@article {dore_global_2022,
	title = {Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts},
	journal = {mSystems},
	year = {2022},
	note = {Publisher: American Society for Microbiology},
	pages = {e00656{\textendash}22},
	abstract = {Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of {\textquotedblleft}who is where{\textquotedblright} by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades.},
	keywords = {RCC1086, RCC1695, RCC2369, rcc2380, RCC2553, RCC2556, RCC2570, rcc791},
	doi = {10.1128/msystems.00656-22},
	url = {https://journals.asm.org/doi/full/10.1128/msystems.00656-22},
	author = {Dor{\'e}, Hugo and Leconte, Jade and Guyet, Ulysse and Breton, Sol{\`e}ne and Farrant, Gregory K. and Demory, David and Ratin, Morgane and Hoebeke, Mark and Corre, Erwan and Pitt, Frances D. and Ostrowski, Martin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Garczarek, Laurence}
}
@article {Humily2013,
	title = {A gene island with two possible configurations is involved in chromatic acclimation in marine synechococcus},
	journal = {PLoS ONE},
	volume = {8},
	number = {12},
	year = {2013},
	note = {Publisher: Public Library of Science tex.mendeley-tags: 2013,macumba,rcc,sbr?hyto?app},
	pages = {e84459},
	abstract = {{\textexclamdown}p{\textquestiondown}{\textexclamdown}italic{\textquestiondown}Synechococcus{\textexclamdown}/italic{\textquestiondown}, the second most abundant oxygenic phototroph in the marine environment, harbors the largest pigment diversity known within a single genus of cyanobacteria, allowing it to exploit a wide range of light niches. Some strains are capable of Type IV chromatic acclimation (CA4), a process by which cells can match the phycobilin content of their phycobilisomes to the ambient light quality. Here, we performed extensive genomic comparisons to explore the diversity of this process within the marine {\textexclamdown}italic{\textquestiondown}Synechococcus{\textexclamdown}/italic{\textquestiondown} radiation. A specific gene island was identified in all CA4-performing strains, containing two genes ({\textexclamdown}italic{\textquestiondown}fciA{\textexclamdown}/italic{\textquestiondown}/b) coding for possible transcriptional regulators and one gene coding for a phycobilin lyase. However, two distinct configurations of this cluster were observed, depending on the lineage. CA4-A islands contain the {\textexclamdown}italic{\textquestiondown}mpeZ{\textexclamdown}/italic{\textquestiondown} gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called {\textexclamdown}italic{\textquestiondown}fciC{\textexclamdown}/italic{\textquestiondown}. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While {\textexclamdown}italic{\textquestiondown}mpeZ{\textexclamdown}/italic{\textquestiondown} is expressed more in blue light than green light, this is the reverse for {\textexclamdown}italic{\textquestiondown}mpeW{\textexclamdown}/italic{\textquestiondown}, although only small phenotypic differences were found among chromatic acclimaters possessing either CA4 island type. This study provides novel insights into understanding both diversity and evolution of the CA4 process.{\textexclamdown}/p{\textquestiondown}},
	keywords = {2013, MACUMBA, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	doi = {10.1371/journal.pone.0084459},
	url = {http://dx.doi.org/10.1371/journal.pone.0084459},
	author = {Humily, Florian and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Farrant, Gregory K and Ratin, Morgane and Marie, Dominique and Garczarek, Laurence}
}
@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}}
}
