Potentials of single-cell genomics in deciphering cellular phenotypes

Single-cell genomics, particularly single-cell transcriptome profiling by RNA sequencing have transformed the possibilities to relate genes to functions, structures, and eventually phe-notypes. We can now observe changes in each cell's tran-scriptome 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 ac-curacy. 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, trajec-tories 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.

Automated summary

Advancements in single-cell genomics, particularly in single-cell transcriptome profiling, have revolutionized our understanding of the relationship between genes and cellular functions, structures, and phenotypes. This paradigm shift enables us to accurately infer causal relationships between transcriptional events.