Single-Cell Genomic Analysis in Plants

Abstract

Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis.

Biological significance of RNA-seq and single-cell genomic research in woody plants

“…Single-cell DNA-sequencing has great potential to gain insights into functions of genes in single plant cells. Applications of single-cell DNA-sequencing will be an important field in plant genomic (Yuan et al 2018). In rice, genome-wide bisulfite sequencing revealed that OsROS1-mediated DNA demethylation restricts the number of aleurone cell layers in (Liu et al 2018).…”

“…In rice, genome-wide bisulfite sequencing revealed that OsROS1-mediated DNA demethylation restricts the number of aleurone cell layers in (Liu et al 2018). Single cell DNA-seq has been applied in different plant species and the procedure of single cell DNA-seq includes; (1) isolation of single cells; (2) amplification of cDNA; (3) construction of cDNA libraries; and (4) sequencing of the cDNA libraies (Brandt et al 2002;Offermann et al 2015;Yuan et al 2018;Zheng et al 2016).…”

“…Single cell sequencing as a promising method for elucidating a set of important biological questions includes single cell DNA sequencing, single cell DNA methylome sequencing, and single-cell RNA sequencing (Grun and van Oudenaarden 2015;Hodzic 2016;Picelli 2017). Single cell DNA sequencing has been used in many organisms and one of the single cell DNA sequencing is multiple displacement amplification (Hane et al 2014;Offermann et al 2015;Utturkar et al 2016;Yuan et al 2018). Single cell DNA methylome sequencing quantifies DNA methylation and the popular method used for single cell methylome sequencing is whole genome bisulfite sequencing (Liu et al 2018;Wuest et al 2013;Yuan et al 2018).…”

Status and Potential of Single‐Cell Transcriptomics for Understanding Plant Development and Functional Biology

“…A few successes have been achieved in successful protoplast isolations in plants such as moss, to load them on commercially available dropletbased platform such as 10x Genomics [39]. The relatively untapped plant systems have the potential to efficiently utilize the modern sc-Omics techniques to enhance our broader understanding of cellular-level plant development and functional trajectories [36]. Single-cell based omics, in particular single-cell transcriptomics has the capability to provide a detailed insight into cell responses to different environmental cues, such as biotic and abiotic stresses and provides the strong basis for understanding of genetic control of more complex traits [40,41].…”

Statistical approaches for analysis of mapping quality for single-cell sequencing data

“…Motivation and Aim: Bioinformatics analysis is essential in providing biological insights for single-cell experiments, such as detecting variants, quantifying gene expression, and subpopulation detection. However, conventional tools developed for bulk-cell genomics cannot be directly applied to single-cell sequencing data [1]. Methods and Algorithms: this low coverage characteristic of single-cell sequencing data has posed difficulties in the variant calling procedure.…”