Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1106074 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28840200_1.fastq.gz | Fastqsanger.gz | |||
| SRR28840200_2.fastq.gz | Fastqsanger.gz | |||
| SRR28840201_1.fastq.gz | Fastqsanger.gz | |||
| SRR28840201_2.fastq.gz | Fastqsanger.gz | |||
| SRR28840202_1.fastq.gz | Fastqsanger.gz |
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Project description:The genetic diversity of tea plant (Camellia sinensis) in Sichuan province (China) based on restriction site-associated DNA sequencing (RAD-seq)
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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 | 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 | GSE138148 | GEO
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:Anthracnose disease is caused by Colletotrichum gloeosporioides, and is common in leaves of the tea plant Camellia sinensis. MicroRNAs (miRNAs) have been known as key modulators of gene expression in defense responses; however, the role of miRNAs in tea plant during defensive responses to C. gloeosporioides remains unexplored. Six miRNA sequencing data sets and two degradome data sets were generated from C. gloeosporioides-inoculated and control tea leaves. A total of 485 conserved and 761 novel miRNAs were identified. Of those, 239 known and 369 novel miRNAs exhibited significantly differential expression under C. gloeosporioides stress. 1134 and 596 mRNAs were identified as targets of 389 and 299 novel and conserved miRNAs by degradome analysis, respectively. The expression levels of twelve miRNAs and their targets were validated by quantitative real-time PCR. The predicted targets of five interesting miRNAs were further validated through 5'RLM-RACE. Furthermore, Gene Ontology and metabolism pathway analysis revealed that most of the target genes were involved in translation, carbohydrate metabolism and signal transduction pathways. This study enriches the resources of defense-responsive miRNAs and their targets in C. sinensis, and thus, provides novel insights into the miRNA-mediated regulatory mechanisms underlying immunity responses to biotic stress in tea plant.
2019-04-10 | GSE119728 | GEO
Project description:Tea plants (Camellia sinensis) present an excellent system to study evolution and diversification of specialized metabolites due to their abundance in classes, numbers and contents. A large number of tea cultivars have been cultivated throughout the world not only because of their adaption to different environments but of selection for specific flavors. The chemical and genetic basis for unique taste and aroma of different tea cultivars remains largely unknown, but is critical for guiding genetic breeding of new cultivars. Using transcriptomic data from 136 representative tea accessions in China, we obtain 925,854 high-quality single-nucleotide polymorphisms (SNPs) useful for marker-assisted breeding. Phylogenetic and population structure analyses separate sampled tea accessions into five major groups. Different major alleles are identified on 1183 SNP sites for the two major types of tea, C. sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS), reflecting fixation of these alleles after population divergence. Non-targeted metabolomic analyses detect 2,818 and 2,311 metabolic features in tea samples in positive and negative ionization modes, respectively, including 355 and 286 metabolites respectively that are differentially accumulated in different tea groups. Each phylogenetic group contains signature metabolites. In particular, CSA tea accessions are featured with high accumulation of diverse classes of flavonoid compounds, such as flavanols, flavonol mono-/di-glycosides and proanthocyanidin dimers. Comparisons of gene expression profiles of different tea groups identify hundreds of differentially expressed genes with some involved in the biosynthesis of characteristic tea metabolites, reflecting a combinational effect of genetic and environmental factors. Taken together, our study provides new insights into the phylogenetic relationships, molecular markers, metabolite compositions, and gene expression profiles of representative cultivated tea accessions in China, which are beneficial for targeted tea breeding and improvement.
2020-10-05 | MTBLS1405 | MetaboLights
Project description:Streptococcus suis is an important zoonosis pathogen that causes significant economic losses worldwide characterized by meningitis, septicaemia, arthritis, bronchopneumonia endocarditis. Streptcoccus suis 2 strain SC19 was isolated in Sichuan province in China, during the outbreak in 2005. Septicemia is most popular symptoms for SC19 infection, and mortality is high. We used human acute monocytic leukemia cell line (THP-1) infected SC19 to analysis the pathomechanism of septicemia in SS2 infection.
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Project description:Cysteine S-nitrosylation is a reversible protein post-translational modification and critically regulates the activity, localization and stability of proteins. Tea (Camellia sinensis (L.)) is one of the most thoroughly studied evergreen crop due to its broad non-alcoholic beverage and huge economic impact in the world. However, to date, little is known about the S-nitrosylome in this plant. Here, we performed a global analysis of cysteine S-nitrosylation in tea leaves. In total, 228 cysteine S-nitrosylation sites were identified in 191 proteins, representing the first extensive data on the S-nitrosylome in tea plants. These S-nitrosylated proteins were located in multiple subcellular compartments, especially in the chloroplast and cytoplasm. The analysis of functional enrichment and PPI network revealed that the S-nitrosylated proteins were mainly involved in carbon metabolism, especially in Calvin cycle and TCA cycle. These results suggested that S-nitrosylated proteins in tea leaves might play critical regulatory roles in the carbon metabolism. Overall, this study not only globally analyzed the functional annotation of cysteine S-nitrosylation in tea leaves, but also preliminarily provided the valuable information for further investigating the functions of cysteine S-nitrosylation in tea plants.
2020-05-26 | PXD012443 | Pride