Recent Applications of RNA Sequencing in Food and Agriculture
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TLDR
This chapter introduces RNA-Seq and surveys its recent food and agriculture applications, ranging from differential gene expression, variants calling and detection, allele-specific expression, alternative splicing, alternative polyadenylation site usage, microRNA profiling, circular RNAs, single-cell RNA- Seq, metatranscriptomics, and systems biology.Abstract:
RNA sequencing (RNA-Seq) is the leading, routine, high-throughput, and cost-effective next-generation sequencing (NGS) approach for mapping and quantifying transcriptomes, and determining the transcriptional structure. The transcriptome is a complete collection of transcripts found in a cell or tissue or organism at a given time point or specific developmental or environmental or physiological condition. The emergence and evolution of RNA-Seq chemistries have changed the landscape and the pace of transcriptome research in life sciences over a decade. This chapter introduces RNA-Seq and surveys its recent food and agriculture applications, ranging from differential gene expression, variants calling and detection, allele-specific expression, alternative splicing, alternative polyadenylation site usage, microRNA profiling, circular RNAs, single-cell RNA-Seq, metatranscriptomics, and systems biology. A few popular RNA-Seq databases and analysis tools are also presented for each application. We began to witness the broader impacts of RNA-Seq in addressing complex biological questions in food and agriculture.read more
Citations
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Journal ArticleDOI
De Novo Transcriptome Analysis Reveals Flowering-Related Genes That Potentially Contribute to Flowering-Time Control in the Japanese Cultivated Gentian Gentiana triflora
Tomoyuki Takase,Motoki Shimizu,Shigekazu Takahashi,Keiichirou Nemoto,Fumina Goto,Chiharu Yoshida,Akira Abe,Masahiro Nishihara +7 more
TL;DR: In this article , the authors obtained transcriptome profiling data using the Gentiana triflora cultivar ‘Maciry’, which typically flowers in late July, and conducted deep RNA sequencing analysis using gentian plants grown under natural field conditions for three months before flowering.
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