Main publications citing or using the Cyanorak information system:
Blot, N., Mella-Flores, D., Six, C., Le Corguillé, G., Boutte, C., Peyrat, A., Monnier, A., Ratin, M., Gourvil, P., Campbell, D.A., and Garczarek, L. (2011). Light history influences the response of the marine cyanobacterium Synechococcus sp. WH7803 to oxidative stress. Plant Physiol 156, 1934-1954.
Bretaudeau, A., Coste, F., Humily, F., Garczarek, L., Le Corguillé, G., Six, C., Ratin, M., Collin, O., Schluchter, W.M., and Partensky, F. (2013). CyanoLyase: a database of phycobilin lyase sequences, motifs and functions. Nucleic Acids Res 41, D396-401.
Breton S, Jouhet J, Guyet U, Gros V, Pittera J, Demory D, Partensky F, Doré H, Ratin M, Maréchal E, Nguyen NA, Garczarek L, Six C. 2019. Unveiling membrane thermoregulation strategies in marine picocyanobacterial. New Phytol. doi: 10.1111/nph.1
Caputi, L., [..], Garczarek L., d'Ortenzio F., Testor P., Not F., Ribera d'Alcala, M., Wincker P., Bowler C., Iudicone D. 2019 Community-level response to natural perturbations in open ocean planktonic ecosystems. Global Biogeochemical Cycles doi: 10.1029/2018GB006022 .
Carrigee L.A., Frick J.P., Karty J.A., Garczarek L., Partensky F. & Schluchter W.M. MpeV is the lyase isomerase for the doubly-linked phycourobilin on the β-subunit of phycoerythrin I & II in marine Synechococcus. Journal of Biological Chemistry 296: 100031.
Doré H., Guyet U., Leconte J., Farrant G.K., Alric B., Ratin M., Ostrowski M., Ferrieux M., Brillet-Guéguen L., Hoebeke M., Siltanen J., Le Corguillé G., Corre E., Wincker P., Scanlan D.J., Eveillard D., Partensky F., Garczarek L. Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies. ISME Journal 17:720-732
Dufresne, A., Ostrowski, M., Scanlan, D.J., Garczarek, L., Mazard, S., Palenik, B.P., Paulsen, I.T., De Marsac, N.T., Wincker, P., Dossat, C., Ferriera, S., Johnson, J., Post, A.F., Hess, W.R., and Partensky, F. (2008). Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Genome Biol 9, R90.
Farrant, GK, Hoebeke, M., Partensky, F., Andres, G. and Garczarek, L. 2011. WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data. BMC Bioinformatics 16:281
Garczarek, L., Dufresne, A., Blot, N., Cockshutt, A.M., Peyrat, A., Campbell, D.A., Joubin, L., and Six, C. (2008). Function and evolutionof the psbA gene family in marine Synechococcus: Synechococcus sp. WH7803 as a case study. ISME J 2, 937-953.
Garczarek, L., Dufresne, A., Rousvoal, S., West, N.J., Mazard, S., Marie, D., Claustre, H., Raimbault, P., Post, A.F., Scanlan, D.J., andPartensky, F. (2007). High vertical and low horizontal diversity of Prochlorococcus ecotypes in the Mediterranean Sea in summer. FEMS Microbiol Ecol 60, 189-206.
Garczarek L., Guyet U., Doré H., Farrant G.K., Hoebeke M., Brillet-Guéguen L., Bisch A., Ferrieux M., Siltanen J., Corre E., Le Corguillé G., Ratin M., Pitt F.D., Ostrowski M., Conan M., Siegel A., Labadie K., Aury J.-M., Wincker P., Scanlan D.J. & F. Partensky (2021). Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. Nucleic Acids Research Volume 49, Issue D1: https://doi.org/10.1093/nar/gkaa958
Grébert T., Doré H., Partensky F., Farrant G.K., Boss E., Picheral M., Acinas S., Kehoe D.J. and Garczarek L. 2018. Light color acclimation:a key process in the global ocean distribution of Synechococcus cyanobacteria. Proc Natl Acad Sci USA 115: E2010-E2019
Grébert T., Garczarek L., Daubin V., Humily F., Marie D., Ratin M., Devailly A., Farrant G.K., Mary I., Mella-Flores D., Tanguy G., Labadie K., Wincker P., Kehoe D.M. & Partensky F. Diversity and evolution of pigment types in marine Synechococcus cyanobacteria. Genome Biology and Evolution 111: evac035
Haney A.M., Sanfilippo J.E., Garczarek L., Partensky F. & Kehoe D.M. Multiple photolyases protect the marine cyanobacterium Synechococcus from ultraviolet radiation. MBio 13(4): e01511-22. https://doi.org/10.1128/mbio.01511-22
Holtzendorff, J., Partensky, F., Mella, D., Lennon, J.F., Hess, W.R., and Garczarek, L. (2008). Genome streamlining results in loss ofrobustness of the circadian clock in the marine cyanobacterium Prochlorococcus marinus PCC 9511. J Biol Rhythms 23, 187-199.
Humily F., Farrant, G.K., Marie D., Partensky F., Mazard S., [..], Scanlan D.J. and Garczarek L. 2014. Development of a targeted metagenomic approachto study a genomic region involved in light harvesting in marine Synechococcus. FEMS Microbiol. Ecol., 88 231-249.
Humily F. Partensky F., Six C., Farrant, G.K., Ratin M., Marie D., and Garczarek L. 2013. A gene island with two possible configurations is involved in chromatic acclimation in marine Synechococcus. PLOS One, vol 8, issue 12, e84459 .
Kolowrat, C., Partensky, F., Mella-Flores, D., Le Corguillé, G., Boutte, C., Blot, N., Ratin, M., Ferreol, M., Lecomte, X., Gourvil, P., Lennon, J.F., Kehoe, D.M., and Garczarek, L. (2010). Ultraviolet stress delays chromosome replication in light/dark synchronized cells of the marine cyanobacterium Prochlorococcus marinus PCC9511. BMC Microbiol 10, 204.
Mahmoud RM., Sanfilippo J.E, Nguyen A.A., Strnat J.A., Partensky F., Garczarek L., El-Kassem N.A. Kehoea D.M. and Schluchter W. M. 2017. Adaptation to blue light in marine Synechococcus requires MpeU, an enzyme with similarity to phycoerythrobilin lyase isomerases. Frontiers in Microbiology (section Microbial Physiology and Metabolism) 8:243. doi: 10.3389/fmicb.2017.00243.
Mazard, S., Ostrowski, M., Partensky, F., and Scanlan, D.J. (2012). Multi-locus sequence analysis, taxonomic resolution and biogeography of marine Synechococcus. Environ Microbiol 14, 372-386.
Mella-Flores, D., Mazard, S., Humily, F., Partensky, F., Mahé, F., Bariat, L., Courties, C., Marie, D., Ras, J., Mauriac, R., Jeanthon, C., Bendif, E.M., Ostrowski, M., Scanlan, D.J., and Garczarek, L.(2011). Is the distribution of Prochlorococcus and Synechococcus ecotypes in the Mediterranean Sea affected by global warming? Biogeosciences 8, 2785-2804
Mella-Flores, D., Six, C., Ratin, M., Partensky, F., Boutte, C., Le Corguillé, G., Marie, D., Blot, N., Gourvil, P., Kolowrat, C., and Garczarek, L. (2012). Prochlorococcus and Synechococcus have Evolved Different Adaptive Mechanisms to Cope with Light and UV Stress. Front Microbiol 3, 285.
Partensky, F., and Garczarek, L. (2010). Prochlorococcus: advantages and limits of minimalism. Ann Rev Mar Sci 2, 305-331.
Partensky F., Mella-Flores D., Six C., Garczarek L., Czjzek M., Kotabova E., Felcmanova K., and Prasil O. 2018. Comparison of photosynthetic performances of marine picocyanobacteria with different configurations of the oxygen-evolving complex. Photosynth Res. 2018 Jun 25. doi: 10.1007/s11120-018-0539-3.
Pittera J., Jouhet J., Breton S., Garczarek L., Partensky F., Maréchal E., Nguyen N.A, Doré H., Ratin M. Pitt F.D., Scanlan D.J. and Six C. 2018. Thermoacclimation and genome adaptation of the membrane lipidome in marine Synechococcus. Environ Microbiol. doi: 10.1111/1462-2920.13985
Sanfilippo JE, Nguyen AA, Garczarek L, Karty JA, Pokhrel S, Strnat JA, Partensky F, Schluchter WM, and Kehoe DM. 2019. Interplay between differentially expressed enzymes contributes to light color acclimation in marine Synechococcus. Proc Natl Acad Sci USA 116 (13) 6457-6462.
Sanfilippo JE, Nguyen AA, Karty JA, Shukla A, Schluchter WM, Garczarek L, Partensky F, Kehoe DM. 2016. A self-regulating genomic island encoding tandem regulators confers chromatic acclimation to marine Synechococcus. Proc Natl Acad Sci USA 113(21):6077-82.
Scanlan, D.J., Ostrowski, M., Mazard, S., Dufresne, A., Garczarek, L., Hess, W.R., Post, A.F., Hagemann, M., Paulsen, I., and Partensky, F. (2009). Ecological genomics of marine picocyanobacteria. Microbiol Mol Biol Rev 73, 249-299.
Six, C., Thomas, J.C., Garczarek, L., Ostrowski, M., Dufresne, A., Blot, N., Scanlan, D.J., and Partensky, F. (2007). Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study. Genome Biol 8, R259
Villar E., Farrant G.K., Follows M., Garczarek L., et al. 2015. Environmental characteristics of Agulhas rings affect interocean plankton transport. Science 348: 6237 p1261447-1 .
Zwirglmaier, K., Jardillier, L., Ostrowski, M., Mazard, S., Garczarek, L., Vaulot, D., Not, F., Massana, R., Ulloa, O., and Scanlan, D.J.(2008). Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes. Environ Microbiol 10, 147-161.