DupGen_finder

DupGen_finder is a computational pipeline for identifying and classifying different modes of gene duplication in plant genomes. The tool analyzes plant genome and transcriptome data to determine the evolutionary consequences of gene duplication events and uncover common principles underlying the retention of duplicate genes.

Key features and findings of DupGen_finder:

1. Identifies genes derived from various duplication modes, including whole-genome duplication (WGD), tandem duplication, proximal duplication, transposed duplication, and dispersed duplication.

2. Reveals differences in abundance, selection pressure, expression divergence, and gene conversion rates among genes derived from different duplication modes.

3. Shows that the number of WGD-derived duplicate genes decreases exponentially with the increasing age of duplication events. In contrast, the frequency of tandem and proximal duplications remains relatively constant over time.

4. Finds that tandem and proximal duplicates experience stronger selective pressure than genes formed by other modes and evolve toward biased functional roles involved in plant self-defense.

5. Observe that the gene conversion rate among WGD-derived gene pairs declines over time, peaking shortly after polyploidization.

DupGen_finder provides a comprehensive landscape of gene duplication modes across 141 plant genomes, offering a solid foundation for further investigation into the dynamic evolution of duplicate genes. The authors also constructed the Plant Duplicate Gene Database to provide a platform for accessing duplicated gene pairs in different plants.