1-COSTA: a database for spatial transcriptome atlas of cotton 1-DPA ovule

Cotton fiber derived from the ovule epidermis provides a natural source for the textile industry. Transcriptional features of the ovule epidermis contribute critical signals and guide fiber development. This study applied the 10× Genomics Visium spatial transcriptome platform to cotton ovules at 1 d post-anthesis (1 DPA), generating high-resolution, tissue-specific gene expression profiles during early ovule development. Following data normalization, dimensionality reduction, and clustering with Seurat, ovule cross-sections were segmented into seven distinct tissue groups based on anatomical features: nucellus/embryo sac; inner integument micropylar end; inner integument chalaza; outer integument chalazal end; outer integument chalaza; outer integument micropylar end; and funicle. These clusters reveal unique transcriptional signatures that closely correspond with the developmental functions of each tissue region. The cotton fiber condensation region on the outer integument chalazal end is characterized by primary cell biosynthesis, while the outer integument micropylar end is enriched with lipid transportation associated with fiber yield. The resulting 1-DPA cotton ovule spatial transcriptome atlas (1-COSTA) captures key gene expression patterns linked to fiber and lint yield regulation. To facilitate data exploration, the 1-COSTA database was established with a user-friendly web interface built on the R Shiny Server, enabling researchers to access core Seurat visualization and analysis tools including 3D expression visualization of genes in a code-free manner. This resource offers an invaluable reference for understanding spatial gene regulation in cotton fiber development and seed yield.