Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1201555 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31800805_1.fastq.gz | Fastqsanger.gz | |||
| SRR31800805_2.fastq.gz | Fastqsanger.gz | |||
| SRR31800806_1.fastq.gz | Fastqsanger.gz | |||
| SRR31800806_2.fastq.gz | Fastqsanger.gz | |||
| SRR31800807_1.fastq.gz | Fastqsanger.gz |
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Project description:The tea plant (Camellia sinensis (L.) O. Kuntze) is often commercially used as a source of non-alcoholic beverages and is an economically important woody crop (Chen et al., 2007). As living standards have improved, the requirement for high-quality life has increased in modern society. ‘Anji Baicha’ (alias ‘Baiye 1’ or ‘White Leaf 1’) is an excellent tea cultivar with albino phenotype and it is popular in producing high-quality green tea. The traits of ‘Anji Baicha’ are as follows. Young ‘Anji Baicha’ shoots are yellow-green when the early spring temperature is below 20°C. As the leaves fully expand, the leaves become white. The leaves gradually return to green when the environmental temperature increases (Cheng et al., 1999; Li et al., 2002, 2011). Previous reports have suggested a positive correlation between amino acid concentration and albinism as well as a negative correlation between tea polyphenols and albinism (Li et al., 1996; Du et al., 2006; Xiong et al., 2013). Therefore, the quality of ‘Anji Baicha’ is much higher when new shoots become albino due to their rich amino acid content and modest tea polyphenol content. Plants adjust their metabolism in response to environmental stimuli to eventually bring about changes in protein activities and levels, and this adaptive process includes posttranslational protein modifications (PTMs) (Prabakaran et al., 2012). PTMs have been reported to regulate various processes, including DNA interaction, protein-protein interactions, enzyme activation and protein stability. Among the hundreds of different PTMs, lysine acetylation is an abundant, reversible and highly regulated PTM (Zhang et al., 2009; Wu et al., 2011).
2018-01-15 | PXD008134 | Pride
Project description:Purpose: In higher plants, perennialism is achieved through axillary buds and side-shoots that stay vegetative. This work aims to analyze the pattern of axillary bud (AB) formation in the perennial model plant Arabis alpina and to study the role of LATERAL SUPPRESSOR (AaLAS) gene in this process. Methods: This study combines stereomicroscopic analysis with RNA sequencing to monitor how patterns of AB formation and gene expression correlate. The role of AaLAS was studied using an RNAi approach. Results: During vegetative development, ABs initiate at a distance to the SAM, whereas after induction of flowering ABs initiate adjacent to the SAM. Dormant buds are established before onset of vernalization. Transcript profiles of ABs initiated at a distance were different from that of the SAM, whereas transcript patterns of buds initiated in close proximity were similar to the corresponding SAM. Knock-down of AaLAS leads to loss of both dormant buds and vegetative side-shoots, strongly compromising perennial life style. Conclusions: AB formation is regulated differently during vegetative and reproductive development. New meristems that show gene expression profiles different from the SAM are established at a distance to the SAM. AaLAS plays an essential role in perennial life cycle modulating the establishment of dormant buds and vegetative side-shoots.
2020-03-03 | GSE140316 | GEO
Project description:In plant axillary bud dormancy and outgrowth are regulated by phytohoromones, but it is still unknown about its molecular mechanism. We reveal that Arabidopsis axillary buds located at axil of rosette leaves show dormancy and that this is broken by the decapitation of main stem, resulting in the bud outgrowth. To investigate about the molecular mechanisms of dormancy and outgrowth, we carried out gene expression analysis during axillary shoot outgrowth in Arabidopsis wild type Columbia accession. Since axillary buds did not initiate outgrowth (dormancy) at 5 day after bolting of main stem, we used 5-day bolted plants as a control (before decapitation). Then, main stems were decapitated, and axillary shoots were collected at 24 hours after decapitation (named as growing shoot). Total RNA was prepared from either control or growing shoots and used for the microarray analysis. We carried out duplicate microarray analysis using independent plant materials.Ref):Tatematsu et al., Plant Physiol. 138: 757-766 (2005). Keywords: Expression profilling by array
2009-11-18 | GSE18987 | 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:Root-synthesized secondary metabolites are critical quality-conferring compounds of foods, plant-derived medicines, and beverages. However, information at a single-cell level on root-specific secondary metabolism remains largely unexplored. L-theanine, an important quality component of tea, is primarily synthesized in roots, from which it is then transported to new tea shoots. In this study, we present a single-cell RNA sequencing (scRNA-seq)-derived map for the tea plant root, which enabled cell-type-specific analysis of glutamate and ethylamine (two precursors of theanine biosynthesis) metabolism, and theanine biosynthesis, storage, and transport. Our findings support a model in which the theanine biosynthesis pathway occurs via multicellular compartmentation and does not require high co-expression levels of transcription factors and their target genes within the same cell cluster. This study provides novel insights into theanine metabolism and regulation, at the single-cell level, and offers an example for studying root-specific secondary metabolism in other plant systems.
2024-10-07 | GSE267845 | GEO
Project description:The green tea made from the etiolation shoots and leaves have fresh taste and strong aroma. ‘Zhonghuang 2 (ZH2) is a natural etiolation mutant and its shoots are etiolation in spring and turn green in summer. Two conditions including the relative high temperature (LT, 26 / 22oC) and the relative low temperature (LT, 18 / 14oC) were to find out the etiolated reason of ZH2. We confirmed ZH2 was a low-temperature sensitive tea plant cultivar, and the reason of shoots etiolation at LT was the reduction of stacked grana, which could cause the lack of photoreaction. We identified 1279 differentially expressed genes (DEGs), most of them were related to cytochrome synthesis and chloroplast development and function by RNA-seq. Through the whole-genome bisulfite sequencing (WGBS) assay, we found that the dynamic of DNA methylation level in three contexts (CG, CHG and CHH) was all decreased at LT, and the change was most obvious in the CHH context. According the result of cross analysis, 56 genes were identified with significant changes in both expression and DNA methylation levels. A large number of them were related to chloroplast development and chlorophyll synthesis. This study demonstrated that the DNA methylation was involved in the low-temperature regulated etiolation process of young shoots in ZH2. Change of the DNA methylation level was associated with the gene expression level, thus affecting the structure and function of chlorophyll and chloroplast, even reduced photosynthesis, which might have a phenotypic impact on the color of shoots and leaves. And it laid the foundation for studying the etiolation process from an epigenetic perspective.
2023-10-19 | GSE234849 | GEO
Project description:In plant axillary bud dormancy and outgrowth are regulated by phytohormones, but it is still unknown about its molecular mechanism. We reveal that Arabidopsis axillary buds located at axil of rosette leaves show dormancy and that this is broken by the decapitation of main stem, resulting in the bud outgrowth. To investigate about the molecular mechanisms of dormancy and outgrowth, we carried out gene expression analysis during axillary shoot outgrowth in Arabidopsis wild type Columbia accession. Since axillary buds did not initiate outgrowth (dormancy) at 5 day after bolting of main stem, we used 5-day bolted plants as a control (before decapitation). Then, main stems were decapitated, and axillary shoots were collected at 24 hours after decapitation (named as growing shoot). Total RNA was prepared from either control or growing shoots and used for the microarray analysis. We carried out duplicate microarray analysis using independent plant materials.Ref):Tatematsu et al., Plant Physiol. 138: 757-766 (2005). Keywords: Expression profilling by array 4 samples were used in this experiment
2009-11-17 | E-GEOD-18987 | biostudies-arrayexpress
Project description:To identificate long noncoding RNAs in rice, we profiled transcriptome of various organs at different developmental stages using nondirectional paired-end RNA-seq based on poly(A) selection. Transcriptom profiling in flower buds, flowers, flag leaves and roots sampled before flowering and after flowering, milk grains and mature seeds.
2015-11-25 | E-GEOD-56462 | biostudies-arrayexpress