Elaeis guineensis
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REPOSITORIES: ENA
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Project description:Proteome data was obtained from the fruit mesocarps of the two oil palm species, namely, the African Elaeis guineensis (commercial tenera or commonly known as D x P and MPOB-Nigerian tenera) and the South American Elaeis oleifera. Total proteins were extracted from randomly selected fruitlets and subjected to proteomics characterisation by means of liquid chromatography mass spectrometry. Number of proteins identified, the grouping of the biological replicates from five developmental weeks after anthesis, and the localisation of gene corresponded to the detected proteins on the oil palm chromosomes, were presented. A total of 4,116, 4,210 and 4,081 proteins were found in commercial tenera and MPOB Nigerian tenera for Elaeis guineensis; and Elaeis oleifera, respectively. Principal component analysis showed two distinct clusters that corresponded to Elaeis guineensis and Elaeis oleifera. Collectively, genes that corresponded to the identified proteins were found to be located in all 16 oil palm chromosomes. A total of 59 proteins from Elaeis guineensis and Elaeis oleifera were down-regulated for >5-fold change during the peak of lipid biosynthesis compared to the onset. The same comparative analysis revealed that 66 proteins were up-regulated for >5-fold change. About 60.0% of the observed proteins were involved in catalytic activity while 28.5% were associated with redox reaction. Based on same datasets, the tricarboxylic acid cycle and 5-hydroxytryptamine degradation pathways were found to be enriched the most (>36-fold change). These data can be used to support the oil palm gene model validation and lipid metabolism research, particularly in the areas of oil yield and quality. The tabulated protein lists of identified proteins and their expression changes from these varieties were provided as supplementary files. Raw MSF and mzid files for all the oil palm species were deposited in the ProteomeXchange (PXD017436).
| S-EPMC7240217 | biostudies-literature
Project description:Identification of differentially expressed genes from RNA-seq data of non-embryogenic and embryogenic ortets. Selected ortets were previously cloned, thereby somatic embryogenesis rates are known for these ortets. Ortets fitting the study criteria were supplied by two agencies, namely L1 and L2. Principal Component Analysis indicated that variance between agencies were higher than the variance between embryogenesis groups within the agency. Therefore, differential analysis was conducted separately for each agency. Differential expression analysis using DESeq2 package suggested the L2 transcriptomes of zero and low embryogenesis groups were more similar compared to the high embryogenesis group. The L1 transcriptomes consisting of zero and low embryogenesis groups similarly showed overlapping clusters. Differential expression analysis was conducted on the L1 samples (low vs. zero embryogenesis) using DESeq2 R package and the identified differentially expressed genes (DEGs) was used for clustering analysis of the L2 samples. The clustering profiles suggested that expression of these DEGs in L2 samples were able to differentiate high embryogenesis from zero-low embryogenesis L2 groups.
2021-02-21 | GSE167149 | GEO
Project description:The production of oil palm (Elaeis guineensis) in Southeast Asia is vital to the economies of Indonesia and Malaysia. Both fertilisers and pesticides used in palm production can contain elevated concentrations of Trace Elements (TEs) which may accumulate in soils and leaf tissues of plants. We hypothesised that leaves from oil palms may be deficient in essential elements, while containing elevated concentrations of non-essential TEs commonly found in agrichemicals. Samples of plant materials (leaves and fruitlets) were collected from active and former plantations in Sumatra, Indonesia, and analysed for essential and non-essential elements. Indonesian palm oil samples were sourced in New Zealand and their elemental concentrations determined. Leaf materials from both active and abandoned production sites were deficient in N, K, S and Mo, while leaf materials from abandoned sites were deficient in P. These deficiencies may have been a contributing factor to the abandonment of production at these sites. Concentrations of non-essential elements were below or comparable to average plant concentrations and no evidence of contamination was found in plant tissues. Palm oil contained low concentrations of TEs, which did not pose any toxicity risks. However, Na and Al were present in concentrations of 1198 and 159 mg kg-1 respectively, which were higher than have been previously reported. Tropical oil palm production could benefit from the determination of bioaccumulation factors for fertiliser contaminants in E. guineensis, to limit the transfer of contaminants to plants and products if increased fertiliser applications were used to correct nutrient deficiencies.
| S-EPMC10800330 | biostudies-literature
Project description:Elaeis guineensis Transcriptome or Gene expression
| PRJNA274848 | ENA
Project description:African oil palm(Elaeis guineensis Jacg) transcriptome,small RNA and degradome
| PRJNA306710 | ENA