Plants form the foundation for our global ecosystem and are essential for environment and human health. With an increasing number of available plant genomes and tractable experimental systems, comparative and functional plant genomics research is greatly expanding our knowledge of the molecular basis of economically and nutritionally important traits in crop plants. Inferences drawn from comparative genomics are motivating experimental investigations of gene function and gene interactions. This special issue aims to highlight recent advances made in comparative and functional genomics research. We invite researchers to contribute original research articles as well as review articles that will stimulate the integration of comparative genomics and functional genomics investigations of plant development, plant-microbe/insect interactions, and plant response to changing abiotic environments. Articles may focus on computational analysis of protein-encoding genes, noncoding RNAs, or regulatory elements among multiple plant species or genotypes and experimental investigation of gene function and gene interactions.

Potential topics include, but are not limited to:

• Comparative analysis of protein-encoding genes in an evolutionary context
• Discovery of lineage-specific and/or tissue-specific noncoding RNAs
• Functional genomics of miRNAs
• Prediction and characterization of protein-protein interactions
• Discovery of promoters driving temporal or tissue-specific gene expression
• Comparative analysis of photosynthetic pathways (C₃, C₄, and crassulacean acid metabolism)
• Evolutionary analysis of genes involved in secondary metabolism
• Signal transduction in plant-microbe/insect interactions and plant response to abiotic stress and climate change
• Functional elucidation of regulatory genes and key enzymes based on integrative genomics
• Development of new computational tools (programs, servers, and databases) for comparative genomics
• Big data analysis tools for genomics research