JGI Plant Gene Atlas

JGI Plant Gene Atlas provides comprehensive transcript abundance assays across 18 distinct plant species to enhance functional gene annotation and identify gene expression responses to environmental stimuli.

Key Features:

• Extensive Transcriptome Data: Expression profiles and transcript abundance assays are aggregated across a wide array of plant genotypes spanning 18 distinct plant species.
• Gene Clustering and Expression Analysis: Co-expression clustering identifies tissue- or condition-specific gene groups and conserved versus condition-specific expression patterns among phylogenetically related species.
• Environmental Response Profiling: Tests for transcriptional responses to environmental cues reveal genes whose expression changes under different conditions and tissues.
• Functional Annotation Enhancement: Expression-derived biological information has been used to assign annotations to approximately 64,495 previously uncharacterized genes.

Scientific Applications:

• Gene Function Discovery: Conserved and condition-specific expression patterns enable inference of potential functions for previously uncharacterized genes.
• Molecular Target Identification: Expression profiles associated with environmental responses support identification of candidate molecular targets for plant improvement strategies such as gene editing.
• Comparative Genomics: Tracking orthologs and expression conservation across species facilitates comparative genomic and evolutionary analyses.

Methodology:

Integrating transcript abundance data across diverse plant genotypes and analyzing these datasets to identify co-expressed gene clusters and phylogenetically constrained expression patterns, then assigning putative functions to genes based on their expression profiles across tissues and environmental conditions.