DupScan: predicting and visualizing vertebrate genome duplication database

Abstract

Duplicated genes prevail in vertebrates and are important in the acquisition of new genes and novelties. Whole genome duplication (WGD) is one of the sources of duplicated genes. It can provide raw materials for natural selection by increasing the flexibility and complexity of the genome. WGDs are the driving force for the evolution of vertebrates and contribute greatly to their species diversity, especially in fish species with complicated WGD patterns. Here, we constructed the DupScan database (https://dupscan.sysumeg.com/) by integrating 106 chromosomal-level genomes, which can analyze and visualize synteny at both the gene and genome scales, visualize the Ka, Ks, and 4DTV values, and browse genomes. DupScan was used to perform functional adaptation for the intricate WGD investigation based on synteny matching. DupScan supports the analysis of five WGD rounds (R): VGD2 (vertebrate genome duplication 2), Ars3R (Acipenser-ruthenus-specific 3R), Pss3R (Polyodon-spathula-specific 3R), Ts3R (teleost-specific duplication 3R), Ss4R (salmonid-specific 4R), and Cs4R (carp-specific 4R). DupScan serves as one-stop analysis platform for synteny and WGD research in which users can analyze and predict synteny and WGD patterns across 106 species of whole genome sequences. This further aided us in elucidating genome evolutionary patterns across over 60,000 vertebrate species with synteny and WGD events.