Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants

• DOI: 10.1371/journal.pbio.3002397
• Publication Date: 2023-12-05T18:31:16Z
• Authors: Sourabh Palande; Joshua A. M. Kaste; Miles D. Roberts; Kenia Segura Abá; Carly Claucherty; Jamell Dacon; Rei Doko; Thilani B. Jayakody; Hannah R. Jeffery; Nathan Kelly; Andriana Manousidaki; Hannah M. Parks; Emily M. Roggenkamp; Ally M. Schumacher; Jiaxin Yang; Sarah Percival; Jeremy Pardo; Aman Y. Husbands; Arjun Krishnan; Beronda L Montgomery; Elizabeth Munch; Addie M. Thompson; Alejandra Rougon-...; Daniel H. Chitwood; Robert VanBuren
• Keywords: Housekeeping gene

Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in most inhospitable environments on earth. At their core, these adaptations been shaped by changes numerous, interconnected pathways genes that collectively give rise emergent biological phenomena. Linking gene expression morphological outcomes remains a grand challenge biology, new approaches are needed begin address this gap. Here, we implemented topological data analysis (TDA) summarize high dimensionality noisiness of using lens functions delineate plant tissue stress responses. Using framework, created representation shape across evolution, development, environment for phylogenetically diverse plants. The TDA-based Mapper graphs form well-defined gradient tissues from leaves seeds, or healthy stressed samples, depending function. This suggests there distinct conserved patterns angiosperms different types responses biotic abiotic stresses. Genes correlate with function enriched central processes such as photosynthetic, growth housekeeping, Together, our results highlight power TDA analyzing complex reveal core backbone defines