Biology subjects

Thomy, J.

Publications and source records attributed to Thomy, J..

3 recordsLinked to original sources

bioRxiv2026

First Evidence of Dicistroviruses Infecting Protists

Molecular surveys suggest that RNA viruses are abundant and diverse in the ocean, but the hosts for most of these viruses are unknown because so few have been cultivated. Here, we present the genomes of five positive-sense, single-stranded RNA (+ssRNA) viruses isolated from tropical seawater that infect green algae in the genus Tetraselmis (order Chlorodendrales). Phylogenetic analyses of multiple genes placed these closely related viruses within the family Dicistroviridae (order Picornavirales) making them the first viruses within the bounds of the Dicistroviridae family demonstrated to infect an organism other than arthropods. The RNA-dependent and capsid gene sequences of the Tetraselmis RNA viruses (TetRNAV01-05) cluster with others recovered from diverse environmental water samples or aquatic invertebrate tissues, and together they form a strongly supported sister clade to viruses in the genus Triatovirus. The TetRNAVs harbor a unique intergenic internal ribosome entry site (IRES), suggesting a translation strategy distinct from that described in arthropod-infecting dicistroviruses. Our results suggest that many uncultivated viruses presumed to infect invertebrates, because they were detected in invertebrate-derived samples and their genes cluster within the family Dicistroviridae, may instead be protist-infecting viruses.

microbiology↗

bioRxiv2025

Genomic analysis of Ostreococcus tauri-infecting viruses reveals a hypervariable region associated with host--virus interactions

While the genus Prasinovirus, known to infect prasinophyte green algae (class Mamiellophyceae), is abundant in the oceans, the genetic mechanisms governing the ecology and (co)evolution of these viruses remain poorly understood. In this study, we sequenced the complete genomes of eighteen viruses infecting the cosmopolitan unicellular green alga Ostreococcus tauri (OtVs) and one specific to Micromonas commoda (McV-20T). Of these viruses, twelve were previously isolated from the coastal Mediterranean Sea and seven were newly isolated from two different geographical locations (i.e., the South Pacific Gyre and the North Sea). Phylogenetic analysis classified these viruses as new members of the Prasinovirus genus and defined three distinct OtV clades: designated OtV-type 1, OtV-type 2a and OtV-type 2b. The OtV-type 1 includes three new viruses isolated from the Pacific Ocean and the previously sequenced genome OtV6. The OtV-type 1 form a large cluster within the Micromonas-infecting virus clade, sharing five unique homologous genes with all Micromonas viruses. In addition, genetic features of OtV-type 1, including a higher number of CDSs ([~]260) and lower GC content ([~]41%), were more closely allied to Micromonas viruses than to those of OtVs, suggesting an alternative host or a recent host switch from Micromonas to O. tauri. By analyzing the OtV genomes, we found a faster-evolving central hypervariable region (HVR), where the OtV-type 2b displayed the largest region, i.e., three times longer than other OtVs. This region encodes genes mainly associated with host cell recognition and attachment and under strong selective pressure (positive and negative). Notably, most viruses associated with OtV-type 2b showed the broadest host range. Infection dynamics between the hosts and the viruses appeared highly specific to host-virus pairs, suggesting complex interactions in the Ostreococcus-prasinovirus system. Finally, by observing viral lysates with electron microscopy, we observed novel morphologies never described for these viruses. Overall, this study provides new insights into the genetic diversity of prasinoviruses and describes for the first time a viral plasticity that might be strongly shaped by antagonistic coevolution with their hosts.

microbiology↗

bioRxiv2025

Evidence for the acquisition of a proteorhodopsin-like rhodopsin by a chrysophyte-infecting giant virus

Chrysophytes are nanoflagellate protists widespread in aquatic ecosystems with diverse trophic roles as primary producers and bacterivores. Molecular evidence suggests that chrysophytes are commonly infected by giant viruses but isolates of such virus-host systems have not been reported. Here, we describe the first cultivated chrysophyte-infecting virus, Chrysophyceae Clade H virus SA1 (ChrysoHV), isolated along with its phago-mixotrophic host alga from surface waters in the tropical North Pacific Ocean. The ChrysoHV capsid (290 {+/-} 40 nm diameter) is associated with a loose, sac-like membrane that extends its effective diameter (720 {+/-} 120 nm) and presents a long (1,200 {+/-} 240 nm), thin (20 {+/-} 2), flexible tail, a morphology unlike any virion yet described. The assembled genome is 1.19 Mbp. Phylogenetic analysis places ChrysoHV as the third cultivated member of the Aliimimivirinae subfamily in the Mimiviridae family of giant viruses. The ChrysoHV genome encodes two heliorhodopsins and one proteorhodopsin. Proteorhodopsins are well known light-driven proton pumps in bacteria but have not been previously reported in a viral genome. The predicted viral proteorhodopsin structure suggests it may not have a functional retinal binding site implying a light-independent function. The genome also encodes two ribosomal proteins and nine genes with closest known homologs in marine cyanobacteria, most annotated as encoding for proteins involved in nutrient uptake. This unusual virus could serve as a model system for exploring viral rhodopsin functions and its genome suggests that phagotrophic protists may serve as an intracellular market for gene exchange between infecting viruses and ingested bacterial prey. ImportanceChrysophytes are abundant eukaryotic phytoplankton with trophic strategies ranging from photosynthesis to phagotrophy. They serve as models of mixotrophy among aquatic protists, but no chrysophyte-infecting viruses had been isolated, leaving a gap in experimental virus-host systems for a major class of protists. This study reports on the characterization of the first isolated chrysophyte-infecting virus, ChrysoHV. The virion morphology is unusual, having a loose membranous sac around a large capsid and a long filamentous tail. The genome contains genes for ribosomal proteins, a rarity in eukaryotic viruses, and multiple genes with homologs in common marine bacteria, one of which is a type of rhodopsin never before reported in a virus. We hypothesize that phago-mixotrophs, through infections and ingestion, may facilitate lateral gene exchange between eukaryote-infecting viruses and bacteria, entities that might not otherwise directly interact. The results expand the observed morphological diversity among viruses and the catalog of known virus genes.

microbiology↗