Recruitment, rewiring, and deep conservation in flowering plant gene regulation

We conducted single-nuclei transcriptome profiling of multiple tissues from a range of flowering plant species. Individual samples from the same species and tissue were integrated to construct celltype-labeled snRNA atlases for four brassica species and one grass species (available as supplementary files). These atlases were used to track the activity of hundreds of transcription factors (TFs) across species and celltypes, by leveraging genome-wide TF binding site data from accompanying multi-species DAP-seq experiments (DAP-seq data available as SRA BioProject PRJNA1177505). The final integrated dataset revealed clear patterns of regulatory conservation across the plant phylogeny, as well as key examples of regulatory re-wiring to enable new cell types and lineage-specific adaptations. Nuclei were extracted from fresh or flash-frozen tissue sampled from seedling roots, seedling shoots, whole seedlings, mature leaves, or flower buds of various flowering plant species grown in control conditions. Single-nuclei transcriptomes were then profiled using either the 10X Chromium droplet-based platform or the BD Rhapsody microwell-based platform. Note that in many cases, nuclei from the same tissue of different species were extracted simultaneously and profiled together in a single combined-species run. Sequences from these samples were then aligned to a combined-species reference and nuclei from each species were separated bioinformatically before downstream analysis.