%0 Journal Article %J Communications Biology %D 2022 %T Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence %A Guérin, Nina %A Ciccarella, Marta %A Flamant, Elisa %A Frémont, Paul %A Mangenot, Sophie %A Istace, Benjamin %A Noel, Benjamin %A Belser, Caroline %A Bertrand, Laurie %A Labadie, Karine %A Cruaud, Corinne %A Romac, Sarah %A Bachy, Charles %A Gachenot, Martin %A Pelletier, Eric %A Alberti, Adriana %A Jaillon, Olivier %A Wincker, Patrick %A Aury, Jean-Marc %A Carradec, Quentin %K Biogeography %K comparative genomics %K metagenomics %K RCC100 %K Water microbiology %X The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment. Genomic inference reveals potential climate change-driven range expansion of the phytoplankton species Pelagomonas calceolata. %B Communications Biology %V 5 %P 1–14 %G eng %U https://www.nature.com/articles/s42003-022-03939-z %R 10.1038/s42003-022-03939-z %0 Journal Article %J BMC Biology %D 2021 %T Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. %A Farhat, Sarah %A Le, Phuong %A Kayal, Ehsan %A Noel, Benjamin %A Bigeard, Estelle %A Corre, Erwan %A Maumus, Florian %A Florent, Isabelle %A Alberti, Adriana %A Aury, Jean-Marc %A Barbeyron, Tristan %A Cai, Ruibo %A Silva, Corinne Da %A Istace, Benjamin %A Labadie, Karine %A Marie, Dominique %A Mercier, Jonathan %A Rukwavu, Tsinda %A Szymczak, Jeremy %A Tonon, Thierry %A Alves-de-Souza, Catharina %A Rouze, Pierre %A de Peer, Yves Van %A Wincker, Patrick %A Rombauts, Stephane %A Porcel, Betina M %A Guillou, Laure %K Dinoflagellate %K genome %K Introner elements %K Non-canonical introns %K parasite %K RCC4383 %K RCC4398 %B BMC Biology %P 1–21 %G eng %R 10.1186/s12915-020-00927-9 %0 Journal Article %J Frontiers in Microbiology %D 2020 %T Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria %A Doré, Hugo %A Farrant, Gregory K. %A Guyet, Ulysse %A Haguait, Julie %A Humily, Florian %A Ratin, Morgane %A Pitt, Frances D. %A Ostrowski, Martin %A Six, Christophe %A Brillet-Guéguen, Loraine %A Hoebeke, Mark %A Bisch, Antoine %A Le Corguillé, Gildas %A Corre, Erwan %A Labadie, Karine %A Aury, Jean-Marc %A Wincker, Patrick %A Choi, Dong Han %A Noh, Jae Hoon %A Eveillard, Damien %A Scanlan, David J. %A Partensky, Frédéric %A Garczarek, Laurence %K amino-acid substitutions %K comparative genomics %K evolution %K genomic islands %K marine cyanobacteria %K niche adaptation %K Prochlorococcus %K rcc1084 %K RCC1085 %K RCC1086 %K RCC1087 %K RCC156 %K RCC158 %K rcc162 %K RCC2033 %K RCC2035 %K RCC2319 %K RCC2366 %K RCC2368 %K RCC2369 %K RCC2374 %K RCC2376 %K RCC2378 %K RCC2379 %K rcc2380 %K RCC2381 %K rcc2382 %K RCC2383 %K RCC2385 %K RCC2433 %K RCC2436 %K RCC2438 %K RCC2527 %K RCC2528 %K RCC2533 %K RCC2534 %K RCC2535 %K RCC2553 %K RCC2554 %K RCC2555 %K RCC2556 %K RCC2571 %K RCC2673 %K RCC278 %K rcc296 %K RCC307 %K RCC328 %K RCC3377 %K RCC407 %K RCC515 %K rcc539 %K rcc555 %K RCC556 %K rcc752 %K RCC753 %K rcc791 %K Synechococcus %B Frontiers in Microbiology %V 11 %P 1–23 %8 sep %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2020.567431/full %R 10.3389/fmicb.2020.567431 %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 Frontiers in Microbiology %D 2018 %T Comparative time-scale gene expression analysis highlights the infection processes of two amoebophrya strains %A Farhat, Sarah %A Florent, Isabelle %A Noel, Benjamin %A Kayal, Ehsan %A Da Silva, Corinne %A Bigeard, Estelle %A Alberti, Adriana %A Labadie, Karine %A Corre, Erwan %A Aury, Jean-Marc %A Rombauts, Stephane %A Wincker, Patrick %A Guillou, Laure %A Porcel, Betina M. %K amoebophrya %K Dinoflagellates %K Gene Expression %K infection %K oxidative stress response %K parasite %K plankton %K RCC1627 %K RCC3596 %K RCC4383 %K RCC4398 %K syndiniales %B Frontiers in Microbiology %V 9 %P 1–19 %8 oct %G eng %U https://www.frontiersin.org/article/10.3389/fmicb.2018.02251/full %R 10.3389/fmicb.2018.02251 %0 Journal Article %J Scientific Reports %D 2016 %T Survey of the green picoalga Bathycoccus genomes in the global ocean %A Vannier, Thomas %A Leconte, Jade %A Seeleuthner, Yoann %A Mondy, Samuel %A Pelletier, Eric %A Aury, Jean-Marc %A de Vargas, Colomban %A Sieracki, Michael %A Iudicone, Daniele %A Vaulot, Daniel %A Wincker, Patrick %A Jaillon, Olivier %K 2016 %K RCC1105 %K RCC715 %K RCC716 %K sbr?hyto$_\textrmd$ipo %K sbr?hyto?ppo %B Scientific Reports %V 6 %P 37900 %8 dec %G eng %U http://www.nature.com/articles/srep37900 %R 10.1038/srep37900 %0 Journal Article %J Proceedings of the National Academy of Sciences %D 2013 %T Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida %A Collen, Jonas %A Porcel, Betina %A Carré, Wilfrid %A Ball, Steven G %A Chaparro, Cristian %A Tonon, Thierry %A Barbeyron, Tristan %A Michel, Gurvan %A Noel, Benjamin %A Valentin, Klaus %A Elias, Marek %A Artiguenave, François %A Arun, Alok %A Aury, Jean-Marc %A Barbosa-Neto, José F %A Bothwell, John H %A Bouget, François-Yves %A Brillet, Loraine %A Cabello-Hurtado, Francisco %A Capella-Gutiérrez, Salvador %A Charrier, Bénédicte %A Cladière, Lionel %A Cock, J Mark %A Coelho, Susana M %A Colleoni, Christophe %A Czjzek, Mirjam %A Da Silva, Corinne %A Delage, Ludovic %A Denoeud, France %A Deschamps, Philippe %A Dittami, Simon M %A Gabaldón, Toni %A Gachon, Claire M M %A Groisillier, Agnès %A Hervé, Cécile %A Jabbari, Kamel %A Katinka, Michael %A Kloareg, Bernard %A Kowalczyk, Nathalie %A Labadie, Karine %A Leblanc, Catherine %A Lopez, Pascal J %A McLachlan, Deirdre H %A Meslet-Cladiere, Laurence %A Moustafa, Ahmed %A Nehr, Zofia %A Nyvall Collén, Pi %A Panaud, Olivier %A Partensky, Frédéric %A Poulain, Julie %A Rensing, Stefan A %A Rousvoal, Sylvie %A Samson, Gaelle %A Symeonidi, Aikaterini %A Weissenbach, Jean %A Zambounis, Antonios %A Wincker, Patrick %A Boyen, Catherine %K RCC299 %X Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements. %B Proceedings of the National Academy of Sciences %V 110 %P 5247–5252 %G eng %U http://www.pnas.org/content/110/13/5247.abstract %R 10.1073/pnas.1221259110