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Physalis

ABSTRACT: RNA-Seq analysis and transcriptome assembly for edible and decorative physalis plants

PROVIDER: PRJDB4299 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	DRR048294_1.fastq.gz	Fastqsanger.gz
	DRR048294_2.fastq.gz	Fastqsanger.gz
	DRR048295_1.fastq.gz	Fastqsanger.gz
	DRR048295_2.fastq.gz	Fastqsanger.gz
	DRR048296_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of floral-fruit Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of plants. The goals of this study are to compare omparatively evaluated both sequence variation and gene expression at the transcriptomic level between two species. Methods: Pooled total RNA of P. floridana flower buds and young fruits, in triplicate, using Illumina HiSeqTM 2000. The sequence reads remove reads with adaptors or unknown nucleotides larger than 5% and low-quality reads using . qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Sequencing the Physalis transcriptome revealed 147,118 unigenes. When aligned to the tomato genome, we estimated that around 30,121 genes were expressed in the Physalis floral-fruit transcriptome, and 10,498 orthologous gene pairs were identified between P. floridana and S. pimpinellifolium.with a fold change ≥1.5 and FER value <0.001, 0.68% of the unigenes in the Physalis floral-fruit transcriptome were developmentally regulated at the floral-fruit transition, and Altered expression of 15 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of floral-fruit 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. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a organ or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2018-12-29 | GSE92998 | GEO

Physalis floridana

Project description:Raw sequencing data of Physalis floridana P106

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