Abstract
Excision of the root tip completely removes its stem cell niche and other specialized tissues and triggers rapid regeneration by recruitment of differentiated cells in the stump. To characterize this process, we used tissue-specific clonal analysis and RNA-Seq profiling of single cells at different time points through regeneration. We show that the stem-cell-niche recovers by "superimposing" its structure on existing cells in the center of the root, which causes rapid loss of original identity and a transient chimeric state. We also show that meristem reorganization affects tissues far from the cut site, as we detect a widespread loss of identity throughout the root meristem.