Single cell mRNA-Seq of developing stem-borne roots in tomato

Plants adjust their growth in response to environmental cues by forming new organs in different development contexts. Underground lateral roots initiate from prepatterned cells in the main root, but cells can also bypass the root/shoot trajectory separation and generate shoot-borne-roots through an unknown mechanism. Here, we mapped tomato (Solanum lycoperiscum) shoot-borne-roots development at single-cell resolution and show that they initiate from differentiated phloem-associated cells via a unique transitional stem-cell-like state. This state required the activity of a transcription factor which we named SHOOTBORNE ROOTLESS (SBRL), a function that was deeply conserved in angiosperms. Phylogenetic analysis revealed that SBRL arose in angiosperms as an ancient duplicated superlocus with its paralogs showing root-type-specific transient expression in wound-induced and lateral root initiation. Mutants in all SBRL-like genes completely lost post-embryonic roots. We propose that the activation of a common transition state by context-specific regulators underlies the plasticity of plant root systems. DR5:VENUS or DR5:mScarleti-NLS TCSn:mNeonGreen tomato plants were grown in growth chamber. At ~4 weeks after germination, stem-borne root primordia were collected from sections of internode 1 under a fluorescent stereoscope. Microdissection sections were transferred to cell wall digestion solution and protoplasts were isolated, sorted using FACS followed by mRNA sequencing.