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

Abstract

The advent of modern "omics" technologies (genomics, transcriptomics, proteomics, and metabolomics) are attributed to innovative breakthroughs in genome sequencing, bioinformatics, and analytic tools. An organism's biological structure and function is the result of the concerted action of single cells in different tissues. Single cell genomics has emerged as a groundbreaking technology that has greatly enhanced our understanding of the complexity of gene expression at a microscopic resolution and holds the potential to revolutionize the way we characterize complex cell assemblies and study their spatial organization, dynamics, clonal distribution, pathways, function, and networking. Mammalian systems have benefitted immensely from these approaches to dissect complex systems such as cancer, immunological disorders, epigenetic controls of diseases, and understanding of developmental biology. However, the applications of single-cell omics in plant research are just starting. The potential to decipher the fundamentals of developmental and functional biology of large and complex plant species at the single-cell resolution are now becoming important drivers of research. In this review, we present the status, challenges and potential of one important and most commonly used single-cell omics technique in plants, namely single cell transcriptomics.

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review

“…Both single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq) have exciting applications [65][66][67][68][69][70][71][72][73][74][75][76][77], for instance: (i) discovering and characterizing cell type in health and diseases, such as cancer [13,[78][79][80][81][82][83][84][85][86][87][88][89], with implications in immunology [90], immune-mediated diseases [91], immunotherapy [92][93][94][95][96][97][98][99][100] and drug resistance [101]; (ii) deciphering the roles of such specific cell types in health and disease [102], including mitochondrial heteroplasmy [33]; and (iii) analyzing cell emergence, development and plasticity in tissues and organisms. These studies are also applied to study plant biology [103,104]. Currently, sc/snRNA-seq are extensively being used in neuroscience research, including analyses of neurodegenerative disorders at the molecular level.…”

Single-cell transcriptome sequencing atlas of cassava tuberous root

“…However, early transcriptome analysis treated the sample as a homogeneous material and averaged differences across hundreds or thousands of cells ( Shaw et al., 2021 ). The patterns of gene expression at the cell level cannot be clearly revealed by a bulk gene expression profile from one tissue ( Iqbal et al., 2020 ).…”

De novo phasing resolves haplotype sequences in complex plant genomes

“…If short‐read sequences (SRS) obtained from Illumina platform analyses of parents with LRS from SMRT or ONT of their offspring are available, accurate offspring phasing is possible by identifying sequences specific to each parent and classifying the contigs of the offspring from the maternal and paternal genomes. In addition to these approaches, gamete‐cell sequencing can be used to generate raw sequences of each haplotype; although this is an ideal method for constructing haplotype‐level assemblies, it has technical limitations (Iqbal et al ., 2020 ; Jia et al ., 2016 ; Shi et al ., 2019 ).…”