Abstract
The precise onset of flowering is crucial for successful reproduction. In longer days, the florigen gene FLOWERING LOCUS T (FT) is induced in specific leaf phloem companion cells in Arabidopsis. However, the molecular nature of these cells remains elusive. Here, we utilized bulk nuclei RNA-seq and single nuclei RNA (snRNA)-seq to investigate transcription in FT-expressing cells and other companion cells. Our bulk nuclei RNA-seq demonstrated that FT-expressing cells in cotyledons and true leaves showed differences in FT repressor gene expression. Within true leaves, our snRNA-seq analysis revealed that companion cells with high FT expression form a unique cluster. The cluster expresses other genes encoding small proteins, including the flowering and stem growth inducer FPF1-LIKE PROTEIN 1 (FLP1) and the anti-florigen BROTHER OF FT AND TFL1 (BFT). We also found that the promoters of FT and the genes co-expressed with FT in the cluster were enriched for the binding motif of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1 (NIGT1). Overexpression of NIGT1.2 and NIGT1.4 repressed FT and delayed flowering under nitrogen-rich conditions, implying the roles of NIGT1s as nitrogen-dependent FT repressors. Taken together, our results indicate that unique FT-expressing phloem cells may produce multiple systemic signals to regulate plant growth and development.