Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.
International audience BACKGROUND: The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence...
Published in: | Genome Biology |
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Main Authors: | , , , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2008
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Subjects: | |
Online Access: | https://hal.science/hal-00338634 https://hal.science/hal-00338634v1/document https://hal.science/hal-00338634v1/file/gb-2008-9-5-r90.pdf https://doi.org/10.1186/gb-2008-9-5-r90 |
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ftinraparis:oai:HAL:hal-00338634v1 |
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record_format |
openpolar |
institution |
Open Polar |
collection |
Institut National de la Recherche Agronomique: ProdINRA |
op_collection_id |
ftinraparis |
language |
English |
topic |
MAXIMUM-LIKELIHOOD ATLANTIC-OCEAN NORTH-ATLANTIC NE ATLANTIC DIVERSITY SEA PROCHLOROCOCCUS ECOTYPES SYNECHOCOCCUS ECOTYPES PHYLOGENETIC ANALYSIS COMMUNITY STRUCTURE MESH: Gene Transfer Horizontal MESH: Genome Bacterial MESH: Seawater MESH: Synechococcus [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces environment [SDE.MCG]Environmental Sciences/Global Changes [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology |
spellingShingle |
MAXIMUM-LIKELIHOOD ATLANTIC-OCEAN NORTH-ATLANTIC NE ATLANTIC DIVERSITY SEA PROCHLOROCOCCUS ECOTYPES SYNECHOCOCCUS ECOTYPES PHYLOGENETIC ANALYSIS COMMUNITY STRUCTURE MESH: Gene Transfer Horizontal MESH: Genome Bacterial MESH: Seawater MESH: Synechococcus [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces environment [SDE.MCG]Environmental Sciences/Global Changes [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology Dufresne, Alexis Ostrowski, Martin Scanlan, David, J. Garczarek, Laurence Mazard, Sophie Palenik, Brian P. Paulsen, Ian, T. de Marsac, Nicole Tandeau Wincker, Patrick Dossat, Carole Ferriera, Steve Johnson, Justin Post, Anton F. Hess, Wolfgang R. Partensky, Frédéric Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. |
topic_facet |
MAXIMUM-LIKELIHOOD ATLANTIC-OCEAN NORTH-ATLANTIC NE ATLANTIC DIVERSITY SEA PROCHLOROCOCCUS ECOTYPES SYNECHOCOCCUS ECOTYPES PHYLOGENETIC ANALYSIS COMMUNITY STRUCTURE MESH: Gene Transfer Horizontal MESH: Genome Bacterial MESH: Seawater MESH: Synechococcus [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces environment [SDE.MCG]Environmental Sciences/Global Changes [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology |
description |
International audience BACKGROUND: The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group. RESULTS: Here, we compare the genomes of 11 marine Synechococcus isolates, representing 10 distinct lineages. Phylogenies inferred from the core genome allowed us to refine the taxonomic relationships between clades by revealing a clear dichotomy within the main subcluster, reminiscent of the two aforementioned lifestyles. Genome size is strongly correlated with the cumulative lengths of hypervariable regions (or 'islands'). One of these, encompassing most genes encoding the light-harvesting phycobilisome rod complexes, is involved in adaptation to changes in light quality and has clearly been transferred between members of different Synechococcus lineages. Furthermore, we observed that two strains (RS9917 and WH5701) that have similar pigmentation and physiology have an unusually high number of genes in common, given their phylogenetic distance. CONCLUSION: We propose that while members of a given marine Synechococcus lineage may have the same broad geographical distribution, local niche occupancy is facilitated by lateral gene transfers, a process in which genomic islands play a key role as a repository for transferred genes. Our work also highlights the need for developing picocyanobacterial systematics based on genome-derived parameters combined with ecological and physiological data. |
author2 |
Ecosystèmes, biodiversité, évolution Rennes (ECOBIO) Université de Rennes (UR)-Institut Ecologie et Environnement - CNRS Ecologie et Environnement (INEE-CNRS) Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR) Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS) Department of Biological Sciences, Warwick University of Warwick Coventry 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) Collection des Cyanobactéries Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS) Scripps Institution of Oceanography (SIO - UC San Diego) University of California San Diego (UC San Diego) University of California (UC)-University of California (UC) Génomique métabolique (UMR 8030) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-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)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) J Craig Venter Institute J. Craig Venter Institute Interuniversity Institute for Marine Science Hebrew University Faculty of Biology, Freiburg Albert-Ludwigs-Universität Freiburg = University of Freiburg ANR-05-BLAN-0122,PHYCOSYN,Evolution, Biosynthèse et Régulation des Phycobilisomes chez les Cyanobactéries Marines du Genre Synechococcus(2005) |
format |
Article in Journal/Newspaper |
author |
Dufresne, Alexis Ostrowski, Martin Scanlan, David, J. Garczarek, Laurence Mazard, Sophie Palenik, Brian P. Paulsen, Ian, T. de Marsac, Nicole Tandeau Wincker, Patrick Dossat, Carole Ferriera, Steve Johnson, Justin Post, Anton F. Hess, Wolfgang R. Partensky, Frédéric |
author_facet |
Dufresne, Alexis Ostrowski, Martin Scanlan, David, J. Garczarek, Laurence Mazard, Sophie Palenik, Brian P. Paulsen, Ian, T. de Marsac, Nicole Tandeau Wincker, Patrick Dossat, Carole Ferriera, Steve Johnson, Justin Post, Anton F. Hess, Wolfgang R. Partensky, Frédéric |
author_sort |
Dufresne, Alexis |
title |
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. |
title_short |
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. |
title_full |
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. |
title_fullStr |
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. |
title_full_unstemmed |
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. |
title_sort |
unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. |
publisher |
HAL CCSD |
publishDate |
2008 |
url |
https://hal.science/hal-00338634 https://hal.science/hal-00338634v1/document https://hal.science/hal-00338634v1/file/gb-2008-9-5-r90.pdf https://doi.org/10.1186/gb-2008-9-5-r90 |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_source |
ISSN: 1465-6906 EISSN: 1474-760X Genome Biology https://hal.science/hal-00338634 Genome Biology, 2008, 9 (5), pp.R90. ⟨10.1186/gb-2008-9-5-r90⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1186/gb-2008-9-5-r90 info:eu-repo/semantics/altIdentifier/pmid/18507822 PUBMED: 18507822 |
op_rights |
info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1186/gb-2008-9-5-r90 |
container_title |
Genome Biology |
container_volume |
9 |
container_issue |
5 |
container_start_page |
R90 |
_version_ |
1812816554680647680 |
spelling |
ftinraparis:oai:HAL:hal-00338634v1 2024-10-13T14:09:33+00:00 Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria. Dufresne, Alexis Ostrowski, Martin Scanlan, David, J. Garczarek, Laurence Mazard, Sophie Palenik, Brian P. Paulsen, Ian, T. de Marsac, Nicole Tandeau Wincker, Patrick Dossat, Carole Ferriera, Steve Johnson, Justin Post, Anton F. Hess, Wolfgang R. Partensky, Frédéric Ecosystèmes, biodiversité, évolution Rennes (ECOBIO) Université de Rennes (UR)-Institut Ecologie et Environnement - CNRS Ecologie et Environnement (INEE-CNRS) Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR) Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS) Department of Biological Sciences, Warwick University of Warwick Coventry 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) Collection des Cyanobactéries Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS) Scripps Institution of Oceanography (SIO - UC San Diego) University of California San Diego (UC San Diego) University of California (UC)-University of California (UC) Génomique métabolique (UMR 8030) Genoscope - Centre national de séquençage Evry (GENOSCOPE) Université Paris-Saclay-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)-Université Paris-Saclay-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS) J Craig Venter Institute J. Craig Venter Institute Interuniversity Institute for Marine Science Hebrew University Faculty of Biology, Freiburg Albert-Ludwigs-Universität Freiburg = University of Freiburg ANR-05-BLAN-0122,PHYCOSYN,Evolution, Biosynthèse et Régulation des Phycobilisomes chez les Cyanobactéries Marines du Genre Synechococcus(2005) 2008 https://hal.science/hal-00338634 https://hal.science/hal-00338634v1/document https://hal.science/hal-00338634v1/file/gb-2008-9-5-r90.pdf https://doi.org/10.1186/gb-2008-9-5-r90 en eng HAL CCSD BioMed Central info:eu-repo/semantics/altIdentifier/doi/10.1186/gb-2008-9-5-r90 info:eu-repo/semantics/altIdentifier/pmid/18507822 PUBMED: 18507822 info:eu-repo/semantics/OpenAccess ISSN: 1465-6906 EISSN: 1474-760X Genome Biology https://hal.science/hal-00338634 Genome Biology, 2008, 9 (5), pp.R90. ⟨10.1186/gb-2008-9-5-r90⟩ MAXIMUM-LIKELIHOOD ATLANTIC-OCEAN NORTH-ATLANTIC NE ATLANTIC DIVERSITY SEA PROCHLOROCOCCUS ECOTYPES SYNECHOCOCCUS ECOTYPES PHYLOGENETIC ANALYSIS COMMUNITY STRUCTURE MESH: Gene Transfer Horizontal MESH: Genome Bacterial MESH: Seawater MESH: Synechococcus [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces environment [SDE.MCG]Environmental Sciences/Global Changes [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology info:eu-repo/semantics/article Journal articles 2008 ftinraparis https://doi.org/10.1186/gb-2008-9-5-r90 2024-09-24T14:49:09Z International audience BACKGROUND: The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group. RESULTS: Here, we compare the genomes of 11 marine Synechococcus isolates, representing 10 distinct lineages. Phylogenies inferred from the core genome allowed us to refine the taxonomic relationships between clades by revealing a clear dichotomy within the main subcluster, reminiscent of the two aforementioned lifestyles. Genome size is strongly correlated with the cumulative lengths of hypervariable regions (or 'islands'). One of these, encompassing most genes encoding the light-harvesting phycobilisome rod complexes, is involved in adaptation to changes in light quality and has clearly been transferred between members of different Synechococcus lineages. Furthermore, we observed that two strains (RS9917 and WH5701) that have similar pigmentation and physiology have an unusually high number of genes in common, given their phylogenetic distance. CONCLUSION: We propose that while members of a given marine Synechococcus lineage may have the same broad geographical distribution, local niche occupancy is facilitated by lateral gene transfers, a process in which genomic islands play a key role as a repository for transferred genes. Our work also highlights the need for developing picocyanobacterial systematics based on genome-derived parameters combined with ecological and physiological data. Article in Journal/Newspaper North Atlantic Institut National de la Recherche Agronomique: ProdINRA Genome Biology 9 5 R90 |