Abstract
RNA-seq and single-cell genomic research emerge as an important research area in the recent years due to its ability to examine genetic information of any number of single cells in all living organisms. The knowledge gained from RNA-seq and single-cell genomic research will have a great impact in many aspects of plant biology. In this review, we summary and discuss the biological significance of RNA-seq and single-cell genomic research in plants including the single-cell DNA-sequencing, RNA-seq and single-cell RNA sequencing in woody plants, methods of RNA-seq and single-cell RNA-sequencing, single-cell RNA-sequencing for studying plant development, and single-cell RNA-sequencing for elucidating cell type composition. We will focus on RNA-seq and single-cell RNA sequencing in woody plants, understanding of plant development through single-cell RNA-sequencing, and elucidation of cell type composition via single-cell RNA-sequencing. Information presented in this review will be helpful to increase our understanding of plant genomic research in a way with the power of plant single-cell RNA-sequencing analysis.
Highlights
RNA-seq and single-cell analysis in the scale of genomewide represents an important research field of plant genomics research in the recent years because the transcriptomic data of thousands of single cells can be investigated in any specific plant species with this technology (Hedlund and Deng 2018)
We summary and discuss the biological significance of RNA-seq and single-cell genomic research in plants including the single-cell DNA-sequencing, RNA-seq and single-cell RNA sequencing in woody plants, methods of RNA-seq and single-cell RNA-sequencing, single-cell RNA-sequencing for studying plant development, and single-cell RNA-sequencing for elucidating cell type composition
RNAseq approach has used to investigate the molecular mechanisms somatic embryogenesis in other woody plant species and the results suggest many gene families may contribute to the development and wood formation (Yakovlev et al 2016)
Summary
RNA-seq and single-cell analysis in the scale of genomewide represents an important research field of plant genomics research in the recent years because the transcriptomic data of thousands of single cells can be investigated in any specific plant species with this technology (Hedlund and Deng 2018). Single-cell genomic analysis examines the DNA or RNA sequence information of individual cells through optimized and powerful sequencing technologies for investigation of function of single cells in a specific plant species (Grun et al 2015; Hedlund and Deng 2018; Picelli 2017). Single cell DNA-seq is popular method that has been used for single cell genome sequencing in different species and application of this method has been reported in various areas including microbial genetics, plant molecular biotechnology, and plant pathology investigation (Hess et al 2011; Libault et al 2010; Pang et al 2009; Wuest et al 2013). RNASeq data analysis has used to determine mechanisms of fruit tree architecture, and to identify promising DNA markers (Okada et al 2016) Both recombination analyses and in silico analyses of RNA-Seq data provide a useful application of plant transcriptomes related to viral genome assembly and recombination (Jo et al 2016). A total of 77,509 unigenes have been identified to be associated with flowering and 107 flowering-time genes were identified and confirmed by qPCR, providing new insight into the molecular mechanisms that regulate flowering time in species of woody plants (Jia et al 2014)
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