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Next Generation Sequencing Facilitates Quantitative Analysis of watermelon fruit small RNA expression

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of watermelon fruit small RNA expression

PROVIDER: PRJNA689613 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13354514.fastq.gz	Fastqsanger.gz
	SRR13354515.fastq.gz	Fastqsanger.gz
	SRR13354516.fastq.gz	Fastqsanger.gz
	SRR13354517.fastq.gz	Fastqsanger.gz
	SRR13354518.fastq.gz	Fastqsanger.gz

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Project description:To determine the differential expression of proteins in leaf and fruit of diploid and tetraploid watermelon

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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.

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