Single-nucleus sequencing deciphers lineage trajectories in rice pistils [bulk RNA-seq]

Angiosperms possess a characteristic life cycle with an alternation of sporophyte and gametophyte generations, which happens in plant organs like pistils. Rice pistils contain ovules and receive pollen for successful fertilization to produce grains. The cellular expression profile in rice pistils is largely unknown. Here we show a cell atlas of rice pistils before fertilization by droplet-based single-nucleus RNA sequencing. The Ab initio marker identification validated by in situ hybridization assists the cell-type annotation, revealing cell heterogeneity between ovule and carpel lineages. Overall design: Perform snRNA-seq for 1N (haploid; gametophyte) and 2N (diploid; sporophyte) nuclei and bulk RNA-seq for nuclei of pistils and whole cells of upper and lower part of pistils