%0 Journal Article %J Science Advances %D 2020 %T Virus-host coexistence in phytoplankton through the genomic lens %A Yau, Sheree %A Krasovec, Marc %A Benites, L. Felipe %A Rombauts, Stephane %A Groussin, Mathieu %A Vancaester, Emmelien %A Aury, Jean-Marc %A Derelle, Evelyne %A Desdevises, Yves %A Escande, Marie-Line %A Grimsley, Nigel %A Guy, Julie %A Moreau, Hervé %A Sanchez-Brosseau, Sophie %A Van de Peer, Yves %A Vandepoele, Klaas %A Gourbière, Sébastien %A Piganeau, Gwenael %K RCC2590 %K RCC2596 %X Virus-microbe interactions in the ocean are commonly described by “boom and bust” dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this “accordion” chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions. %B Science Advances %V 6 %P eaay2587 %8 apr %G eng %U https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aay2587 %R 10.1126/sciadv.aay2587 %0 Journal Article %J Science Advances %D 2017 %T Population genomics of picophytoplankton unveils novel chromosome hypervariability %A Blanc-Mathieu, Romain %A Krasovec, Marc %A Hebrard, Maxime %A Yau, Sheree %A Desgranges, Elodie %A Martin, Joel %A Schackwitz, Wendy %A Kuo, Alan %A Salin, Gerald %A Donnadieu, Cecile %A Desdevises, Yves %A Sanchez-Ferandin, Sophie %A Moreau, Hervé %A Rivals, Eric %A Grigoriev, Igor V. %A Grimsley, Nigel %A Eyre-Walker, Adam %A Piganeau, Gwenael %K RCC1105 %K RCC1108 %K RCC1110 %K RCC1112 %K RCC1114 %K RCC1115 %K RCC1116 %K RCC1117 %K RCC1118 %K RCC1123 %K RCC1558 %K RCC1559 %K RCC1561 %K RCC299 %K RCC4221 %K RCC809 %B Science Advances %V 3 %P e1700239 %8 jul %G eng %U http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1700239 %R 10.1126/sciadv.1700239 %0 Journal Article %J Protist %D 2017 %T Revision of the genus micromonas manton et parke (chlorophyta, mamiellophyceae), of the type species m. pusilla (butcher) manton & parke and of the species m. commoda van baren, bachy and worden and description of two new species based on the genetic %A Simon, Nathalie %A Foulon, Elodie %A Grulois, Daphne %A Six, Christophe %A Desdevises, Yves %A Latimier, Marie %A Le Gall, Florence %A Tragin, Margot %A Houdan, Aude %A Derelle, Evelyne %A Jouenne, Fabien %A Marie, Dominique %A Le Panse, Sophie %A Vaulot, Daniel %A Marin, Birger %K 2017 %K ASSEMBLE %K rcc %K RCC1109 %K RCC114 %K RCC2306 %K RCC2308 %K RCC299 %K RCC372 %K RCC373 %K RCC418 %K RCC434 %K RCC447 %K RCC448 %K RCC449 %K RCC450 %K RCC451 %K RCC461 %K RCC465 %K RCC472 %K RCC497 %K RCC498 %K RCC570 %K RCC629 %K RCC647 %K RCC658 %K RCC676 %K RCC692 %K RCC746 %K RCC803 %K RCC804 %K RCC805 %K RCC806 %K RCC807 %K RCC808 %K RCC828 %K RCC829 %K RCC830 %K RCC831 %K RCC833 %K RCC834 %K RCC835 %K RCC836 %K SBR$_\textrmP$hyto$_\textrmD$IPO %K SBR$_\textrmP$hyto$_\textrmP$PM %K sbr?hyto$_\textrmd$ipo %B Protist %V 168 %P 612–635 %8 nov %G eng %U http://linkinghub.elsevier.com/retrieve/pii/S1434461017300780 %R 10.1016/j.protis.2017.09.002 %0 Journal Article %J BMC Evolutionary Biology %D 2014 %T Cophylogenetic interactions between marine viruses and eukaryotic picophytoplankton %A Bellec, Laure %A Clerissi, Camille %A Edern, Roseline %A Foulon, Elodie %A Simon, Nathalie %A Grimsley, Nigel %A Desdevises, Yves %K rcc %K RCC1105 %K rcc1107 %K RCC1108 %K RCC1109 %K RCC114 %K RCC2482 %K RCC2483 %K RCC2484 %K RCC2485 %K RCC344 %K RCC356 %K RCC373 %K RCC418 %K RCC461 %K RCC464 %K RCC465 %K RCC629 %K RCC658 %K RCC745 %K RCC789 %K RCC834 %K SBR$_\textrmP$hyto$_\textrmD$PO %X BACKGROUND:Numerous studies have investigated cospeciation (or cophylogeny) in various host-symbiont systems, and different patterns were inferred, from strict cospeciation where symbiont phylogeny mirrors host phylogeny, to complete absence of correspondence between trees. The degree of cospeciation is generally linked to the level of host specificity in the symbiont species and the opportunity they have to switch hosts. In this study, we investigated cophylogeny for the first time in a microalgae-virus association in the open sea, where symbionts are believed to be highly host-specific but have wide opportunities to switch hosts. We studied prasinovirus-Mamiellales associations using 51 different viral strains infecting 22 host strains, selected from the characterisation and experimental testing of the specificities of 313 virus strains on 26 host strains.RESULTS:All virus strains were restricted to their host genus, and most were species-specific, but some of them were able to infect different host species within a genus. Phylogenetic trees were reconstructed for viruses and their hosts, and their congruence was assessed based on these trees and the specificity data using different cophylogenetic methods, a topology-based approach, Jane, and a global congruence method, ParaFit. We found significant congruence between virus and host trees, but with a putatively complex evolutionary history.CONCLUSIONS:Mechanisms other than true cospeciation, such as host-switching, might explain a part of the data. It has been observed in a previous study on the same taxa that the genomic divergence between host pairs is larger than between their viruses. It implies that if cospeciation predominates in this algae-virus system, this would support the hypothesis that prasinoviruses evolve more slowly than their microalgal hosts, whereas host switching would imply that these viruses speciated more recently than the divergence of their host genera. %B BMC Evolutionary Biology %V 14 %P 59 %G eng %U http://www.biomedcentral.com/1471-2148/14/59 %R 10.1186/1471-2148-14-59 %0 Journal Article %J Applied and Environmental Microbiology %D 2014 %T Unveiling of the diversity of prasinoviruses (phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-Amplified DNA polymerase and major capsid protein genes %A Clerissi, Camille %A Grimsley, Nigel %A Ogata, Hiroyuki %A Hingamp, Pascal %A Poulain, Julie %A Desdevises, Yves %K Micromonas %K rcc %K TARA-Oceans %X Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale. %B Applied and Environmental Microbiology %V 80 %P 3150–3160 %G eng %U http://aem.asm.org/content/80/10/3150.abstract %R 10.1128/aem.00123-14 %0 Journal Article %J Protist %D 2013 %T Morphology, genome plasticity, and phylogeny in the genus ostreococcus reveal a cryptic species, o. mediterraneus sp. nov. (mamiellales, mamiellophyceae) %A Subirana, Lucie %A Péquin, Bérangère %A Michely, Stéphanie %A Escande, Marie-Line %A Meilland, Julie %A Derelle, Evelyne %A Marin, Birger %A Piganeau, Gwenael %A Desdevises, Yves %A Moreau, Hervé %A Grimsley, Nigel H %K barcode %K Chromosome %K culture %K ITS2 %K karyotype %K picoeukaryote %K rcc %K RCC1112 %K RCC1114 %K RCC1117 %K RCC143 %K RCC1620 %K RCC1621 %K RCC1623 %K RCC1624 %K RCC2572 %K RCC2573 %K RCC2574 %K RCC2575 %K RCC2577 %K RCC2578 %K RCC2579 %K RCC2582 %K RCC2583 %K RCC2584 %K RCC2585 %K RCC2587 %K RCC2590 %K RCC344 %K RCC356 %K RCC393 %K rcc501 %K RCC745 %K RCC809 %K ribosomal gene %X Coastal marine waters in many regions worldwide support abundant populations of extremely small (1-3 ??m diameter) unicellular eukaryotic green algae, dominant taxa including several species in the class Mamiellophyceae. Their diminutive size conceals surprising levels of genetic diversity and defies classical species' descriptions. We present a detailed analysis within the genus Ostreococcus and show that morphological characteristics cannot be used to describe diversity within this group. Karyotypic analyses of the best-characterized species O. tauri show it to carry two chromosomes that vary in size between individual clonal lines, probably an evolutionarily ancient feature that emerged before species' divergences within the Mamiellales. By using a culturing technique specifically adapted to members of the genus Ostreococcus, we purified ¿30 clonal lines of a new species, Ostreococcus mediterraneus sp. nov., previously known as Ostreococcus clade D, that has been overlooked in several studies based on PCR-amplification of genetic markers from environment-extracted DNA. Phylogenetic analyses of the S-adenosylmethionine synthetase gene, and of the complete small subunit ribosomal RNA gene, including detailed comparisons of predicted ITS2 (internal transcribed spacer 2) secondary structures, clearly support that this is a separate species. In addition, karyotypic analyses reveal that the chromosomal location of its ribosomal RNA gene cluster differs from other Ostreococcus clades. %B Protist %V 164 %P 643–659 %G eng %U http://www.sciencedirect.com/science/article/pii/S1434461013000497 %R 10.1016/j.protis.2013.06.002 %0 Journal Article %J Journal of Virology %D 2012 %T Prasinoviruses of the marine green alga Ostreococcus tauri are mainly species specific %A Clerissi, Camille %A Desdevises, Yves %A Grimsley, Nigel %K rcc %K RCC1110 %K RCC1114 %K RCC1115 %K RCC1116 %K RCC1117 %K RCC1123 %K RCC1558 %K RCC1561 %K RCC745 %X Prasinoviruses infecting unicellular green algae in the order Mamiellales (class Mamiellophyceae) are commonly found in coastal marine waters where their host species frequently abound. We tested 40 Ostreococcus tauri viruses on 13 independently isolated wild-type O. tauri strains, 4 wild-type O. lucimarinus strains, 1 Ostreococcus sp. (“Ostreococcus mediterraneus”) clade D strain, and 1 representative species of each of two other related species of Mamiellales, Bathycoccus prasinos and Micromonas pusilla. Thirty-four out of 40 viruses infected only O. tauri, 5 could infect one other species of the Ostreococcus genus, and 1 infected two other Ostreococcus spp., but none of them infected the other genera. We observed that the overall susceptibility pattern of Ostreococcus strains to viruses was related to the size of two host chromosomes known to show intraspecific size variations, that genetically related viruses tended to infect the same host strains, and that viruses carrying inteins were strictly strain specific. Comparison of two complete O. tauri virus proteomes revealed at least three predicted proteins to be candidate viral specificity determinants. %B Journal of Virology %V 86 %P 4611–4619 %G eng %U http://jvi.asm.org/content/86/8/4611.abstract %R 10.1128/jvi.07221-11 %0 Journal Article %J Journal of Virology %D 2010 %T Marine Prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer %A Moreau, Hervé %A Piganeau, Gwenael %A Desdevises, Yves %A Cooke, Richard %A Derelle, Evelyne %A Grimsley, Nigel %K RCC1105 %K RCC745 %X Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates. %B Journal of Virology %V 84 %P 12555–12563 %G eng %R 10.1128/jvi.01123-10 %0 Journal Article %J PLoS ONE %D 2008 %T Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga ¡i¿Ostreococcus tauri¡/i¿ %A Derelle, Evelyne %A Ferraz, Conchita %A Escande, Marie-Line %A Eychenié, Sophie %A Cooke, Richard %A Piganeau, Gwenael %A Desdevises, Yves %A Bellec, Laure %A Moreau, Hervé %A Grimsley, Nigel %K rcc %X Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon. %B PLoS ONE %V 3 %P e2250 %G eng %U http://dx.doi.org/10.1371/journal.pone.0002250 %R 10.1371/journal.pone.0002250