Detailed materials and methods are provided in the SI Appendix. This includes information on field work, flow sorting, whole-genome amplification, amplicon library construction and sequencing, data processing, assembly and analysis, including gene predictions, as well as phylogenetic, crystallization and phylogenomic analyses. The final ChoanoV1 genome assembly was assembled from 13,802,665 quality-filtered reads, and viral contigs were differentiated from the cellular assembly by tetranucleotide frequency and GC content. The ChoanoV1 assembly consisted of 11 contigs with average coverage of 215 ± 157×. For eastern North Pacific Ocean gene expression analyses, reads from metatranscriptomes were mapped to ChoanoVirus genomes at >95% nucleotide identity with bbmap. For 18S V4 amplicon sequencing, we had on average 131,385 ± 121,027 amplicons well−1 (the lowest number being 1,037) clustered at 99% and classified via the Protistan Ribosomal Reference database. Rhodopsin functionality of viral VirRDTS was determined via heterologous expression in E. coli. The VirRDTS crystallization samples were produced by a cell-free system, and crystals were grown using the in meso approach. Accession numbers and DOI for alignment and tree files are available in Dataset S2.