AGV: a web-based visualization tool for reconstructed ancestral genomes

Abstract

The ancestral genome is the genome of the common ancestor of extant species. Ancestral genome reconstruction infers evolutionary events from extant genomes to recover the genomic states of extinct ancestors. Although this approach provides a powerful framework for studying genome evolution, the resulting reconstructions are often structurally complex, thus making it challenging to interpret the rearrangement patterns and their evolutionary implications. Effective visualization is therefore essential for facilitating the intuitive interpretation and comparative analysis of ancestral genome structures. We developed Ancestral Genome Visualization (AGV), a web-based visualization tool for reconstructed ancestral genomes. AGV incorporates a data transformation pipeline that converts outputs from DESCHRAMBLER into a web interface. Furthermore, it enables users to effectively explore the reconstructed ancestral genome, thereby identifying structural changes and the ancestral genome’s state. Through a case study of the primate lineage, AGV enabled the identification of conserved genomic regions and lineage-specific evolutionary patterns. The observed patterns in the synteny blocks and adjacency scores revealed differences in structural stability between the ingroup and outgroup species, thereby demonstrating that AGV supports the intuitive visualization and quantitative assessment of genome evolution. AGV is available at https://github.com/ibclab-hub/AGV . AGV offers an accessible, intuitive platform for exploring patterns in ancestral genome reconstruction. By integrating visual exploration with the reconstruction results, AGV facilitates a deeper understanding of genome evolution and provides a foundation for broader comparative genomic studies across diverse lineages.