P. Johnson and J. Sieburth, Chroococcoid cyanobacteria in the sea: A ubiquitous and diverse phototrophic biomass1, Limnology and Oceanography, vol.24, issue.5, pp.928-935, 1979.
DOI : 10.4319/lo.1979.24.5.0928

J. Waterbury, S. Watson, R. Guillard, and L. Brand, Widespread occurrence of a unicellular, marine, planktonic, cyanobacterium, Nature, vol.35, issue.5694, pp.293-294, 1979.
DOI : 10.1146/annurev.mi.31.100177.001301

R. Gradinger and J. Lenz, Seasonal occurrence of picocyanobacteria in the Greenland Sea and central Arctic Ocean, Polar Biology, vol.15, issue.6, pp.447-452, 1995.
DOI : 10.1007/BF00239722

F. Partensky, J. Blanchot, F. Lantoine, J. Neveux, and M. D. , Vertical structure of picophytoplankton at different trophic sites of the tropical northeastern Atlantic Ocean. Deep-Sea Res I, pp.1191-1213, 1996.

M. Zubkov, M. Sleigh, G. Tarran, P. Burkill, and R. Leakey, Picoplanktonic community structure on an Atlantic transect from 50 degrees N to 50 degrees S. Deep-Sea Res I, pp.1339-1355, 1998.

J. Waterbury, S. Watson, F. Valois, and D. Franks, Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus, Can Bull Fish Aquat Sci, vol.472, pp.71-120, 1986.

R. Olson, E. Zettler, E. Armbrust, and S. Chisholm, Pigments, size, and distributions of Synechococcus in the North Atlantic and Pacific Oceans, Limnology and Oceanography, vol.35, issue.1, pp.45-58, 1990.
DOI : 10.4319/lo.1990.35.1.0045

F. Partensky, J. Blanchot, D. Vaulot, L. Charpy, and L. A. Monaco, Differential distribution and ecology of Prochlorococcus and Synechococcus in oceanic waters: a review, Marine Cyanobacteria, pp.457-475

D. Scanlan and N. West, Molecular ecology of the marine cyanobacterial genera Prochlorococcus and Synechococcus, FEMS Microbiology Ecology, vol.40, issue.1, pp.1-12, 2002.
DOI : 10.1111/j.1574-6941.2002.tb00930.x

D. Scanlan, Physiological diversity and niche adaptation in marine Synechococcus, Adv Microb Physiol, vol.47, pp.1-64, 2003.
DOI : 10.1016/S0065-2911(03)47001-X

A. Glazer, R. Williams, S. Yeh, and J. Clark, Kinetics of Energy Flow in the Phycobilisome Core, Science, vol.230, issue.4729, pp.1051-1053, 1985.
DOI : 10.1126/science.230.4729.1051

A. Glazer, Light guides -directional energy transfer in a photosynthetic antenna, J Biol Chem, vol.264, pp.1-4, 1989.

A. Grossman, M. Schaefer, G. Chiang, and J. Collier, The Responses of Cyanobacteria to Environmental Conditions: Light and Nutrients, The Molecular Biology of Cyanobacteria Edited by, pp.677-692
DOI : 10.1007/978-94-011-0227-8_21

R. Maccoll and . Cyanobacterial-phycobilisomes, Cyanobacterial Phycobilisomes, Journal of Structural Biology, vol.124, issue.2-3, pp.311-334, 1998.
DOI : 10.1006/jsbi.1998.4062

W. Sidler, Phycobilisome and phycobiliprotein structure In The Molecular Biology of Cyanobacteria Edited by, pp.139-216

L. Ong and A. Glazer, R-phycocyanin II, a new phycocyanin occurring in marine Synechococcus species, J Biol Chem, vol.262, pp.6323-6327, 1987.

L. Ong and A. Glazer, Structural studies of phycobiliproteins in unicellular marine cyanobacteria In Light-energy Transduction in Photosynthesis: Higher Plant and Bacterial Models Edited by, pp.102-121

L. Ong and A. Glazer, Phycoerythrins of marine unicellular cyanobacteria. I. Bilin types and locations and energy transfer pathways in Synechococcus spp. phycoerythrins, J Biol Chem, vol.266, pp.9515-9527, 1991.

C. Six, J. Thomas, L. Thion, Y. Lemoine, F. Zal et al., Two Novel Phycoerythrin-Associated Linker Proteins in the Marine Cyanobacterium Synechococcus sp. Strain WH8102, Journal of Bacteriology, vol.187, issue.5, pp.1685-1694, 2005.
DOI : 10.1128/JB.187.5.1685-1694.2005

R. Everroad and A. Wood, COMPARATIVE MOLECULAR EVOLUTION OF NEWLY DISCOVERED PICOCYANOBACTERIAL STRAINS REVEALS A PHYLOGENETICALLY INFORMATIVE VARIABLE REGION OF ??-PHYCOERYTHRIN, Journal of Phycology, vol.19, issue.6, pp.1300-1311, 2006.
DOI : 10.1111/j.1529-8817.2006.00282.x

S. Wilbanks and A. Glazer, Rod structure of a phycoerythrin IIcontaining phycobilisome. II. Complete sequence and bilin attachment site of a phycoerythrin ? subunit, J Biol Chem, vol.268, pp.1236-1241, 1993.

E. Urbach, D. Scanlan, D. Distel, J. Waterbury, and S. Chisholm, Rapid Diversification of Marine Picophytoplankton with Dissimilar Light-Harvesting Structures Inferred from Sequences of Prochlorococcus and Synechococcus (Cyanobacteria), Journal of Molecular Evolution, vol.46, issue.2, pp.188-201, 1998.
DOI : 10.1007/PL00006294

N. Fuller, D. Marie, F. Partensky, D. Vaulot, A. Post et al., Clade-Specific 16S Ribosomal DNA Oligonucleotides Reveal the Predominance of a Single Marine Synechococcus Clade throughout a Stratified Water Column in the Red Sea, Applied and Environmental Microbiology, vol.69, issue.5, pp.2430-2443, 2003.
DOI : 10.1128/AEM.69.5.2430-2443.2003

N. Ahlgren and G. Rocap, Culture Isolation and Culture-Independent Clone Libraries Reveal New Marine Synechococcus Ecotypes with Distinctive Light and N Physiologies, Applied and Environmental Microbiology, vol.72, issue.11, pp.7193-7204, 2006.
DOI : 10.1128/AEM.00358-06

F. Chen, K. Wang, J. Kan, M. Suzuki, and K. Wommack, Diverse and Unique Picocyanobacteria in Chesapeake Bay, Revealed by 16S-23S rRNA Internal Transcribed Spacer Sequences, Applied and Environmental Microbiology, vol.72, issue.3, pp.2239-2243, 2006.
DOI : 10.1128/AEM.72.3.2239-2243.2006

M. Herdman, R. Castenholz, J. Waterbury, and R. Rippka, Form-genus XIII. Synechococcus. In Bergey's Manual of Systematic Bacteriology, pp.508-512, 2001.

J. Waterbury, R. Rippka, and . Rippka, Order Chroococcales Wettstein Emend In Bergey's Manual of Systematic Bacteriology Edited by, pp.1728-1746, 1979.

G. Toledo, B. Palenik, and B. Brahamsha, Swimming marine Synechococcus strains with widely different photosynthetic pigment ratios form a monophyletic group, Appl Environ Microbiol, vol.65, pp.5247-5251, 1999.

S. Penno, D. Lindell, and A. Post, Diversity of Synechococcus and Prochlorococcus populations determined from DNA sequences of the N-regulatory gene ntcA, Environmental Microbiology, vol.230, issue.7, pp.1200-1211, 2006.
DOI : 10.1046/j.1462-2920.2003.00403.x

A. Wood, D. Phinney, and C. Yentsch, Water column transparency and the distribution of spectrally distinct forms of phycoerythrin-containing organisms, Marine Ecology Progress Series, vol.162, pp.25-31, 1998.
DOI : 10.3354/meps162025

A. Wood, M. Lipsen, and P. Coble, Fluorescence-based characterization of phycoerythrin-containing cyanobacterial communities in the Arabian Sea during the Northeast and early Southwest Monsoon Deep-Sea Res II, pp.1769-1790, 1994.

C. Six, J. Thomas, B. Brahamsha, Y. Lemoine, and F. Partensky, Photophysiology of the marine cyanobacterium Synechococcus sp. WH8102, a new model organism, Aquatic Microbial Ecology, vol.35, pp.17-29, 2004.
DOI : 10.3354/ame035017

B. Palenik, Chromatic Adaptation in Marine Synechococcus Strains, Applied and Environmental Microbiology, vol.67, issue.2, pp.991-994, 2001.
DOI : 10.1128/AEM.67.2.991-994.2001

C. Everroad, C. Six, F. Partensky, J. Thomas, J. Holtzendorff et al., Biochemical Bases of Type IV Chromatic Adaptation in Marine Synechococcus spp., Journal of Bacteriology, vol.188, issue.9, pp.3345-3356, 2006.
DOI : 10.1128/JB.188.9.3345-3356.2006

H. Jones, M. Ostrowski, and D. Scanlan, A Suppression Subtractive Hybridization Approach Reveals Niche-Specific Genes That May Be Involved in Predator Avoidance in Marine Synechococcus Isolates, Applied and Environmental Microbiology, vol.72, issue.4, pp.2730-2737, 2006.
DOI : 10.1128/AEM.72.4.2730-2737.2006

R. Alberte, A. Wood, T. Kursar, and R. Guillard, Novel Phycoerythrins in Marine Synechococcus spp. : Characterization and Evolutionary and Ecological Implications, PLANT PHYSIOLOGY, vol.75, issue.3, pp.732-739, 1984.
DOI : 10.1104/pp.75.3.732

S. Wilbanks and A. Glazer, Rod structure of a phycoerythrin IIcontaining phycobilisome. I. Organization and sequence of the gene cluster encoding the major phycobiliprotein rod components in the genome of marine Synechococcus sp. WH8020, J Biol Chem, vol.268, pp.1226-1235, 1993.

N. Frankenberg, K. Mukougawa, T. Kohchi, and J. Lagarias, Functional Genomic Analysis of the HY2 Family of Ferredoxin-Dependent Bilin Reductases from Oxygenic Photosynthetic Organisms, THE PLANT CELL ONLINE, vol.13, issue.4, pp.965-978, 2001.
DOI : 10.1105/tpc.13.4.965

J. Cobley, A. Clark, S. Weerasurya, F. Queseda, J. Xiao et al., CpeR is an activator required for expression of the phycoerythrin operon (cpeBA) in the cyanobacterium Fremyella diplosiphon and is encoded in the phycoerythrin linker-polypeptide operon (cpeCDESTR), Molecular Microbiology, vol.9, issue.1, pp.1517-1531, 2002.
DOI : 10.1046/j.1365-2958.2002.02966.x

B. Montgomery, E. Casey, A. Grossman, and D. Kehoe, AplA, a Member of a New Class of Phycobiliproteins Lacking a Traditional Role in Photosynthetic Light Harvesting, Journal of Bacteriology, vol.186, issue.21, pp.7420-7428, 2004.
DOI : 10.1128/JB.186.21.7420-7428.2004

V. Capuano, A. Braux, N. Tandeau-de-marsac, and J. Houmard, The "anchor polypeptide" of cyanobacterial phycobilisomes. Molecular characterization of the Synechococcus sp. PCC 6301 apcE gene, J Biol Chem, vol.266, pp.7239-7247, 1991.

C. Fairchild, J. Zhao, J. Zhou, S. Colson, D. Bryant et al., Phycocyanin alpha-subunit phycocyanobilin lyase., Proceedings of the National Academy of Sciences, vol.89, issue.15, pp.7017-7021, 1992.
DOI : 10.1073/pnas.89.15.7017

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC49636

C. Fairchild and A. Glazer, Oligomeric structure, enzyme kinetics , and substrate specificity of the phycocyanin alpha subunit phycocyanobilin lyase, J Biol Chem, vol.269, pp.8686-8694, 1994.

R. Bhalerao, L. Lind, and P. Gustafsson, Cloning of the cpcE and cpcF genes from Synechococcus sp. PCC 6301 and their inactivation in Synechococcus sp. PCC 7942, Plant Molecular Biology, vol.267, issue.1, pp.313-326, 1994.
DOI : 10.1007/BF00039542

R. Swanson, J. Zhou, J. Leary, T. Williams, R. De-lorimier et al., Characterization of phycocyanin produced by cpcE and cpcF mutants and identification of an intergenic suppressor of the defect in bilin attachment, J Biol Chem, vol.267, pp.16146-16154, 1992.

K. Zhao, D. Wu, L. Zhang, M. Zhou, S. Bohm et al., Chromophore attachment in phycocyanin. Functional amino acids of phycocyanobilin -alpha-phycocyanin lyase and evidence for chromophore binding, FEBS Journal, vol.702, issue.6, pp.1262-1274, 2006.
DOI : 10.1006/abio.1976.9999

K. Zhao, M. Deng, M. Zheng, M. Zhou, A. Parbel et al., Novel activity of a phycobiliprotein lyase: both the attachment of phycocyanobilin and the isomerization to phycoviolobilin are catalyzed by the proteins PecE and PecF encoded by the phycoerythrocyanin operon, FEBS Letters, vol.286, issue.1, pp.9-13, 2000.
DOI : 10.1016/S0014-5793(00)01245-X

K. Zhao, S. Ping, S. Bohm, S. Bo, Z. Ming et al., Reconstitution of phycobilisome core???membrane linker, LCM, by autocatalytic chromophore binding to ApcE, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1706, issue.1-2, pp.81-87, 2005.
DOI : 10.1016/j.bbabio.2004.09.008

G. Shen, N. Saunée, S. Williams, E. Gallo, W. Schluchter et al., Identification and Characterization of a New Class of Bilin Lyase: THE cpcT GENE ENCODES A BILIN LYASE RESPONSIBLE FOR ATTACHMENT OF PHYCOCYANOBILIN TO CYS-153 ON THE beta-SUBUNIT OF PHYCOCYANIN IN SYNECHOCOCCUS SP. PCC 7002, Journal of Biological Chemistry, vol.281, issue.26, pp.17768-17778, 2006.
DOI : 10.1074/jbc.M602563200

K. Zhao, P. Su, J. Li, J. Tu, M. Zhou et al., Chromophore Attachment to Phycobiliprotein beta-Subunits: PHYCOCYANOBILIN:CYSTEINE-beta84 PHYCOBILIPROTEIN LYASE ACTIVITY OF CpeS-LIKE PROTEIN FROM ANABAENA Sp. PCC7120, Journal of Biological Chemistry, vol.281, issue.13, pp.8573-8581, 2006.
DOI : 10.1074/jbc.M513796200

K. Zhao, P. Su, J. Tu, X. Wang, H. Liu et al., Phycobilin:cystein-84 biliprotein lyase, a near-universal lyase for cysteine-84-binding sites in cyanobacterial phycobiliproteins, Proceedings of the National Academy of Sciences, vol.104, issue.36, pp.14300-14305, 2007.
DOI : 10.1073/pnas.0706209104

K. Kahn, D. Mazel, J. Houmard, N. Tandeau-de-marsac, and M. Schaefer, A role for cpeYZ in cyanobacterial phycoerythrin biosynthesis., Journal of Bacteriology, vol.179, issue.4, pp.998-1006, 1997.
DOI : 10.1128/jb.179.4.998-1006.1997

M. Jacobson, K. Brigle, L. Bennett, R. Setterquist, M. Wilson et al., Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii., Journal of Bacteriology, vol.171, issue.2, pp.1017-1027, 1989.
DOI : 10.1128/jb.171.2.1017-1027.1989

Y. Hagiwara, M. Sugishima, Y. Takahashi, and K. Fukuyama, Crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IX??, a key enzyme in the biosynthesis of phycocyanobilin, Proceedings of the National Academy of Sciences, vol.103, issue.1, pp.27-32, 2006.
DOI : 10.1073/pnas.0507266103

P. Bickel, K. Kechris, P. Spector, G. Wedemayer, and A. Glazer, Finding important sites in protein sequences, Proceedings of the National Academy of Sciences, vol.99, issue.23, pp.14764-14771, 2002.
DOI : 10.1073/pnas.222508899

D. Kehoe and A. Gutu, Responding to Color: The Regulation of Complementary Chromatic Adaptation, Annual Review of Plant Biology, vol.57, issue.1, pp.127-150, 2006.
DOI : 10.1146/annurev.arplant.57.032905.105215

A. Ducret, S. Muller, K. Goldie, A. Hefti, W. Sidler et al., Reconstitution, characterisation and mass analysis of the pentacylindrical allophycocyanin core complex from the cyanobacterium Anabaena sp. PCC 712011Edited by R. Huber, Journal of Molecular Biology, vol.278, issue.2, pp.369-388, 1998.
DOI : 10.1006/jmbi.1998.1678

K. Elmorjani, J. Thomas, and P. Sebban, Phycobilisomes of wild type and pigment mutants of the cyanobacterium Synechocystis PCC 6803, Archives of Microbiology, vol.257, issue.2, pp.186-191, 1986.
DOI : 10.1007/BF00402349

A. Glazer, Phycobilisome a macromolecular complex optimized for light energy transfer, Biochimica et Biophysica Acta (BBA) - Reviews on Bioenergetics, vol.768, issue.1, pp.29-51, 1984.
DOI : 10.1016/0304-4173(84)90006-5

N. Federspiel and A. Grossman, Characterization of the light-regulated operon encoding the phycoerythrin-associated linker proteins from the cyanobacterium Fremyella diplosiphon., Journal of Bacteriology, vol.172, issue.7, pp.4072-4081, 1990.
DOI : 10.1128/jb.172.7.4072-4081.1990

T. Haverkamp, S. Acinas, M. Doeleman, M. Stomp, J. Huisman et al., Diversity and phylogeny of Baltic Sea picocyanobacteria inferred from their ITS and phycobiliprotein operons, Environmental Microbiology, vol.162, issue.0, 2007.
DOI : 10.1111/j.1574-6941.2006.00060.x

K. Apt, J. Collier, and A. Grossman, Evolution of the Phycobiliproteins, Journal of Molecular Biology, vol.248, issue.1, pp.79-96, 1995.
DOI : 10.1006/jmbi.1995.0203

D. Lindell, M. Sullivan, Z. Johnson, A. Tolonen, F. Rohwer et al., Transfer of photosynthesis genes to and from Prochlorococcus viruses, Proceedings of the National Academy of Sciences, vol.101, issue.30, pp.11013-11018, 2004.
DOI : 10.1073/pnas.0401526101

N. Mann, M. Clokie, A. Millard, A. Cook, W. Wilson et al., The Genome of S-PM2, a "Photosynthetic" T4-Type Bacteriophage That Infects Marine Synechococcus Strains, Journal of Bacteriology, vol.187, issue.9, pp.3188-3200, 2005.
DOI : 10.1128/JB.187.9.3188-3200.2005

M. Clokie and N. Mann, Marine cyanophages and light, Environmental Microbiology, vol.179, issue.12, pp.2074-2082, 2006.
DOI : 10.1111/j.1462-2920.2005.00833.x

M. Sullivan, M. Coleman, P. Weigele, F. Rohwer, and S. Chisholm, Three Prochlorococcus Cyanophage Genomes: Signature Features and Ecological Interpretations, PLoS Biology, vol.183, issue.5, pp.790-806, 2005.
DOI : 10.1371/journal.pbio.0030144.sg006

URL : http://doi.org/10.1371/journal.pbio.0030144

R. Rippka, T. Coursin, W. Hess, C. Lichtlé, D. Scanlan et al., Prochlorococcus marinus Chisholm et al. 1992 subsp. pastoris subsp. nov. strain PCC 9511, the first axenic chlorophyll a2/b2-containing cyanobacterium (Oxyphotobacteria)., International Journal of Systematic and Evolutionary Microbiology, vol.50, issue.5, pp.1833-1847, 2000.
DOI : 10.1099/00207713-50-5-1833

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

A. Enright, S. Van-dongen, and C. Ouzounis, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research, vol.30, issue.7, pp.1575-1584, 2002.
DOI : 10.1093/nar/30.7.1575

J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

S. Gadagkar, M. Rosenberg, and S. Kumar, Inferring species phylogenies from multiple genes: Concatenated sequence tree versus consensus gene tree, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol.42, issue.1, pp.64-74, 2005.
DOI : 10.1002/jez.b.21026

N. Galtier, M. Gouy, and C. Gautier, SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny, Bioinformatics, vol.12, issue.6, pp.543-548, 1996.
DOI : 10.1093/bioinformatics/12.6.543

URL : https://hal.archives-ouvertes.fr/hal-00435028

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

S. Kumar, K. Tamura, and M. Nei, MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment, Briefings in Bioinformatics, vol.5, issue.2, pp.150-163, 2004.
DOI : 10.1093/bib/5.2.150

M. Berlyn, Linkage map of Escherichia coli K-12, edition 10: the traditional map, Microbiol Mol Biol Rev, vol.62, pp.814-984, 1998.