The single-cell transcriptome program of nodule development cellular lineages in Medicago truncatula

Medicago truncatula engages in root nodule symbiosis by developing a de novo plant organ (known as nodule) in its roots in response to the infection by rhizobia. These nodules are de novo plant organs that provide an optimal environment for the rhizobia to fix nitrogen in exchange for photosynthates. The establishment of root nodule symbioses (RNS) requires the coordination of two distinct processes: bacterial infection and nodule organogenesis. In this study we used single-cell RNA-seq to investigate the first hours of the establishment of the root nodule symbiosis aiming to identify the transcriptional mechanisms governing this process. Two genotypes of M. truncatula were used, a wild-type Jemalong A17 a hypernodulating sunn-4 mutant. Root segments were isolated at 0h (control), and at 24h, 48h and 96h after the infection with S. meliloti. Nuclei extraction was performed, followed by Fluorescence-activated cell sorting (FACS). Nuclei were then used to generate single-cell libraries using 10x Chromium technology. Sequencing was performed using Illumina platforms.