Charting plant gene functions in the multi-omics and single-cell era.

Despite the increased access to high-quality plant genome sequences, the set of genes with a known function remains far from complete. With the advent of novel bulk and single-cell omics profiling methods, we are entering a new era where advanced and highly integrative functional annotation strategies are being developed to elucidate the functions of all plant genes. Here, we review different multi-omics approaches to improve functional and regulatory gene characterization and highlight the power of machine learning and network biology to fully exploit the complementary information embedded in different omics layers. Finally, we discuss the potential of emerging single-cell methods and algorithms to further increase the resolution, allowing generation of functional insights about plant biology. Different omics profiling methods are becoming available for a variety of plant species, offering new opportunities to explore new gene functions at various molecular levels. The combination of multiple omics data types enables the characterization of different levels of gene regulation for a biological process of interest. Studies targeting a specific biological process, as well as untargeted multi-omics approaches, shed light on novel gene functions in plant biology. Different integration strategies offer a practical solution to exploit the information captured by complementary omics layers and allow the generation of new testable hypotheses for various biological processes and pathways. New computational methods, modeling coexpression and regulatory networks, are being developed to accommodate the technological advances in omics profiling and fully exploit the information available in functional genomics databases. [ABSTRACT FROM AUTHOR]