摘要：SummaryA full understanding of the developmental process requires fine-scale characterization of cell divisions and cell types, which are naturally organized as the developmental cell lineage tree (CLT). Technological breakthroughs facilitated determination of more CLTs, but complete comprehension of the data remains difficult without quantitative comparison among CLTs. We hereby quantified phenotypic similarity between CLTs using a novel computational method that exhaustively searches for optimal correspondence between individual cells meanwhile retaining their topological relationships. The revealed CLT similarities allowed us to infer functional similarity at the transcriptome level, identify cell fate transformations, predict functional relationships between mutants, and find evolutionary correspondence between cell types of different species. By allowing quantitative comparison between CLTs, our work is expected to greatly enhance the interpretability of relevant data and help answer the myriad of questions surrounding the developmental process.Graphical AbstractDisplay OmittedHighlights•Align cell lineage trees (CLTs) to search/quantify their phenotypic similarities•Aligning worm CLTs captured known genetic/developmental programs•Similarities between knockdown CLTs revealed functional relationships between genes•CLT alignments between species gave insight on the evolution of cell typesCell Biology; Developmental Biology; Bioinformatics
