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Updated: Jul 25, 2025

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants
Yu-Chen Song1, Debatosh Das2, Youjun Zhang3
1State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.
Proteogenomics (PG) advances plant functional genomics by integrating proteomic data with genomic and transcriptomic information. This approach refines gene models and enhances understanding of plant development and stress responses.
Area of Science:
- Plant Science
- Genomics
- Proteomics
Background:
- Proteogenomics (PG) integrates proteomic data with genomic and transcriptomic information.
- Single-cell (SC) assays combined with PG can distinguish cellular heterogeneity.
- Spatial information integration with PG reveals cellular circuitry.
Purpose of the Study:
- To summarize existing plant proteogenomics research.
- To introduce the technical features of various PG methods.
- To highlight the contribution of PG to functional genomics in plants.
Main Methods:
- Integration of proteome, genome, and transcriptome data.
- Application of single-cell assays and spatial information.
- Combination of PG with metabolomics and peptidomics.
Main Results:
- PG refines gene models and annotation.
- PG effectively distinguishes heterogeneity among cell groups using SC assays.
- PG investigates dynamic changes in protein-coding genes during plant growth, development, and stress.
Conclusions:
- Proteogenomics offers foundational knowledge for plant functional genomics.
- Combining PG with other omics provides deeper insights into gene functions.
- PG is crucial for understanding plant responses to environmental stimuli.
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