@booklet {dennu_biological_2023,
	title = {Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and major structural variations},
	year = {2023},
	note = {Pages: 2023.10.16.562038 Section: New Results},
	month = {oct},
	publisher = {bioRxiv},
	abstract = {Population-scale sequencing has become a standard practice to explore the natural genetic diversity underlying adaptation, notably in land plants. However, current sequencing initiatives for eukaryotic phytoplankton primarily concentrate on creating reference genomes for model organisms and characterizing natural communities through metagenomics approaches. Consequently, few species have been thoroughly sequenced and intraspecific genetic diversity remains virtually undescribed, limiting our understanding of diversity and adaptation mechanisms. Here we report a biological and genomic resource to explore the genetic diversity of the cosmopolitan and ecologically important Bathycoccus genus. To span broad geographical and temporal scales, we selected available strains but also isolated and genotyped strains from both the Banyuls bay (Mediterranean sea) and the Baffin bay (Arctic ocean). By combining ONT long reads and Illumina short reads technologies, we produced and annotated 28 Bathycoccus sp. de novo assembled genomes of high quality, including 24 genomes of Bathycoccus prasinos strains along a latitudinal gradient between 40{\textdegree} and 78{\textdegree} North, one reference genome of the Bathycoccus calidus species and 3 genomes of a yet undescribed Bathycoccus species named Bathycoccus catiminus. We assessed the genetic diversity of this genus through phylogenomic analyses and highlighted the central role of this genomic resource in providing new insights into the diversity of outlier chromosomal structures. The Bathycoccus biological and genomic resources offer a robust framework for investigating the diversity and adaptation mechanisms of eukaryotic phytoplankton in the Ocean. Significance statement Comparative and functional approaches for the study of eukaryotic phytoplankton and their adaptation to latitudes and seasons that rely on extensive biological and genomic resources are currently lacking. Here we report such resources and describe the natural diversity of the cosmopolitan phytoplankton Bathycoccus, providing insights into its species and intraspecific diversity and establishing it as a robust model for functional and ecological studies.},
	keywords = {RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685, RCC716},
	doi = {10.1101/2023.10.16.562038},
	url = {https://www.biorxiv.org/content/10.1101/2023.10.16.562038v1},
	author = {Dennu, Louis and Devic, Martine and Rigonato, Janaina and Falciatore, Angela and Lozano, Jean-Claude and Verg{\'e}, Val{\'e}rie and Mariac, C{\'e}dric and Jaillon, Olivier and Team, The Dark Edge genomics sampling and Sabot, Fran{\c c}ois and Bouget, Fran{\c c}ois-Yves}
}
@article {sands_genetic_2023,
	title = {Genetic and physiological responses to light quality in a deep ocean ecotype of Ostreococcus, an ecologically important photosynthetic picoeukaryote},
	journal = {Journal of Experimental Botany},
	year = {2023},
	pages = {erad347},
	abstract = {Abstract Phytoplankton are exposed to dramatic variations in light quality when cells are carried by upwelling or downwelling currents or encounter sediment. We investigated the potential impact of light quality changes in Ostreococcus, a key marine photosynthetic picoeukaryote, by analysing changes in its transcriptome, pigment content and photophysiology after acclimation to monochromatic red, green or blue light. The clade B species RCC809, isolated from the deep euphotic zone of the tropical Atlantic Ocean, responded to blue light by accelerating cell division at the expense of storage reserves and by increasing the relative level of blue-light absorbing pigments. RCC809 responded to red and green light by increasing its potential for photoprotection. In contrast, the clade A species OTTH0595, which originates from a shallow water environment, showed no difference in photosynthetic properties and minor differences in carotenoid contents between light qualities. This was associated with the loss of candidate lightquality responsive promoter motifs identified in RCC809 genes. These results demonstrate that light quality can have a major influence on the physiology of eukaryotic phytoplankton and suggest that different light quality environments can drive selection for diverse patterns of responsiveness and environmental niche partitioning.},
	keywords = {Rcc141, RCC4221, RCC745, RCC809},
	issn = {0022-0957, 1460-2431},
	doi = {10.1093/jxb/erad347},
	url = {https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erad347/7258950},
	author = {Sands, Elizabeth and Davies, Sian and Puxty, Richard John and Verg{\'e}, Val{\'e}rie and Bouget, Fran{\c c}ois-Yves and Scanlan, David John and Carr{\'e}, Isabelle Alice}
}
@booklet {devic_indel_2023,
	title = {An INDEL genomic approach to explore population diversity of phytoplankton : \textit{Bathycoccus , a case study},
	year = {2023},
	publisher = {Ecology},
	type = {preprint},
	abstract = {Abstract Although metabarcoding has generated large dataset on world-wide phytoplankton species diversity, little is known about the intraspecies diversity underlying adaptation to environmental niches. To gain insight into population diversity, a novel INDEL based method was developed on Bathycoccus prasinos . Oxford Nanopore Technology (ONT) sequencing was first used to characterise structural variants (SV) among the genomes of Bathycoccus sampled from geographically distinct regions in the world ocean. Markers derived from INDEL were validated by PCR and sequencing in the world-wide strains. These markers were then used to genotype 55 Bathycoccus strains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer. With five markers, eight Multi Loci Genotypes (MLG) were determined, two of which represented 53\% and 29\% of the isolates. Physiological studies confirmed that isolates are phenotypically different, cells isolated in February growing better at low temperature than those isolated in December and January. When tested directly on environmental samples, two diversity markers showed a similar allele frequency in sea water as in individual Bathycoccus strains isolated at the same period. We conclude that these markers constitute a resource to identify the most abundant variant alleles in a given bloom. A follow-up on three consecutive blooms revealed differences in allele abundance during the course of a bloom, particularly at initiation and between years. This INDEL-based genotyping constitutes a new methodological approach that may be used to assess the population structure and diversity of other species.},
	keywords = {RCC1613, RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685},
	doi = {10.1101/2023.02.09.527951},
	url = {http://biorxiv.org/lookup/doi/10.1101/2023.02.09.527951},
	author = {Devic, Martine and Mariac, C{\'e}dric and Verg{\'e}, Val{\'e}rie and Schatt, Philipe and Dennu, Louis and Lozano, Jean-Claude and Bouget, Fran{\c c}ois-Yves and Sabot, Fran{\c c}ois}
}
@booklet {devic_population_2023,
	title = {Population dynamics of the cosmopolitan eukaryotic picophytoplankton Bathycoccus during seasonal blooms in the bay of Banyuls sur Mer (North Western Mediterranean sea)},
	year = {2023},
	publisher = {BioRxiv},
	type = {preprint},
	abstract = {Abstract Although Bathycoccus is one of the most abundant picophytoplankton, little is known about the genetic diversity underlying its adaptation to ecological niches. In this study, the diversity of Bathycoccus populations during their annual bloom in the Mediterranean bay of Banyuls France was assessed by an INDEL based approach. Oxford Nanopore Technology (ONT) was used to characterise structural variants (SV) among the genomes of Bathycoccus sampled from geographically distinct regions in the world ocean. Markers derived from INDEL were validated by PCR and sequencing in the world-wide strains. These markers were then used to genotype 55 Bathycoccus strains isolated during the winter bloom 2018-2019 in Banyuls. With five markers, eight Multi Loci Genotypes (MLG) were determined, two of which represented 53\% and 29\% of the isolates. Physiological studies confirmed that isolates are phenotypically different, cells isolated in February growing better at low temperature than those isolated in December. When tested on environmental samples, two diversity markers showed a similar allele frequency in sea water as in individual Bathycoccus strains isolated at the same period. We conclude that these markers constitute a resource to identify the most abundant variant alleles in a given bloom. A follow-up on three consecutive blooms revealed differences in allele abundance during the course of a bloom, particularly at initiation, and between years. In addition to Bathycoccus prasinos , two other species of Bathycoccus were identified including the recently described species B. calidus and a novel species B. catiminus , suggesting that species diversity of the genus Bathycoccus may be underestimated.},
	keywords = {RCC1613, RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685},
	doi = {10.1101/2023.02.09.527951},
	url = {http://biorxiv.org/lookup/doi/10.1101/2023.02.09.527951},
	author = {Devic, Martine and Mariac, C{\'e}dric and Verg{\'e}, Val{\'e}rie and Schatt, Philipe and Dennu, Louis and Lozano, Jean-Claude and Bouget, Fran{\c c}ois-Yves and Sabot, Fran{\c c}ois}
}
@article {Annunziata2018,
	title = {A bHLH-PAS protein regulates light-dependent rhythmic processes in the marine diatom Phaeodactylum tricornutum},
	journal = {bioRxiv},
	year = {2018},
	note = {tex.mendeley-tags: RCC2967},
	pages = {271445},
	abstract = {Periodic light dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diurnal rhythms in growth, cell cycle and gene expression, the molecular bases controlling these processes are still obscure. By exploring the regulatory landscape of diatom diurnal rhythms, we here unveil the key function of a Phaeodactylum tricornutum bHLH-PAS protein, named Pt bHLH1a, in the regulation of light-dependent rhythms. Peak expression of Pt bHLH1a mRNA occurs at the end of the light period and it is adjusted to photoperiod changes. Ectopic over-expression of Pt bHLH1a results in lines with altered cell division and gene expression and showing a phase shift in diurnal responses, compared to the wild-type cells. Reduced oscillations in gene expression are also observed in continuous darkness, showing that the regulation of rhythmicity by Pt bHLH1a is not directly dependent on light inputs and cell division. Pt bHLH1a orthologs are widespread in both pennate and centric diatom genomes, hinting at a common function in many species. This study adds new elements to understand diatom biology and ecology and offers new perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but still underinvestigated branch of the tree of life.},
	keywords = {RCC2967},
	doi = {10.1101/271445},
	url = {https://www.biorxiv.org/content/early/2018/02/25/271445},
	author = {Annunziata, Rossella and Ritter, Andr{\'e}s and Fortunato, Antonio Emidio and Cheminant-Navarro, Soizic and Agier, Nicolas and Huysman, Marie J. J. and Winge, Per and Bones, Atle and Bouget, Fran{\c c}ois-Yves and Lagomarsino, Marco Cosentino and Bouly, Jean Pierre and Falciatore, Angela}
}
@article {Guyon2018,
	title = {Comparative analysis of culture conditions for the optimization of carotenoid production in several strains of the picoeukaryote ostreococcus},
	journal = {Marine Drugs},
	volume = {16},
	number = {3},
	year = {2018},
	note = {tex.mendeley-tags: 2018,RCC745,RCC802,RCC809,rcc},
	pages = {76},
	abstract = {Microalgae are promising sources for the sustainable production of compounds of interest for biotechnologies. Compared to higher plants, microalgae have a faster growth rate and can be grown in industrial photobioreactors. The microalgae biomass contains specific metabolites of high added value for biotechnology such as lipids, polysaccharides or carotenoid pigments. Studying carotenogenesis is important for deciphering the mechanisms of adaptation to stress tolerance as well as for biotechnological production. In recent years, the picoeukaryote Ostreococcus tauri has emerged as a model organism thanks to the development of powerful genetic tools. Several strains of Ostreococcus isolated from different environments have been characterized with respect to light response or iron requirement. We have compared the carotenoid contents and growth rates of strains of Ostreococcus (OTTH595, RCC802 and RCC809) under a wide range of light, salinity and temperature conditions. Carotenoid profiles and productivities varied in a strain-specific and stress-dependent manner. Our results also illustrate that phylogenetically related microalgal strains originating from different ecological niches present specific interests for the production of specific molecules under controlled culture conditions.},
	keywords = {2018, carotenoids, GROWTH RATE, Light, Ostreococcus, rcc, RCC745, RCC802, RCC809, salinity, temperature},
	issn = {1660-3397},
	doi = {10.3390/md16030076},
	url = {http://www.mdpi.com/1660-3397/16/3/76},
	author = {Guyon, Jean-baptiste and Schatt, Philippe and Lozano, Jean-Claude and Liennard, Marion and Bouget, Fran{\c c}ois-Yves}
}
@article {Henriquez-Castillo2018,
	title = {Ostreococcus tauri luminescent reporter lines as biosensors for detecting pollution from copper-mine tailing effluents in coastal environments},
	journal = {Frontiers in Environmental Science},
	volume = {6},
	number = {May},
	year = {2018},
	note = {tex.mendeley-tags: RCC745},
	month = {may},
	pages = {1{\textendash}11},
	keywords = {biosensors, CDKA, copper pollution, ferritin, frontiers in environmental science, frontiersin, luciferase reporter, mine tailings, org, Ostreococcus, RCC745, www},
	issn = {2296-665X},
	doi = {10.3389/fenvs.2018.00022},
	url = {https://www.frontiersin.org/article/10.3389/fenvs.2018.00022/full},
	author = {Henr{\'\i}quez-Castillo, Carlos and Botebol, Hugo and Mouton, Adelaide and Ram{\'\i}rez-Flandes, Salvador and Lozano, Jean-Claude and Lelandais, Gaelle and Andrade, Santiago and Trefault, Nicole and de la Iglesia, Rodrigo and Bouget, Fran{\c c}ois-Yves}
}
@article {Paerl2016,
	title = {Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton},
	journal = {The ISME Journal},
	volume = {11},
	number = {3},
	year = {2017},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc3401,rcc745},
	month = {mar},
	pages = {753{\textendash}765},
	keywords = {rcc3401, RCC745},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.145},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2016.145},
	author = {Paerl, Ryan W and Bouget, Fran{\c c}ois-Yves and Lozano, Jean-Claude and Verg{\'e}, Val{\'e}rie and Schatt, Philippe and Allen, Eric E and Palenik, Brian and Azam, Farooq}
}
@article {Morrissey2014,
	title = {A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake},
	journal = {Current Biology},
	volume = {25},
	number = {3},
	year = {2014},
	note = {tex.mendeley-tags: rcc},
	month = {dec},
	pages = {364{\textendash}371},
	abstract = {Numerous cellular functions including respiration require iron. Plants and phytoplankton must also maintain the iron-rich photosynthetic electron transport chain, which most likely evolved in the iron-replete reducing environments of the Proterozoic ocean [1]. Iron bioavailability has drastically decreased in the contemporary ocean [1], most likely selecting for the evolution of efficient iron acquisition mechanisms among modern phytoplankton. Mesoscale iron fertilization experiments often result in blooms dominated by diatoms [2], indicating that diatoms have adaptations that allow survival in iron-limited waters and rapid multiplication when iron becomes available. Yet the genetic and molecular bases are unclear, as very few iron uptake genes have been functionally characterized from marine eukaryotic phytoplankton, and large portions of diatom iron starvation transcriptomes are genes encoding unknown functions [3{\textendash}5]. Here we show that the marine diatom Phaeodactylum tricornutum utilizes ISIP2a to concentrate Fe(III) at the cell surface as part of a novel, copper-independent and thermodynamically controlled iron uptake system. ISIP2a is expressed in response to iron limitation several days prior to the induction of ferrireductase activity, and it facilitates significant Fe(III) uptake during the initial response to Fe limitation. ISIP2a is able to directly bind Fe(III) and increase iron uptake when heterologously expressed, whereas knockdown of ISIP2a in P. tricornutum decreases iron uptake, resulting in impaired growth and chlorosis during iron limitation. ISIP2a is expressed by diverse marine phytoplankton, indicating that it is an ecologically significant adaptation to the unique nutrient composition of marine environments.},
	keywords = {rcc},
	issn = {09609822},
	doi = {10.1016/j.cub.2014.12.004},
	url = {http://www.sciencedirect.com/science/article/pii/S0960982214015632},
	author = {Morrissey, Joe and Sutak, Robert and Paz-Yepes, Javier and Tanaka, Atsuko and Moustafa, Ahmed and Veluchamy, Alaguraj and Thomas, Yann and Botebol, Hugo and Bouget, Fran{\c c}ois-Yves and McQuaid, Jeffrey B. and Tirichine, Leila and Allen, Andrew E. and Lesuisse, Emmanuel and Bowler, Chris}
}
@article {Collen2013,
	title = {Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {110},
	number = {13},
	year = {2013},
	note = {tex.mendeley-tags: RCC299},
	pages = {5247{\textendash}5252},
	abstract = {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.},
	keywords = {RCC299},
	doi = {10.1073/pnas.1221259110},
	url = {http://www.pnas.org/content/110/13/5247.abstract},
	author = {Collen, Jonas and Porcel, Betina and Carr{\'e}, Wilfrid and Ball, Steven G and Chaparro, Cristian and Tonon, Thierry and Barbeyron, Tristan and Michel, Gurvan and Noel, Benjamin and Valentin, Klaus and Elias, Marek and Artiguenave, Fran{\c c}ois and Arun, Alok and Aury, Jean-Marc and Barbosa-Neto, Jos{\'e} F and Bothwell, John H and Bouget, Fran{\c c}ois-Yves and Brillet, Loraine and Cabello-Hurtado, Francisco and Capella-Guti{\'e}rrez, Salvador and Charrier, B{\'e}n{\'e}dicte and Cladi{\`e}re, Lionel and Cock, J Mark and Coelho, Susana M and Colleoni, Christophe and Czjzek, Mirjam and Da Silva, Corinne and Delage, Ludovic and Denoeud, France and Deschamps, Philippe and Dittami, Simon M and Gabald{\'o}n, Toni and Gachon, Claire M M and Groisillier, Agn{\`e}s and Herv{\'e}, C{\'e}cile and Jabbari, Kamel and Katinka, Michael and Kloareg, Bernard and Kowalczyk, Nathalie and Labadie, Karine and Leblanc, Catherine and Lopez, Pascal J and McLachlan, Deirdre H and Meslet-Cladiere, Laurence and Moustafa, Ahmed and Nehr, Zofia and Nyvall Coll{\'e}n, Pi and Panaud, Olivier and Partensky, Fr{\'e}d{\'e}ric and Poulain, Julie and Rensing, Stefan A and Rousvoal, Sylvie and Samson, Gaelle and Symeonidi, Aikaterini and Weissenbach, Jean and Zambounis, Antonios and Wincker, Patrick and Boyen, Catherine}
}
@article {Derelle2006,
	title = {Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {103},
	number = {31},
	year = {2006},
	note = {tex.mendeley-tags: RCC745},
	pages = {11647{\textendash}11652},
	abstract = {The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world{\textquoteright}s smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C4 photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.},
	keywords = {rcc, RCC745, SBR$_\textrmP$hyto},
	doi = {10.1073/pnas.0604795103},
	url = {http://www.pnas.org/cgi/content/abstract/103/31/11647},
	author = {Derelle, Evelyne and Ferraz, Conchita and Rombauts, Stephane and Rouze, Pierre and Worden, Alexandra Z and Robbens, Steven and Partensky, Fr{\'e}d{\'e}ric and Degroeve, Sven and Echeynie, Sophie and Cooke, Richard and Saeys, Yvan and Wuyts, Jan and Jabbari, Kamel and Bowler, Chris and Panaud, Olivier and Piegu, Benoit and Ball, Steven G and Ral, Jean-Philippe and Bouget, Fran{\c c}ois-Yves and Piganeau, Gwenael and De Baets, Bernard and Picard, Andr{\'e} and Delseny, Michel and Demaille, Jacques and Van de Peer, Yves and Moreau, Herv{\'e}}
}
