Unravelling the predominant genetic paths for asexual reproduction in Kalanchoe

How somatic cells acquire totipotency and subsequently develop into a whole plant (plantlet) remains a mystery in plant biology. Here we used three Kalanchoe species to address this fundamental question. By assembling high-quality chromosome-level reference genomes and conducting comparative genomic analyses, we reveal hidden signatures of gene expansion, contraction and loss during the evolution of Kalanchoe species and elucidate conserved temporal gene expression signatures and epigenetic states during plantlet formation. Remarkably, we uncover three innovations contributing to the plantlet formation in Kalanchoe. Specifically, our results suggest that the loss of the F-box gene LCR is a prerequisite for plantlet formation. Both gene duplication and increased chromatin accessibility of pluripotency-associated genes further create conditions that enhance the potential of plantlet formation. The previously uncharacterized gene KdLBD19 could be leveraged to improve crop transformation efficiency. Overall, this study reveals the genetic basis underlying the acquisition of totipotency and plantlet formation in Kalanchoe.