plantannot

plantannot identifies and annotates proteins of unknown function (PUFs) in 53 angiosperms by integrating orthology, coexpression networks, and genomic data to support discovery of candidate genes associated with abiotic stress responses.

Key Features:

• Genomic Data Aggregation: Aggregates genomes and RNA sequence data from Phytozome and NCBI covering 53 angiosperms, comprising 1,862,010 genes and 2,332,974 RNA sequences.
• PUF Identification: Uses Diamond and InterproScan to identify 72,266 proteins of unknown function (PUFs) across the analyzed organisms.
• Coexpression Network Construction: Processes RNA-seq abiotic stress datasets from NCBI/GEO with LSTrAP to build coexpression networks and clusters of correlated transcripts.
• Orthology Analysis: Generates orthologous groups with OrthoMCL across 2,332,974 proteins to group homologous proteins among species.
• Guilt-by-Association Functional Inference: Infers potential functions of PUFs by associating them with orthologous groups and coexpression clusters.

Scientific Applications:

• Functional inference of PUFs: Enables prediction of functions for proteins lacking annotation through orthology and coexpression associations.
• Candidate gene discovery for abiotic stress tolerance: Identifies novel gene candidates associated with plant responses to abiotic stresses for use in breeding or genetic modification efforts.
• Integrated gene function prediction framework: Provides an orthology-plus-coexpression framework to support hypothesis generation about molecular mechanisms underlying stress responses.

Methodology:

Genomes and RNA sequences from Phytozome and NCBI (53 angiosperms; 1,862,010 genes, 2,332,974 RNAs) were aggregated; proteins were analyzed with Diamond and InterproScan to identify PUFs; RNA-seq datasets from NCBI/GEO were processed with LSTrAP to build coexpression networks and clusters; OrthoMCL generated orthologous groups across 2,332,974 proteins; PUF functions were inferred by associating PUFs with orthologous groups and coexpression clusters (guilt-by-association).