GenTree

GenTree integrates age inference and coding-potential annotation to study the evolutionary origins and functions of primate-specific coding genes (PSGs).

Key Features:

• Age Inference Methods: Incorporates three methods for gene age inference: a synteny-based pipeline (SBP), protein-family-based approaches, and additional comparative techniques.
• Manual Evaluation: Provides a manually curated dataset for PSGs dated with the SBP and masks less-certain syntenic regions to improve age-assignment reliability.
• Functional Annotation and Coding Potential: Assesses coding potential using evolutionary constraint analysis and peptide evidence from proteomic data, and includes a curated list of 254 PSGs and 41 candidate misannotated pseudogenes encoding primate-specific short proteins.
• Coexpression Analysis: Performs coexpression analysis to identify recruitment of PSGs into rapidly evolving pathways and organs, highlighting involvement in spermatogenesis, immune response, mother-fetus interaction, and brain development.

Scientific Applications:

• Evolutionary Biology: Elucidates origins and evolutionary trajectories of new genes to aid study of phenotypic evolution in humans.
• Genomics and Proteomics: Integrates genomic and proteomic data to refine annotation of gene function and coding potential.
• Developmental Biology: Identifies primate-specific KRAB zinc-finger proteins (KZNFs) up-regulated during the mid-fetal stage of brain development, implicating roles in developmental evolution.

Methodology:

Applies a genome-wide comparison of three age-inference methods (synteny-based pipeline, protein-family-based approaches, and other comparative techniques), manual curation with syntenic-region masking for SBP-dated PSGs, evolutionary constraint analysis, peptide evidence from proteomics, and coexpression analysis.