Papillomaviruses (PVs) are a ubiquitous group of DNA viruses that infect a wide range of vertebrate hosts, including human. It is well established that the infection of some PV types (e.g., HPV16 and HPV18) are strongly associated with the occurrence and progression of cancers in human, but it remains elusive how such pathogenicity got evolved at the genomic level. Here we curated and annotated a compendium of 3,562 PV genomes (including 3,329 human PVs and 233 animal PVs) and performed the corresponding comparative genomics analyses.