Spatiotemporal transcriptome atlas of ovule development in gymnosperms reveals co-regulatory patterns of gene expression associated with polarity establishment
Ovule, as the precursor to seed, represents a key evolutionary innovation in seed plants, enhancing their adaptability and biodiversity. Researches in model angiosperms have revealed that ovule development involves the establishment of polarity, which drives cell differentiation and organ formation. However, studies on gymnosperms have primarily focused on morphological comparisons and limited gene function analyses, leaving the core regulatory networks underlying ovule organogenesis in the common ancestor of seed plants a subject of ongoing debate. We employed spatial transcriptome sequencing to dissect the dynamic gene expression profiles across various tissues during early ovule development in four representative gymnosperm species: Ginkgo biloba, Gnetum montanum, Pinus tabulaeformis and Cycas panzhihuaensis. The analyses reveal distinct trajectories of cell types during formation of tissues, uncovering critical genes and pathways involved in the initiation and differentiation of ovule primordium, as well as the subsequent formation of chalaza, integument and nucellus. The spatial and temporal expression patterns of key regulatory genes, particularly those associated with proximal-distal polarity establishment, strongly support the hypothesis that early-formed chalaza regions constitute the meristematic cells, giving rise to the formation of integument and nucellus. Furthermore, specific gene expression patterns in the developing integument exhibit clear adaxial-abaxial distribution, offering clues for understanding the molecular mechanisms driving integument formation. The spatial transcriptome analyses in this study provide a detailed landscape of gene activity during ovule organogenesis in multiple gymnosperms, and offer valuable resources for future genomic and evolutionary studies on seed development. Overall design: We performed spatial transcriptome sequencing on ovule tissues from four representative gymnosperms species, Ginkgo biloba, Gnetum montanum, Pinus tabuliformis and Cycas panzhihuaensis, covering most of major gymnosperms clades . The dataset comprises over fifty samples spanning multiple developmental stages, from the presence of meristematic regions to near-mature organs, included in ten slides.