Phyllostachys bambusoides
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB16709 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR505689_1.fastq.gz | Fastqsanger.gz | |||
| DRR505689_2.fastq.gz | Fastqsanger.gz | |||
| DRR505690_1.fastq.gz | Fastqsanger.gz | |||
| DRR505690_2.fastq.gz | Fastqsanger.gz | |||
| DRR505691_1.fastq.gz | Fastqsanger.gz |
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Project description:Moso bamboo (Phyllostachys edulis (Carrière) J. Houz.), ) is one of the most importantessential economic bamboo species in China. However, the woods quality and yield of bamboo shoots were significantly threatened by diverse environmental conditions. significantly threaten the quality of wood and yield of bamboo shoots. In this study, to explore the molecular mechanism of abiotic stress response, we report the RNA-seq analyses of mosoMoso bamboo treated with drought, salt, SA and ABA at three -time courses. A total of 224.4 Gb clean data were generate in to explore the molecular mechanism of the abiotic stress response. The full-length transcriptome sequencing of these four treatments generated a total of 224.4 Gb data after quality trimming, and approximately 5.83Gban average of 6.615 Gb clean data were per sample was generated in per sample. The comparative analyses of the generated transcriptome data in this study will provide a valuable resource for identifying regulatory genes and potential pathways involved in various abiotic stresses in mosoMoso bamboo.
2021-10-01 | GSE169067 | GEO
Project description:Purpose:Bamboo shoots rapidly lose water and accumulate lignin when stored under room temperature, while low temperature conditioning (LTC, 4℃) can alleviate lignification and reduce weightlessness rate. However, few transcriptional response and profiling datasets are available to explore the LTC mechanism of bamboo shoots.The goal of this study is to provides insights into the regulation of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage by transcriptome analysis. Methods:Total RNA was extracted using RNAiso Plus (Takara, Japan) according to the protocol, and after quality testing, was used for library construction and transcriptome sequencing by Illumina Novaseq™ 6000. The quality-controlled reads were aligned to the Phyllostachys edulis reference genome (http://gigadb.org/dataset/100498). The edgeR program25 was used for differential expression analyses. Results: After raw data filtering, a high clean data rate from each sample was achieved, and the assessment result for the clean data by FastQC all demonstrated that our sequencing data was of high quality, full representativeness and validity. Compared with CK, a total of 7,452 DEGs were identified during LT storage. The Pearson’s correlation coefficient (r) and principle component analysis (PCA) results all suggested a high correlation among all samples. The above results suggest an effective LT treatment of postharvest bamboo shoots and a high-quality bioinformatics analysis of our RNA-seq results. Conclusions: Our study represents the first detailed analysis of Lei bamboo (Phyllostachys violascens) shoots during postharvest cold storage transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would reveal the essence of ripening and senescence of fruits and vegetables.
2020-10-01 | GSE149182 | GEO
Project description:Brassinosteroids (BRs) are a group of plant steroid hormones that play crucial roles various of growth and developmental processes. Biological function and signal transduction pathway of BR has been well characterized in model plants like Arabidopsis and rice. However, their biological roles are still unclear in tree species, especially in an important non-timber plant moso bamboo, which has great ecological and economic value and distinguish fast-growth feature. Here we reported that reduce endogenous brassinosteroid by biosynthesis inhibitor propiconazole reduced both root and shoot growth in seedling stage. Exogenous BR application promoted shoot bract elongation and inclination of lamina joint and bract. Genome-wide transcriptome analysis were performed to identify hundreds of differential expressed genes by BR and propiconazole treatment in shoot and root parts of bamboo seedling, respectively. GO analysis revealed that BR regulates cell wall related genes, hydrogen peroxide catabolic genes and auxin related genes to promote bamboo root development and elongation. Our study identified BR response genes and provides a comprehensive resource for molecular mechanism research of bamboo growth.
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Project description:Transcriptome, Metabolome, and Hormonome Analyses of Rice Calli
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Project description:We adopted the high-throughput sequencing technology and compared the transcriptomes of Moso bamboo rhizome buds in germination stage and late development stage. We found that the development of Moso bamboo rhizome lateral buds was coordinated by multiple pathways, including meristem development, sugar metabolism and phytohormone signaling. Phytohormones have fundamental impacts on the plant development. We found the evidence of several major hormones participating in the development of Moso bamboo rhizome lateral bud. Furthermore, we showed direct evidence that Gibberellic Acids (GA) signaling participated in the Moso bamboo stem elongation.
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Project description:Auxin is essential for plant growth and development by altering downstream gene expression. Although large progresses have been made on auxin-concentration, distribution and signaling pathways in model plants like Arabidopsis and rice, little is known in moso bamboo which belongs to grass family, and has great economic and social value. Here we performed genome-wide analysis of the key components related to auxin action, and identified 13 YUCCA genes for auxin synthesis, 14 PIN-FORMED/PIN-like (PIN/PILS) proteins 7 AUXIN1/LIKE-AUX1 (AUX1/LAX) family members for auxin transport, 10 auxin binding factors (AFB) for auxin perception, 43 auxin/indole-3-aceticacid (AUX/IAA) and 41 auxin response transcription factors (ARF) genes for auxin signaling in moso bamboo genome. We further performed phylogenetic analysis of those auxin action related genes from Arabidopsis, Oryza sativa and moso bamboo. To know those genes’ ability to response exogenous auxin and to generate a comprehensive transcriptome overview of auxin response in moso Bamboo, we performed RNA_seq analysis. Our data showed that auxin regulates genes related its biosynthesis, transport, signaling. Moreover, we present the interaction between auxin and other phytohormones at the level of transcription. In summary, we identified the key gene families involved in the auxin action pathways in moso bamboo, and generated a transcriptional overview of the auxin response in moso bamboo. Our data open up an opportunity to uncover the precise roles of auxin action pathways in this important species.
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Project description:Transcriptome, Metabolome, and Hormonome Analyses of Tobacco SR1 Calli
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Project description:Moso bamboo is a fast-growing bamboo species with high economic, social and cultural value. The method of transplanting moso bamboo seedlings for afforestation has become a more economical and effective method. The effect of light on the growth of plant seedlings is mainly reflected in the regulation of different light quality on the growth and development of seedlings, including light morphogenesis, photosynthesis and secondary metabolites. Therefore, studying the effects of specific wavelength light on the physiology and proteome of moso bamboo seedlings will play an important role in growing seedlings and seed cultivation of moso bamboo. Here, moso bamboo seeds were germinated in the dark and then were transferred to the blue and red-light conditions. After 14 days, we observed the effects of different light treatments on the growth and development of seedlings, and then compared and analyzed their proteome.
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