Merit of integrating in situ transcriptomics and anatomical information for cell annotation and lineage construction in single-cell analyses of Populus
Ying‐Lan Chen, Jo‐Wei Allison Hsieh, Shang‐Che Kuo, Chung‐Ting Kao, Chia-Chun Tung, Jhong‐He Yu, Tien‐Hsien Chang, Chuan Ku, Jianbo Xie, Deqiang Zhang, Quanzi Li, Ying‐Chung Jimmy Lin
Abstract
Cell type annotation and lineage construction are two of the most critical tasks conducted in the analyses of single-cell RNA sequencing (scRNA-seq). Four recent scRNA-seq studies of differentiating xylem propose four models on differentiating xylem development in Populus. The differences are mostly caused by the use of different strategies for cell type annotation and subsequent lineage interpretation. Here, we emphasize the necessity of using in situ transcriptomes and anatomical information to construct the most plausible xylem development model.
Topics & Concepts
BiologyXylemAnnotationTranscriptomeLineage (genetic)Computational biologyEvolutionary biologyCell typeIn situCellBotanyGeneticsGeneGene expressionMeteorologyPhysicsGenomics and Phylogenetic StudiesSingle-cell and spatial transcriptomicsPlant Molecular Biology Research