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Abstract

Comparative transcriptomics and proteomics (T&P) have brought biological
insight into development, gene function, and physiological stress responses.
However, RNA-seq and high-throughput proteomics remain underutilised in
studies of plant adaptation. These methodologies have created discovery tools
with the potential to significantly advance our understanding of adaptive diversification.
We outline experimental recommendations for their application. We
discuss analysis models and approaches that accelerate the identification of
adaptive gene sets and integrate transcriptome, proteome, phenotypic, and
environmental data. Finally, we encourage widespread uptake and future
developments in T&P that will advance our understanding of evolution and
adaptation.