Salvador-Martínez Irepan
Centro Nacional de Análisis Genómico, Barcelona, Spain.
Methods Mol Biol. 2025;2886:355-373. doi: 10.1007/978-1-0716-4310-5_18.
The recent development of genetic lineage recorders, designed to register the genealogical history of cells using induced somatic mutations, has opened the possibility of reconstructing complete animal cell lineages. To reconstruct a cell lineage tree from a molecular recorder, it is crucial to use an appropriate reconstruction algorithm. Current approaches include algorithms specifically designed for cell lineage reconstruction and the repurposing of phylogenetic algorithms. These methods have, however, the same objective: to uncover the hierarchical relationships between cells and the sequence of cell divisions that have occurred during development. In this chapter, I will use the phylogenetic software FastTree to reconstruct a lineage tree, in a step-by-step manner, using data from a simulated CRISPR-Cas9 recorder. To ensure reproducibility, the code is presented as a Jupyter Notebook, available (together with the necessary input files) at https://github.com/irepansalvador/lineage_reconstruction_chapter .
基因谱系记录器是利用诱导体细胞突变来记录细胞谱系历史的工具，其最新进展为重建完整的动物细胞谱系提供了可能。要从分子记录器重建细胞谱系树，使用合适的重建算法至关重要。当前的方法包括专门为细胞谱系重建设计的算法以及对系统发育算法的重新利用。然而，这些方法的目标是一致的：揭示细胞之间的层次关系以及发育过程中发生的细胞分裂顺序。在本章中，我将使用系统发育软件FastTree，以逐步的方式，利用来自模拟CRISPR-Cas9记录器的数据重建谱系树。为确保可重复性，代码以Jupyter Notebook的形式呈现，可在https://github.com/irepansalvador/lineage_reconstruction_chapter获取（连同必要的输入文件）。
