Browsing by Author "Vega Thurber, Rebecca L."

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    Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes
    (Springer Nature, 2023) Veglia, Alex J.; Bistolas, Kalia S. I.; Voolstra, Christian R.; Hume, Benjamin C. C.; Ruscheweyh, Hans-Joachim; Planes, Serge; Allemand, Denis; Boissin, Emilie; Wincker, Patrick; Poulain, Julie; Moulin, Clémentine; Bourdin, Guillaume; Iwankow, Guillaume; Romac, Sarah; Agostini, Sylvain; Banaigs, Bernard; Boss, Emmanuel; Bowler, Chris; de Vargas, Colomban; Douville, Eric; Flores, Michel; Forcioli, Didier; Furla, Paola; Galand, Pierre E.; Gilson, Eric; Lombard, Fabien; Pesant, Stéphane; Reynaud, Stéphanie; Sunagawa, Shinichi; Thomas, Olivier P.; Troublé, Romain; Zoccola, Didier; Correa, Adrienne M. S.; Vega Thurber, Rebecca L.
    Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
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    Filamentous virus-like particles are present in coral dinoflagellates across genera and ocean basins
    (Oxford University Press, 2023) Howe-Kerr, Lauren I.; Knochel, Anna M.; Meyer, Matthew D.; Sims, Jordan A.; Karrick, Carly E.; Grupstra, Carsten G. B.; Veglia, Alex J.; Thurber, Andrew R.; Vega Thurber, Rebecca L.; Correa, Adrienne M. S.
    Filamentous viruses are hypothesized to play a role in stony coral tissue loss disease (SCTLD) through infection of the endosymbiotic dinoflagellates (Family Symbiodiniaceae) of corals. To evaluate this hypothesis, it is critical to understand the global distribution of filamentous virus infections across the genetic diversity of Symbiodiniaceae hosts. Using transmission electron microscopy, we demonstrate that filamentous virus-like particles (VLPs) are present in over 60% of Symbiodiniaceae cells (genus Cladocopium) within Pacific corals (Acropora hyacinthus, Porites c.f. lobata); these VLPs are more prevalent in Symbiodiniaceae of in situ colonies experiencing heat stress. Symbiodiniaceae expelled from A. hyacinthus also contain filamentous VLPs, and these cells are more degraded than their in hospite counterparts. Similar to VLPs reported from SCTLD-affected Caribbean reefs, VLPs range from ~150 to 1500 nm in length and 16–37 nm in diameter and appear to constitute various stages in a replication cycle. Finally, we demonstrate that SCTLD-affected corals containing filamentous VLPs are dominated by diverse Symbiodiniaceae lineages from the genera Breviolum, Cladocopium, and Durusdinium. Although this study cannot definitively confirm or refute the role of filamentous VLPs in SCTLD, it demonstrates that filamentous VLPs are not solely observed in SCTLD-affected corals or reef regions, nor are they solely associated with corals dominated by members of a particular Symbiodiniaceae genus. We hypothesize that filamentous viruses are a widespread, common group that infects Symbiodiniaceae. Genomic characterization of these viruses and empirical tests of the impacts of filamentous virus infection on Symbiodiniaceae and coral colonies should be prioritized.