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, genomics, and potential viral-host interactions of reverse-transcriptase-containing viruses (RTVs) remain poorly understood. Here, we identified 74729 RTVs from public genomic and metagenomic datasets to establish six viral-derived RT super clades (RTSCs), including two viral-derived RTSCs that possibly shared ancestry 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 RTSCs. The genome-content-based analysis has revealed that RTVs tend to form independent clusters compared to other<i> </i>caudoviruses. Most RTVs colonized in host-associated environments, with <i>Bacteroidota,</i> <i>Bacillota</i>, and <i>Pseudomonadota</i> being the main host lineages. The endogenous RTVs were shared between multiple bacterial genera of<i> </i><i>Bacteroidota</i> and <i>Bacillota</i>. The endogenous RTVs from <i>Pseudomonadota</i> were not shared between genera. Our results highlight the neglected diversity of RTVs and their potential host spectrums.