Dissection of a Cell Atlas of Developing Somatic Embryos in Cotton by Single-cell RNA-sequencing and Spatial Transcriptomic and Metabolomic Analyses

Abstract Somatic embryogenesis is a major pathway for the regeneration of cotton in tissue culture, and a major technique used for cotton breeding and improvement. The signaling pathway regulating the process of somatic embryogenesis in cotton are extremely complex and still poorly characterized. Little is known about the mechanisms regulating the changes that occur in gene expression and metabolites during somatic embryogenesis at a single-cell resolution. Here, we investigated the spatial and single-cell expression profiles of key genes and metabolic patterns of key metabolites by integrated single-cell RNA-sequencing, spatial transcriptomics, and spatial metabolomics. To evaluate the results of the above analyses, we characterized the potential roles of two representative marker genes AATP1 and DOX2 in the regulation of somatic embryo development. A publicly accessible web-based resource database (http://cottonsomaticembryo.cricaas.com.cn) was generated to facilitate future studies designed to analyze the expression patterns of marker genes at specific developmental stages.