DupGen_finder

DupGen_finder identifies and classifies modes of gene duplication across plant genomes to analyze their evolutionary consequences.

Key Features:

• Identification of Duplication Modes: Detects whole-genome duplication (WGD), tandem, proximal, transposed, and dispersed duplications in plant genomes.
• Abundance and Age Trends: Quantifies abundance and age-related trends, noting that WGD-derived gene numbers decline with increasing age while tandem and proximal duplicates maintain consistent frequency.
• Selective Pressure and Expression Divergence Analysis: Assesses selective pressure and expression divergence, reporting stronger selection on tandem and proximal duplicates and tendencies toward functional specialization.
• Gene Conversion Dynamics: Examines gene conversion rates among WGD-derived gene pairs, observing an initial post-polyploidization peak followed by decline over time.
• Comparative Genomics: Performs comparative analyses across 141 sequenced plant genomes to provide a landscape of duplication modes.
• Database Integration: Integrates results into the Plant Duplicate Gene Database to provide a consolidated dataset of duplicate genes.

Scientific Applications:

• Evolutionary Biology: Elucidating contributions of different duplication mechanisms to genetic diversity and adaptation in plants.
• Functional Genomics: Investigating functional divergence and specialization of duplicated genes via selection and expression analyses.
• Plant Defense Mechanisms: Studying the enrichment and evolution of duplicates involved in plant self-defense mechanisms.

Methodology:

Performs a systematic survey of sequenced plant genomes, comparing 141 genomes and integrating findings into the Plant Duplicate Gene Database.