Potentials of single-cell genomics in deciphering cellular phenotypes

Curr Opin Plant Biol. 2021 Oct:63:102059. doi: 10.1016/j.pbi.2021.102059. Epub 2021 Jun 8.


Single-cell genomics, particularly single-cell transcriptome profiling by RNA sequencing have transformed the possibilities to relate genes to functions, structures, and eventually phenotypes. We can now observe changes in each cell's transcriptome and among its neighborhoods, interrogate the sequence of transcriptional events, and assess their influence on subsequent events. This paradigm shift in biology enables us to infer causal relationships in these events with high accuracy. Here we review the latest single-cell studies in plants that uncover how cellular phenotypes emerge as a result of the transcriptome process such as waves of expression, trajectories of development and responses to the environment, and spatial information. With an eye on the advances made in animal and human studies, we further highlight some of the needed areas for future research and development, including computational methods.

Keywords: Causal inference; Chromatin accessibility; Expression waves; Multi-omics; Plant biology; Pseudotime; RNA sequencing; Single cell; Spatial transcriptomics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Review

MeSH terms

  • Animals
  • Computational Biology*
  • Genomics
  • Phenotype
  • Sequence Analysis, RNA
  • Single-Cell Analysis*