A2TEA

A2TEA identifies candidate genes underlying stress adaptation by integrating comparative genomics and RNA-Seq transcriptomics to connect gene family expansions, differential expression, phylogeny, and protein function.

Key Features:

• Integration of omics data: Combines protein family, phylogeny, expression, and protein function analyses to assess evolutionary adaptations.
• Cross-species analysis: Facilitates genome comparisons between stress-tolerant and stress-sensitive species using RNA-Seq datasets to reveal adaptive genetic differences.
• Gene family expansion detection: Identifies expanded gene families that show differential expression under stress conditions as candidate adaptive loci.
• Automated workflow: Implements data transformation and filtering steps within a Snakemake pipeline for reproducible cross-species omics integration.

Scientific Applications:

• Plant stress adaptation studies: Identifies genetic factors contributing to traits such as drought tolerance in plants.
• Crop improvement: Pinpoints candidate genes involved in stress responses for use in breeding and genetic improvement programs.
• Evolutionary biology research: Supports investigation of species- or clade-specific adaptations by linking gene family dynamics, expression changes, and phylogeny.

Methodology:

Computational steps include identification of protein family expansions via comparative genomics; differential expression analysis of RNA-Seq data from stress experiments; correlation of expanded families and differentially expressed genes with phylogenetic information and functional annotations to nominate candidate genes; and workflow implementation in Snakemake.