Peat metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA883528 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR21679849_1.fastq.gz | Fastqsanger.gz | |||
| SRR21679849_2.fastq.gz | Fastqsanger.gz | |||
| SRR21679850_1.fastq.gz | Fastqsanger.gz | |||
| SRR21679850_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 73 |
Similar Datasets
Project description:Oil palm breeding and seed development have been hindered due to the male parent's incapacity to produce male inflorescence as a source of pollen under normal conditions. On the other hand, a young oil palm plantation has a low pollination rate due to a lack of male flowers. These are the common problem of sex ratio in the oil palm industry. Nevertheless, the regulation of sex ratio in oil palm plants is a complex mechanism and remains an open question until now. Researchers have previously used complete defoliation to induce male inflorescences, but the biological and molecular mechanisms underlying this morphological change have yet to be discovered. Here, we present an RNA-seq dataset from three early stages of an oil palm inflorescence under normal conditions and complete defoliation stress. This transcriptomic dataset is a valuable resource to improve our understanding of sex determination mechanisms in oil palm inflorescence.
2021-10-23 | GSE186394 | GEO
Project description:Malaysian Oil Palm Peat Soil Metagenome
| PRJNA804311 | ENA
Project description:The oil palm fruit abnormality, mantled, is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for breeding and oil production. Widely regarded as epigenetic, mantling had defied explanation, and has become an icon of unsustainability in environmentally sensitive tropical plantation crops. We identified the MANTLED gene using Epigenome Wide Association analysis of genetically identical palms from multiple clonal lineages. Hypomethylation of a LINE retrotransposon related to rice Karma, found in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is correlated with alternative splicing and loss of small RNA. DNA methylation is regained in spontaneous revertants accounting for non-Medelian inheritance of the Good Karma and Bad Karma epialleles. Thus epigenetic regulation of transposable elements results in somaclonal variation and provides a means to cull mantled nursery palms before committing limiting plantation resources to clonal propagation. DNA methylation profiling was performed using the McrBC DNA methylation dependent fractionation and microarray hybridization method as described in Lippman, Z., Gendrel, A. V., Colot, V. & Martienssen, R. Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods 2, 219-224 (2005).
2015-09-09 | GSE68410 | GEO
Project description:The oil palm fruit abnormality, mantled, is a somaclonal variant arising from tissue culture that drastically reduces yield, and has largely halted efforts to clone elite hybrids for breeding and oil production. Widely regarded as epigenetic, mantling had defied explanation, and has become an icon of unsustainability in environmentally sensitive tropical plantation crops. We identified the MANTLED gene using Epigenome Wide Association analysis of genetically identical palms from multiple clonal lineages. Hypomethylation of a LINE retrotransposon related to rice Karma, found in the intron of the homeotic gene DEFICIENS, is common to all mantled clones and is correlated with alternative splicing and loss of small RNA. DNA methylation is regained in spontaneous revertants accounting for non-Medelian inheritance of the Good Karma and Bad Karma epialleles. Thus epigenetic regulation of transposable elements results in somaclonal variation and provides a means to cull mantled nursery palms before committing limiting plantation resources to clonal propagation. DNA methylation profiling was performed using the McrBC DNA methylation dependent fractionation and microarray hybridization method as described in Lippman, Z., Gendrel, A. V., Colot, V. & Martienssen, R. Profiling DNA methylation patterns using genomic tiling microarrays. Nat Methods 2, 219-224 (2005). DNA methylation profiling was performed on 54 parthenocarpic mantled ramet, 43 normal ramet and 1 ortet adult leaf samples. For each sample, two independent fractionations of total genomic DNA and DNA methylation-depleted DNA were performed. Each total DNA/methylation-depleted DNA pair was differentially labeled and hydrized to a custon Nimblegen microarray in a dye-swapped design (4 array hybridizations per sample).
2015-09-09 | E-GEOD-68410 | biostudies-arrayexpress
Project description:Sago palm is an important agricultural starch producing plant which contributes to the economics of Malaysia where the trunk is the main plant part which the starch is stored. However, there are sago palms that planted on peat soil failed to develop its trunk even after 17 years been planted. This phenomenon is known as 'non-trunking', which eliminates the economic value of the plants. Numeral researches have been done to address the phenomenon but the molecular mechanisms of sago palm respond toward the responsible stresses are still lacking. Therefore, in this study we collected samples from Trunking (Normal) and Non-Trunking sago palm leaf samples which planted on peat soil for total RNA extraction followed by next generation sequencing using BGISEQ-500 platform. The raw reads were cleaned and de novo assembled using TRINITY software package. Total of 40.11 Gb bases were sequenced from the sago palm leaf samples and after assembled producing 102,447 unigenes, with N50 score 1,809 bp and GC ratio of 44.34%. Unigenes by aligning with 7 (NR, NT, GO, KOG, KEGG, SwissProt & InterPro) functional databases and 65,523 (63.96%) unigenes were annotated. Functional annotation results in the detection of 46,335 Coding DNA sequences by Transdecoder. 30,039 Simple-sequence repeats distributed on 21,676 Unigenes were detected using Primer3 software, and 2,355 Transcription Factor coding Unigenes were predicted using getorf and hmmseach software. A total of 492 up-regulated and 444 down-regulated at least two-fold differential expressed gene were detected using DESeq2 algorithm with 95% confidence.
2021-12-13 | GSE189085 | GEO
Project description:Oil palm (Elaeis guineensis) is a highly productive oil crop and the most consumed vegetable oil globally due to its unique oil characteristics. Palm oil production is affected by abiotic stresses, leading to food security issues and huge economic losses. To understand the oil palm responses to different abiotic stresses at the transcriptional level, we performed RNA-Seq analyses of oil palm leaves treated with drought, high salinity, heat, cold and flood stresses compared with controls. A total of 18 libraries (three biological replicates per treatment) were generated with approximately 843 million of total clean reads after data filtering. Clean reads were mapped to the oil palm reference genome at a total mapping rate of more than 70%. The quantification of expression analysis enabled the identification of potential abiotic stress-responsive genes, co-expressed under multiple abiotic stresses and unigenes that were induced by a specific abiotic stress. The availability of these RNA-Seq datasets will provide a better understanding of the abiotic stress response mechanisms to develop climate-resilient oil palm planting materials.
2024-12-14 | GSE242922 | GEO
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.
2023-01-10 | GSE222528 | GEO
Project description:Schlöppnerbrunnen omics: 13 metagenome-assembled genomes
| PRJNA412580 | ENA
Project description:H3K4me3 profiling of OSCC secondary (2ary) recipient primary tumors (PTs) following in vivo exposure to control (CTRL) or palm oil-enriched (PALM) diet in primary recipient mice
2021-11-16 | GSE149047 | GEO