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1. Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

Author

Doré, Hugo, Guyet, Ulysse, Leconte, Jade, Farrant, Gregory K., Alric, Benjamin, Ratin, Morgane, Ostrowski, Martin, Ferrieux, Mathilde, Brillet-Guéguen, Loraine, Hoebeke, Mark, Siltanen, Jukka, Le Corguillé, Gildas, Corre, Erwan, Wincker, Patrick, Scanlan, David J., Eveillard, Damien, Partensky, Frédéric, and Garczarek, Laurence

Published
2023
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5. Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts

Author

Doré, Hugo, primary, Leconte, Jade, additional, Guyet, Ulysse, additional, Breton, Solène, additional, Farrant, Gregory K., additional, Demory, David, additional, Ratin, Morgane, additional, Hoebeke, Mark, additional, Corre, Erwan, additional, Pitt, Frances D., additional, Ostrowski, Martin, additional, Scanlan, David J., additional, Partensky, Frédéric, additional, Six, Christophe, additional, and Garczarek, Laurence, additional

Published
2022
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6. Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

Author

Doré, Hugo, primary, Guyet, Ulysse, additional, Leconte, Jade, additional, Farrant, Gregory K., additional, Alric, Benjamin, additional, Ratin, Morgane, additional, Ostrowski, Martin, additional, Ferrieux, Mathilde, additional, Brillet-Guéguen, Loraine, additional, Hoebeke, Mark, additional, Siltanen, Jukka, additional, Corguillé, Gildas Le, additional, Corre, Erwan, additional, Wincker, Patrick, additional, Scanlan, David J., additional, Eveillard, Damien, additional, Partensky, Frédéric, additional, and Garczarek, Laurence, additional

Published
2022
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7. Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria

Author

Grébert, Théophile, primary, Garczarek, Laurence, additional, Daubin, Vincent, additional, Humily, Florian, additional, Marie, Dominique, additional, Ratin, Morgane, additional, Devailly, Alban, additional, Farrant, Gregory K, additional, Mary, Isabelle, additional, Mella-Flores, Daniella, additional, Tanguy, Gwenn, additional, Labadie, Karine, additional, Wincker, Patrick, additional, Kehoe, David M, additional, and Partensky, Frédéric, additional

Published
2022
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8. Global phylogeography of marine Synechococcus in coastal areas reveals strikingly different communities than in the open ocean

Author

Doré, Hugo, primary, Leconte, Jade, additional, Guyet, Ulysse, additional, Breton, Solène, additional, Farrant, Gregory K., additional, Demory, David, additional, Ratin, Morgane, additional, Hoebeke, Mark, additional, Corre, Erwan, additional, Pitt, Frances D., additional, Ostrowski, Martin, additional, Scanlan, David J., additional, Partensky, Frédéric, additional, Six, Christophe, additional, and Garczarek, Laurence, additional

Published
2022
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10. Diversity and evolution of pigment types and the phycobilisome rod gene region of marine Synechococcus cyanobacteria

Author

Grébert, Théophile, primary, Garczarek, Laurence, additional, Daubin, Vincent, additional, Humily, Florian, additional, Marie, Dominique, additional, Ratin, Morgane, additional, Devailly, Alban, additional, Farrant, Gregory K., additional, Mary, Isabelle, additional, Mella-Flores, Daniella, additional, Tanguy, Gwen, additional, Labadie, Karine, additional, Wincker, Patrick, additional, Kehoe, David M., additional, and Partensky, Frédéric, additional

Published
2021
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11. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Author

Doré, Hugo, Farrant, Gregory K., Guyet, Ulysse, Haguait, Julie, Humily, Florian, Ratin, Morgane, Pitt, Frances Diana, Ostrowski, Martin, Six, Christophe, Brillet-Guéguen, Loraine, Hoebeke, Mark, Bisch, Antoine, Le Corguillé, Gildas, Corre, Erwan, Labadie, Karine, Aury, Jean-Marc, Wincker, Patrick, Choi, Dong Han, Noh, Jae Hoon, Eveillard, Damien, Scanlan, David J., Partensky, Frédéric, Garczarek, Laurence, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Combinatoire et Bioinformatique (COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Combinatoire et Bioinformatique (LS2N - équipe COMBI), ANR-13-ADAP-0010,SAMOSA,Synechococcus as a model genus for studying adaptation of marine phytoplankton to environmental changes(2013), ANR-17-CE02-0014,CINNAMON,Analyse multi-échelle de l'adaptation à la carence en Fer chez un organisme clé du phytoplancton marin, dans un contexte de changement global(2017), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), and Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Marine cyanobacteria 1, amino-acid substitutions 6, amino-acid substitutions, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], comparative genomics, Microbiology, genomic islands, QH301, comparative genomics 4, evolution, QH426, 0502 Environmental Science and Management, 0503 Soil Sciences, 0605 Microbiology, ComputingMilieux_MISCELLANEOUS, Synechococcus 3, Original Research, Prochlorococcus, niche adaptation, Synechococcus, marine cyanobacteria, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], QR, niche adaptation 5, evolution 8, Prochlorococcus2, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], genomic islands 7, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton.

Published
2020
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12. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Author

Garczarek, Laurence, primary, Guyet, Ulysse, additional, Doré, Hugo, additional, Farrant, Gregory K, additional, Hoebeke, Mark, additional, Brillet-Guéguen, Loraine, additional, Bisch, Antoine, additional, Ferrieux, Mathilde, additional, Siltanen, Jukka, additional, Corre, Erwan, additional, Le Corguillé, Gildas, additional, Ratin, Morgane, additional, Pitt, Frances D, additional, Ostrowski, Martin, additional, Conan, Maël, additional, Siegel, Anne, additional, Labadie, Karine, additional, Aury, Jean-Marc, additional, Wincker, Patrick, additional, Scanlan, David J, additional, and Partensky, Frédéric, additional

Published
2020
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13. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author

Villar, Emilie, Farrant, Gregory K, Follows, Michael, Garczarek, Laurence, Speich, Sabrina, Audic, Stéphane, Bittner, Lucie, Blanke, Bruno, Brum, Jennifer R, Brunet, Christophe, Casotti, Raffaella, Chase, Alison, Dolan, John R, d'Ortenzio, Fabrizio, Gattuso, Jean-Pierre, Grima, Nicolas, Guidi, Lionel, Hill, Christopher N, Jahn, Oliver, Jamet, Jean-Louis, Le Goff, Hervé, Lepoivre, Cyrille, Malviya, Shruti, Pelletier, Eric, Romagnan, Jean-Baptiste, Roux, Simon, Santini, Sébastien, Scalco, Eleonora, Schwenck, Sarah M, Tanaka, Atsuko, Testor, Pierre, Vannier, Thomas, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans coordinators, Acinas, Silvia G, Bork, Peer, Boss, Emmanuel, de Vargas, Colomban, Gorsky, Gabriel, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, Bowler, Chris, Not, Fabrice, Hingamp, Pascal, and Iudicone, Daniele

Subjects
fungi
Abstract

Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic., プランクトンの世界 : 新しいフロンティア -タラ海洋探査からの最新情報-. 京都大学プレスリリース. 2015-05-22.

Published
2015

14. WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data

Author

Farrant, Gregory K., Hoebeke, Mark, Partensky, Frédéric, Andres, Gwendoline, Corre, Erwan, Garczarek, Laurence, MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), and Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP)

Subjects
Synechococcus, Marine Synechococcus, Genome, Genome assembly, Methodology Article, Genome scaffolding, Chromosome Mapping, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Genome finishing, Biochemistry, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Next-generation sequencing, Humans, Molecular Biology
Abstract

Background The sequencing depth provided by high-throughput sequencing technologies has allowed a rise in the number of de novo sequenced genomes that could potentially be closed without further sequencing. However, genome scaffolding and closure require costly human supervision that often results in genomes being published as drafts. A number of automatic scaffolders were recently released, which improved the global quality of genomes published in the last few years. Yet, none of them reach the efficiency of manual scaffolding. Results Here, we present an innovative semi-automatic scaffolder that additionally helps with chimerae resolution and generates valuable contig maps and outputs for manual improvement of the automatic scaffolding. This software was tested on the newly sequenced marine cyanobacterium Synechococcus sp. WH8103 as well as two reference datasets used in previous studies, Rhodobacter sphaeroides and Homo sapiens chromosome 14 (http://gage.cbcb.umd.edu/). The quality of resulting scaffolds was compared to that of three other stand-alone scaffolders: SSPACE, SOPRA and SCARPA. For all three model organisms, WiseScaffolder produced better results than other scaffolders in terms of contiguity statistics (number of genome fragments, N50, LG50, etc.) and, in the case of WH8103, the reliability of the scaffolds was confirmed by whole genome alignment against a closely related reference genome. We also propose an efficient computer-assisted strategy for manual improvement of the scaffolding, using outputs generated by WiseScaffolder, as well as for genome finishing that in our hands led to the circularization of the WH8103 genome. Conclusion Altogether, WiseScaffolder proved more efficient than three other scaffolders for both prokaryotic and eukaryotic genomes and is thus likely applicable to most genome projects. The scaffolding pipeline described here should be of particular interest to biologists wishing to take advantage of the high added value of complete genomes. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0705-y) contains supplementary material, which is available to authorized users.

Published
2015
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15. Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria

Author

European Commission, Natural Environment Research Council (UK), France Génomique, Agence Nationale de la Recherche (France), Farrant, Gregory K., Cornejo-Castillo, Francisco M., Acinas, Silvia G., Garczarek, Laurence, European Commission, Natural Environment Research Council (UK), France Génomique, Agence Nationale de la Recherche (France), Farrant, Gregory K., Cornejo-Castillo, Francisco M., Acinas, Silvia G., and Garczarek, Laurence

Abstract

Prochlorococcus and Synechococcus are the two most abundant and widespread phytoplankton in the global ocean. To better understand the factors controlling their biogeography, a reference database of the high-resolution taxonomic marker petB, encoding cytochrome b6, was used to recruit reads out of 109 metagenomes from the Tara Oceans expedition. An unsuspected novel genetic diversity was unveiled within both genera, even for the most abundant and well-characterized clades, and 136 divergent petB sequences were successfully assembled from metagenomic reads, significantly enriching the reference database. We then defined Ecologically Significant Taxonomic Units (ESTUs)—that is, organisms belonging to the same clade and occupying a common oceanic niche. Three major ESTU assemblages were identified along the cruise transect for Prochlorococcus and eight for Synechococcus. Although Prochlorococcus HLIIIA and HLIVA ESTUs codominated in iron-depleted areas of the Pacific Ocean, CRD1 and the yet-to-be cultured EnvB were the prevalent Synechococcus clades in this area, with three different CRD1 and EnvB ESTUs occupying distinct ecological niches with regard to iron availability and temperature. Sharp community shifts were also observed over short geographic distances—for example, around the Marquesas Islands or between southern Indian and Atlantic Oceans—pointing to a tight correlation between ESTU assemblages and specific physico-chemical parameters. Together, this study demonstrates that there is a previously overlooked, ecologically meaningful, fine-scale diversity within some currently defined picocyanobacterial ecotypes, bringing novel insights into the ecology, diversity, and biology of the two most abundant phototrophs on Earth

Published
2016

16. Environmental characteristics of Agulhas rings affect interocean plankton transport.

Author

70291432, Villar, Emilie, Farrant, Gregory K, Follows, Michael, Garczarek, Laurence, Speich, Sabrina, Audic, Stéphane, Bittner, Lucie, Blanke, Bruno, Brum, Jennifer R, Brunet, Christophe, Casotti, Raffaella, Chase, Alison, Dolan, John R, d'Ortenzio, Fabrizio, Gattuso, Jean-Pierre, Grima, Nicolas, Guidi, Lionel, Hill, Christopher N, Jahn, Oliver, Jamet, Jean-Louis, Le Goff, Hervé, Lepoivre, Cyrille, Malviya, Shruti, Pelletier, Eric, Romagnan, Jean-Baptiste, Roux, Simon, Santini, Sébastien, Scalco, Eleonora, Schwenck, Sarah M, Tanaka, Atsuko, Testor, Pierre, Vannier, Thomas, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans coordinators, Acinas, Silvia G, Bork, Peer, Boss, Emmanuel, de Vargas, Colomban, Gorsky, Gabriel, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, Bowler, Chris, Not, Fabrice, Hingamp, Pascal, Iudicone, Daniele, 70291432, Villar, Emilie, Farrant, Gregory K, Follows, Michael, Garczarek, Laurence, Speich, Sabrina, Audic, Stéphane, Bittner, Lucie, Blanke, Bruno, Brum, Jennifer R, Brunet, Christophe, Casotti, Raffaella, Chase, Alison, Dolan, John R, d'Ortenzio, Fabrizio, Gattuso, Jean-Pierre, Grima, Nicolas, Guidi, Lionel, Hill, Christopher N, Jahn, Oliver, Jamet, Jean-Louis, Le Goff, Hervé, Lepoivre, Cyrille, Malviya, Shruti, Pelletier, Eric, Romagnan, Jean-Baptiste, Roux, Simon, Santini, Sébastien, Scalco, Eleonora, Schwenck, Sarah M, Tanaka, Atsuko, Testor, Pierre, Vannier, Thomas, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans coordinators, Acinas, Silvia G, Bork, Peer, Boss, Emmanuel, de Vargas, Colomban, Gorsky, Gabriel, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, Bowler, Chris, Not, Fabrice, Hingamp, Pascal, and Iudicone, Daniele

Abstract

Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.

Published
2015

17. Correction: Corrigendum: Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

Author

Veluchamy, Alaguraj, primary, Lin, Xin, additional, Maumus, Florian, additional, Rivarola, Maximo, additional, Bhavsar, Jaysheel, additional, Creasy, Todd, additional, O’Brien, Kimberly, additional, Sengamalay, Naomi A., additional, Tallon, Luke J., additional, Smith, Andrew D., additional, Rayko, Edda, additional, Ahmed, Ikhlak, additional, Crom, Stéphane Le, additional, Farrant, Gregory K., additional, Sgro, Jean-Yves, additional, Olson, Sue A., additional, Bondurant, Sandra Splinter, additional, Allen, Andrew E., additional, Rabinowicz, Pablo D., additional, Sussman, Michael R., additional, Bowler, Chris, additional, and Tirichine, Leïla, additional

Published
2014
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19. Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

Author

Veluchamy, Alaguraj, primary, Lin, Xin, additional, Maumus, Florian, additional, Rivarola, Maximo, additional, Bhavsar, Jaysheel, additional, Creasy, Todd, additional, O’Brien, Kimberly, additional, Sengamalay, Naomi A., additional, Tallon, Luke J., additional, Smith, Andrew D., additional, Rayko, Edda, additional, Ahmed, Ikhlak, additional, Crom, Stéphane Le, additional, Farrant, Gregory K., additional, Sgro, Jean-Yves, additional, Olson, Sue A., additional, Bondurant, Sandra Splinter, additional, Allen, Andrew E., additional, Rabinowicz, Pablo D., additional, Sussman, Michael R., additional, Bowler, Chris, additional, and Tirichine, Leïla, additional

Published
2013
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21. Corrigendum: Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum.

Author

Veluchamy, Alaguraj, Lin, Xin, Maumus, Florian, Rivarola, Maximo, Bhavsar, Jaysheel, Creasy, Todd, O'Brien, Kimberly, Sengamalay, Naomi A., Tallon, Luke J., Smith, Andrew D., Rayko, Edda, Ahmed, Ikhlak, Crom, Stéphane Le, Farrant, Gregory K., Sgro, Jean-Yves, Olson, Sue A., Bondurant, Sandra Splinter, Allen, Andrew E., Rabinowicz, Pablo D., and Sussman, Michael R.

Published
2014
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22. A Gene Island with Two Possible Configurations Is Involved in Chromatic Acclimation in Marine Synechococcus.

Author

Humily, Florian, Partensky, Frédéric, Six, Christophe, Farrant, Gregory K., Ratin, Morgane, Marie, Dominique, and Garczarek, Laurence

Subjects
ACCLIMATIZATION, SYNECHOCOCCUS, MARINE bacteria, PHOTOSYNTHETIC bacteria, CYANOBACTERIA, BACTERIAL diversity, PHYCOBILISOMES, PHYCOBILINS, CHROMATIN
Abstract

Synechococcus, 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 Synechococcus radiation. A specific gene island was identified in all CA4-performing strains, containing two genes (fciA/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 mpeZ gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called fciC. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While mpeZ is expressed more in blue light than green light, this is the reverse for mpeW, 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. [ABSTRACT FROM AUTHOR]

Published
2013
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23. A Gene Island with Two Possible Configurations Is Involved in Chromatic Acclimation in Marine Synechococcus.

Author

Humily, Florian, Partensky, Frédéric, Six, Christophe, Farrant, Gregory K., Ratin, Morgane, Marie, Dominique, and Garczarek, Laurence

Subjects
*ACCLIMATIZATION, *SYNECHOCOCCUS, *MARINE bacteria, *PHOTOSYNTHETIC bacteria, *CYANOBACTERIA, *BACTERIAL diversity, *PHYCOBILISOMES, *PHYCOBILINS, *CHROMATIN
Abstract

Synechococcus, 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 Synechococcus radiation. A specific gene island was identified in all CA4-performing strains, containing two genes (fciA/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 mpeZ gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called fciC. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While mpeZ is expressed more in blue light than green light, this is the reverse for mpeW, 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. [ABSTRACT FROM AUTHOR]

Published
2013
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24. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes.

Author

Garczarek L, Guyet U, Doré H, Farrant GK, Hoebeke M, Brillet-Guéguen L, Bisch A, Ferrieux M, Siltanen J, Corre E, Le Corguillé G, Ratin M, Pitt FD, Ostrowski M, Conan M, Siegel A, Labadie K, Aury JM, Wincker P, Scanlan DJ, and Partensky F

Subjects
Bacterial Proteins genetics, Geography, Likelihood Functions, Phylogeny, User-Computer Interface, Aquatic Organisms genetics, Cyanobacteria genetics, Data Curation, Databases, Genetic, Genome, Bacterial, Information Systems
Abstract

Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2021
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25. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria.

Author

Doré H, Farrant GK, Guyet U, Haguait J, Humily F, Ratin M, Pitt FD, Ostrowski M, Six C, Brillet-Guéguen L, Hoebeke M, Bisch A, Le Corguillé G, Corre E, Labadie K, Aury JM, Wincker P, Choi DH, Noh JH, Eveillard D, Scanlan DJ, Partensky F, and Garczarek L

Abstract

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus , we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters ( Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton., (Copyright © 2020 Doré, Farrant, Guyet, Haguait, Humily, Ratin, Pitt, Ostrowski, Six, Brillet-Guéguen, Hoebeke, Bisch, Le Corguillé, Corre, Labadie, Aury, Wincker, Choi, Noh, Eveillard, Scanlan, Partensky and Garczarek.)

Published
2020
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