 positions of the viral genome. Non-synonymous mutations were detected in several hypothetical proteins, and 15 nudivirus core genes such as gp034, lef-8, lef-4 and vp91. We found limited evidence of variation in viral gene expression among geographic populations. Only a few genes such as gp01, gp022 and gp107 were differentially expressed among different strains. Additionally, small RNA sequencing from SI population suggests that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21nt small RNAs. Some of these structural changes are specific to the geographic population and could be related to particular phenotypic characteristics of the strain, such as viral pathogenicity or transmissibility, and this requires further investigation.
Project description:Oil palm (Elaeis guineensis Jacq.) is one of the most important oil-producing crops in the world. However, the demand for oil from this crop will increase in the future. A comparative gene expression profile of the oil palm leaves was needed in order to understand the key factors that influence the oil production. Here, we reported an RNA-seq dataset from three different oil yields and three different genetic populations of oil palm. All raw sequencing reads were obtained from an Illumina NextSeq 500 platform. We also provide a list of the genes and their expression levels resulting from the RNA-sequencing. This transcriptomic dataset will provide a valuable resource for increasing oil yield.
Project description:To investigate the role of lncRNAs on lipid metabolism, we did RNAseq to find the difference among large yellow croaker fed with fish oil (FO), soybean oil (SO), olive oil (OO), and palm oil (PO) diets
