Virophages are unique double-stranded DNA (dsDNA) viruses that parasitize viruses of Nucleocytoviricota (NCVs). While conventionally viewed as a viral group, growing evidence suggests that "virophage" is better understood as a parasitic lifestyle, rather than a natural group. Despite this conceptual shift, their diversity and evolution remain largely obscure and contentious. Through deep mining of protein-primed type B DNA polymerase (pPolB) in 7,041 eukaryotic genomes and 12,053 metagenomes sampled globally, we expand the diversity of pPolB-carrying mavirus virophage-related elements (pMVREs), which include virophages, transpovirons, and Polinton-like viruses (PLVs). Our phylogenomic and metagenomic mining reveals the widespread distribution of pMVREs in eukaryotic genomes (97/7,041, 1.38%) and global environments (2,450/12,053, 20.33%). pMVREs possess genome architectures of high plasticity and promiscuity. The presence of pMVREs and NCVs is statistically correlated in both eukaryotic genomes and global metagenomes, supporting a specific co-occurrence association between pMVREs and NCVs. Moreover, pMVRE diversity and composition exhibit strong heterogeneity across global ecosystems. Together, this study unveils a vast diversity of virophage-related elements and provides insights into the intricate relationship among virophages, transpovirons, PLVs, pMVREs, and NCVs. • We expand the diversity of protein-primed type B DNA polymerase (pPolB)-carrying mavirus virophage-related elements (pMVREs). • pMVREs are widespread in eukaryotic genomes and global environments. • The presence of pMVREs and Nucleocytoviricota is correlated.
Wei et al. (Sun,) studied this question.