Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1050642 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27163355_subreads.fastq.gz | Fastqsanger.gz |
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Project description:To identify the important genetic resources of tea oil accumulation and quality formation in Camellia oleifera, an important woody edible oil tree native to Southern China, we have designed and customized an expression profile chip of C. oleifera with 8×60 K on the basis of transcriptome sequencing of multiple tissue samples including kernels, roots, and leaves from multiple varieties. we used the mcroarrays to determine the gene expressions in kernel development of C. oleifera elite varieties'Huashuo' , 'Huaxin' , 'Huajin' and 'Jujian' respectively. Microarray results indicated a total of 10710 gene probes showed stable differential expression in the comparation of August vs June and 9987 in the comparation of October vs August. PATHWAY enrichment results of DEGs indicated that the oil synthesis and accumulation occured in the whole kernel development of C. oleifera, but were mainly concentrated from the nutrition high-speed synthesis period to the seed mature period, which was consistent with the variation trend of oil content and fatty acide composition in C. oleifera kernel development.
2020-03-11 | GSE146709 | GEO
Project description:<p>The section <em>Oleifera</em> (Theaceae) has attracted attention for the high levels of unsaturated fatty acids found in its seeds. Here, we report the chromosome-scale genome of the sect. <em>Oleifera</em> using diploid wild <em>Camellia lanceoleosa</em> with a final size of 3.00 Gb and an N50 scaffold size of 186.43 Mb. Repetitive sequences accounted for 80.63% and were distributed unevenly across the genome. <em>Camellia lanceoleosa</em> underwent a whole-genome duplication event approximately 65 million years ago (65 Mya), prior to the divergence of <em>C</em>. <em>lanceoleosa</em> and <em>Camellia sinensis</em> (approx. 6-7 Mya). Syntenic comparisons of these two species elucidated the genomic rearrangement, appearing to be driven in part by the activity of transposable elements. The expanded and positively selected genes in <em>C</em>. <em>lanceoleosa</em> were significantly enriched in oil biosynthesis, and the expansion of homomeric <em>acetyl-coenzyme A carboxylase</em> (<em>ACCase</em>) genes and the seed-biased expression of genes encoding heteromeric ACCase, diacylglycerol acyltransferase, glyceraldehyde-3-phosphate dehydrogenase and stearoyl-ACP desaturase could be of primary importance for the high oil and oleic acid content found in <em>C. lanceoleosa</em>. Theanine and catechins were present in the leaves of <em>C</em>. <em>lanceoleosa</em>. However, caffeine can not be dectected in the leaves but was abundant in the seeds and roots. The functional and transcriptional divergence of genes encoding SAM-dependent <em>N</em>-methyltransferases may be associated with caffeine accumulation and distribution. Gene expression profiles, structural composition and chromosomal location suggest that the late-acting self-incompatibility of <em>C. lanceoleosa</em> is likely to have favoured a novel mechanism co-occurring with gametophytic self-incompatibility. This study provides valuable resources for quantitative and qualitative improvements and genome assembly of polyploid plants in sect. <em>Oleifera</em>.</p>
2022-07-14 | MTBLS3769 | MetaboLights
Project description:Tea (Camellia sinensis (L.) O. Kuntze) is an important non-alcoholic commercial beverage crop. Tea tree is a perennial plant, and winter dormancy is its part of biological adaptation to environmental changes. We recently discovered a novel tea tree cultivar that can generate tender shoots in winter, but the regulatory mechanism of this ever-growing tender shoot development in winter is not clear. In this study, we conducted a proteomic analysis for identification of key genes and proteins differentially expressed between the winter and spring tender shoots, to explore the putative regulatory mechanisms and physiological basis of its ever-growing character during winter.
2022-02-23 | PXD008958 | Pride
Project description:Purpose: High-throughput RNA sequencing has been used to examine mRNA expression profiles in fungal cells treated with essential oils. The goals of this study are to analyze the global gene expression profiles in Botrytis cinerea with or without tea tree oil and its two characteristic components treatment by RNA-Seq. Methods: The mRNA profiles of Botrytis cinerea with or without tea tree oil and its two characteristic components treatment were generated by deep sequencing, in triplicate, using Illumina HiSeq™ 2500 sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR was performed to verified the sensitivity of the RNA-seq method. Results: After high-throughput RNA sequencing, reads were filtered to yield 111.22 Gb of clean sequence data. The GC content for all samples exceeded 45%. The Q20 ratio (used to evaluate reads quality) was greater than 94%, and Q30 base percentage was at least 87.07%. Altered expression of 7 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Most differentially expressed genes (DEGs) from B. cinera cells treated with terpinen-4-ol participated in biosynthesis of secondary metabolites, and the metabolism of amino acid, carbohydrate and lipid. 1,8-cineole mainly affected DEGs involved in genetic information processing, and thus inducing cell death. Conclusions: Terpinen-4-ol exerts antifungal activity mainly by blocking the expression of genes related to cell integrity and mitochondrial function. 1,8-cineole primarily affects genes involved in genetic information processing including DNA replication, transcription and repair. This study provides insight into the molecular mechanism by which tea tree oil acts against Botrytis cinerea based on the data from RNA-seq.
2019-10-03 | GSE138291 | GEO
Project description:MicroRNAs (miRNAs) are a type of small non-coding RNAs, which play important roles in plant growth, development and stress responses. Tea (Camellia sinensis) prepared from tea tree is the oldest and most popular nonalcoholic beverages in the world, and has large economic, medicinal and cultural significance. Nevertheless, there are a few studies on the miRNAs and their functions in Camellia sinensis. We sequenced 9 small RNA libraries and 9 RNA-Seq libraries from roots, leaves and flowers tissues. Through comprehensive computational analyses of 9 small RNA profiles, we identified 200 conserved miRNAs of which 138 have not been reported, and 56 novel miRNAs with 33 have not been reported. Nearly, two thousands genes have significantly different expression levels in tissues. In order to identify targets of miRNAs, we sequenced two degradome profiles from leaves and roots, respectively. Totally, more than 3,000 putative targets of conserved miRNAs were identified in both degradome profiles by using the SeqTar algorithm. These results clearly enhanced our understanding about small RNA guided gene regulations in Camellia sinensis.
2020-12-31 | GSE138149 | GEO
Project description:MicroRNAs (miRNAs) are a type of small non-coding RNAs, which play important roles in plant growth, development and stress responses. Tea (Camellia sinensis) prepared from tea tree is the oldest and most popular nonalcoholic beverages in the world, and has large economic, medicinal and cultural significance. Nevertheless, there are a few studies on the miRNAs and their functions in Camellia sinensis. We sequenced 9 small RNA libraries and 9 RNA-Seq libraries from roots, leaves and flowers tissues. Through comprehensive computational analyses of 9 small RNA profiles, we identified 200 conserved miRNAs of which 138 have not been reported, and 56 novel miRNAs with 33 have not been reported. Nearly, two thousands genes have significantly different expression levels in tissues. In order to identify targets of miRNAs, we sequenced two degradome profiles from leaves and roots, respectively. Totally, more than 3,000 putative targets of conserved miRNAs were identified in both degradome profiles by using the SeqTar algorithm. These results clearly enhanced our understanding about small RNA guided gene regulations in Camellia sinensis.
2020-12-31 | GSE138150 | GEO
Project description:MicroRNAs (miRNAs) are a type of small non-coding RNAs, which play important roles in plant growth, development and stress responses. Tea (Camellia sinensis) prepared from tea tree is the oldest and most popular nonalcoholic beverages in the world, and has large economic, medicinal and cultural significance. Nevertheless, there are a few studies on the miRNAs and their functions in Camellia sinensis. We sequenced 9 small RNA libraries and 9 RNA-Seq libraries from roots, leaves and flowers tissues. Through comprehensive computational analyses of 9 small RNA profiles, we identified 200 conserved miRNAs of which 138 have not been reported, and 56 novel miRNAs with 33 have not been reported. Nearly, two thousands genes have significantly different expression levels in tissues. In order to identify targets of miRNAs, we sequenced two degradome profiles from leaves and roots, respectively. Totally, more than 3,000 putative targets of conserved miRNAs were identified in both degradome profiles by using the SeqTar algorithm. These results clearly enhanced our understanding about small RNA guided gene regulations in Camellia sinensis.
2020-12-31 | GSE138148 | GEO
Project description:RNA sequencing (RNA-Seq) was used in our study to elucidate the mechanism of Tea tree oil (TTO) as a potential antibacterial agent to evaluate differentially expressed genes and functional network analysis in S. aureus ATCC 29213 biofilms.
2016-08-19 | GSE85787 | GEO