4.1 RNA virus study description
Dinoflagellate-infecting RNA viruses (dinoRNAVs) are positive-sense, single-stranded RNA viruses hypothesized to infect the dinoflagellate symbionts (Family Symbiodiniaceae) that live in the tissues of reef-building stony corals (Correa et al., 2013; Grupstra et al., 2022; Veglia et al., 2022). Although dinoRNAVs can be prevalent in coral colonies (Grupstra et al., 2022; Howe-Kerr et al., 2022; Montalvo-Proaño et al., 2017; Veglia et al., 2022), it is unclear how dinoRNAVs (or Symbiodiniaceae infected by dinoRNAVs) are transmitted among colonies. Recent work has shown that corallivorous (coral-eating) fishes disperse 100s of millions of live Symbiodiniaceae cells across reefscapes in their feces each day (Grupstra et al., 2021). To assess the extent to which corallivorous fish feces disperse dinoRNAVs in their feces (as in Grupstra et al., 2022), we characterized the presence and diversity of dinoRNAVs in various environmental reservoirs using amplicon sequencing of the dinoRNAV major capsid protein (mcp ) gene. Given that dinoRNAV communities can vary across coral species and colonies (Grupstra et al., 2022; Howe-Kerr, 2022; Montalvo-Proaño et al., 2017) and that corallivorous fish actively ‘sample’ corals while feeding (Grupstra et al., 2021), we hypothesized that corallivorous fish feces are a reservoir of dinoRNAVs and that fish feces-associated dinoRNAV communities exhibit higher alpha diversity than coral colony-associated dinoRNAV communities. We generated 19 dinoRNAV mcp amplicon sequencing libraries from coral colony biopsies (Acroporahyacinthus , n=8; Pocillopora species complex, n=5), as well as the feces of corallivorous fishes (Chaetodon reticulatus , n=4; Chaetodon ornatissimus, n=2). All samples were collected from reefs off the north shore of Moorea, French Polynesia (South Pacific). Methods for sampling and sample processing to generate virus amplicon sequencing libraries are described in Grupstra et al. (2021,2022) and Howe-Kerr et al. (2022). DinoRNAV mcp amplicon libraries were processed and analyzed using vAMPirus (see doi.org/10.5281/zenodo.7574173).