Supplementary materials

Viral-encoded reverse transcriptase (RT) is a key component in replication (reverse transcribing viruses, generating complementary DNA from an RNA template) and genomic mutations (bacteriophage diversity-generating retroelement). However, the diversity of viral RTs remains poorly understood. Here, we identified 76,208 viral-derived RTs from publicly available genomic and metagenomic datasets to establish 13 viral-derived RT clusters (RTCs), belonging to six phylogenetic RT super clades. These include two viral-derived RT phylogenetic clades that have a close relationship with bacterial Retrons-like and Group II Introns-like RT. Phylogenetic inference of viral terminase-related proteins has revealed the differentiated evolutionary status of RTVs from various RT phylogenetic clades. The genome-content-based network suggests that RTVs tend to form independent clusters compared to other caudoviruses. Most RTVs are colonized in host-associated environments, with <i>Bacteroidota</i>, <i>Bacillota</i>, and <i>Pseudomonadota</i> being the main host lineages. The integrated RTVs were shared between multiple bacterial genera of <i>Bacteroidota</i> and <i>Bacillota</i>. The integrated RTVs from <i>Pseudomonadota</i> are genus-specific. Our results highlight the neglected diversity of RTVs and their potential host spectrums.