Spatially Resolved Transcriptome Profiling in Model Plant Species

Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analyzing high-throughput spatial expression profiles were developed for a limited range of organisms - primarily mammals. We present the first available method to generate high-resolution, spatially-resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. Here we first demonstrate feasibility by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections (Arabidopsis thaliana, Populus tremula and Picea abies). We achieved high reproducibility of our method in the three species, and identify a high specificity (92.9%), and a low false positive rate (6.5%).

It is well established that most biological characteristics arise from complex interactions and coordination between the numerous and multi-layered components of a cell, which act across the genome-to-phenotype continuum. Our approach enables to combine morphological information with single and global level gene expression analyses. In A. thalianawe used the spatial data to identify 141 differential expressed genes and 189 altered pathways among eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling represents a powerful new strategy that can be applied to a broad range of plant species, providing an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology. To facilitate this goal, the data have been made available to the community for visual exploration, representing the first high-resolution spatially resolved gene expression resource in plants.

Title: Spatially resolved transcriptome profiling in model plant species

Submitter's E-mail Address: stefania.giacomello@scilifelab.se

Session Selection: Functional genomics

First author

Presenting Author

Stefania Giacomello
Royal Institute of Technology (KTH),
Science for Life Laboratory, Stockholm, Sweden
Email: stefania.giacomello@scilifelab.se

Back to: Functional Genomics

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Meeting Information

When:

January 13 - 18, 2017

Where:

San Diego, CA