DupScan

DupScan provides visualization and analysis of synteny and whole genome duplication (WGD) events across vertebrate genomes to support studies of genome evolution.

Key Features:

• Synteny Visualization: Detailed visualization of synteny at both gene and genome scales to explore conservation of gene order across species.
• Genome Duplication Analysis: Analysis and visualization of whole genome duplication events including Ka (nonsynonymous substitution rate), Ks (synonymous substitution rate), and 4DTV (fourfold degenerate third codon transversion) values for duplicated genes.
• Functional Adaptation Studies: Synteny matching to investigate functional divergence and adaptation of duplicated genes following WGD.
• Support for Multiple WGD Rounds: Accommodation of analyses for VGD2, Ars3R (Acipenser-ruthenus-specific 3R), Pss3R (Polyodon-spathula-specific 3R), Ts3R (teleost-specific duplication 3R), Ss4R (salmonid-specific 4R), and Cs4R (carp-specific 4R).
• Integrated Genomic Dataset: Integration of 106 chromosomal-level genomes enabling analysis and prediction of synteny and WGD patterns across those vertebrate genomes and supporting investigations spanning more than 60,000 vertebrate species.

Scientific Applications:

• Vertebrate Genome Evolution: Investigation of the role of gene duplications and synteny conservation in vertebrate evolutionary history.
• WGD Detection and Dating: Use of Ka, Ks, and 4DTV metrics to detect and assess divergence timing of WGD events.
• Functional Genomics: Tracing functional divergence and adaptation of duplicated genes after WGD.
• Comparative Analysis of Fish Lineages: Comparative studies of lineage-specific WGDs such as salmonid, carp, Acipenser, Polyodon, and teleost duplications.

Methodology:

Integration of 106 chromosomal-level genomes, synteny visualization at gene and genome scales, calculation and visualization of Ka, Ks, and 4DTV values, synteny matching for functional analysis, and accommodation of analyses for specified WGD rounds.