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Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants
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Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants
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Journal Article
Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants
2023
Overview
Proteogenomics can further improve draft plant genomes, correct gene annotation, discover new translation initial sites, ORFs, and alternative splicing, and verify novel genes of the peptide/protein level as well as provide comprehensive information for the study of gene expression patterns.Single-cell proteogenomics will refine annotations at the single-cell level to present the state of cells in a more refined way, effectively better reflecting the heterogeneity of different cell groups. Spatial proteogenomics is also of great value because of its multidimensional data integration. High-resolution spatial single-cell proteogenomics will thereby pave the way for considerable future research avenues in plants.Based on proteogenomics technology, multi-omics integrations will allow the exploration of different life activity-changing patterns of plants across many aspects, including metabolism, immunity, and signal transduction as well as developing the utilization of plants and their natural products.
Proteogenomics (PG) integrates the proteome with the genome and transcriptome to refine gene models and annotation. Coupled with single-cell (SC) assays, PG effectively distinguishes heterogeneity among cell groups. Affiliating spatial information to PG reveals the high-resolution circuitry within SC atlases. Additionally, PG can investigate dynamic changes in protein-coding genes in plants across growth and development as well as stress and external stimulation, significantly contributing to the functional genome. Here we summarize existing PG research in plants and introduce the technical features of various methods. Combining PG with other omics, such as metabolomics and peptidomics, can offer even deeper insights into gene functions. We argue that the application of PG will represent an important font of foundational knowledge for plants.
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