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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, Partensky F. Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes. Nucleic Acids Res 2021; 49:D667-D676. [PMID: 33125079 PMCID: PMC7779031 DOI: 10.1093/nar/gkaa958] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/22/2020] [Accepted: 10/28/2020] [Indexed: 12/05/2022] Open
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.
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Affiliation(s)
- Laurence Garczarek
- Sorbonne Université & CNRS, UMR 7144 'Adaptation & Diversity in the Marine Environment' (AD2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Ulysse Guyet
- Sorbonne Université & CNRS, UMR 7144 'Adaptation & Diversity in the Marine Environment' (AD2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Hugo Doré
- Sorbonne Université & CNRS, UMR 7144 'Adaptation & Diversity in the Marine Environment' (AD2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Gregory K Farrant
- Sorbonne Université & CNRS, UMR 7144 'Adaptation & Diversity in the Marine Environment' (AD2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France.,CNRS & Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), F-29680 Roscoff, France
| | - Mark Hoebeke
- CNRS & Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), F-29680 Roscoff, France
| | - Loraine Brillet-Guéguen
- CNRS & Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), F-29680 Roscoff, France.,Sorbonne Université & CNRS, UMR 8227 'Integrative Biology of Marine Models' (LBI2M), Station Biologique de Roscoff (SBR), F-29680 Roscoff, France
| | - Antoine Bisch
- Sorbonne Université & CNRS, UMR 7144 'Adaptation & Diversity in the Marine Environment' (AD2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France.,CNRS & Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), F-29680 Roscoff, France
| | - Mathilde Ferrieux
- Sorbonne Université & CNRS, UMR 7144 'Adaptation & Diversity in the Marine Environment' (AD2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Jukka Siltanen
- CNRS & Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), F-29680 Roscoff, France
| | - Erwan Corre
- CNRS & Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), F-29680 Roscoff, France
| | - Gildas Le Corguillé
- CNRS & Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), F-29680 Roscoff, France
| | - Morgane Ratin
- Sorbonne Université & CNRS, UMR 7144 'Adaptation & Diversity in the Marine Environment' (AD2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Frances D Pitt
- University of Warwick, School of Life Sciences, Coventry CV4 7AL, UK
| | - Martin Ostrowski
- University of Warwick, School of Life Sciences, Coventry CV4 7AL, UK
| | - Maël Conan
- Université de Rennes 1, INSERM, EHESP, IRSET, F-35043 Rennes, France
| | - Anne Siegel
- Université de Rennes 1, INRIA, CNRS, IRISA, F-35000 Rennes, France
| | - Karine Labadie
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91000 Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, F-91000 Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d'Évry, Université Paris-Saclay, F-91000 Evry, France
| | - David J Scanlan
- University of Warwick, School of Life Sciences, Coventry CV4 7AL, UK
| | - Frédéric Partensky
- Sorbonne Université & CNRS, UMR 7144 'Adaptation & Diversity in the Marine Environment' (AD2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
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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, Garczarek L. Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria. Front Microbiol 2020; 11:567431. [PMID: 33042072 PMCID: PMC7522525 DOI: 10.3389/fmicb.2020.567431] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022] Open
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.
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Affiliation(s)
- Hugo Doré
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Gregory K Farrant
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Ulysse Guyet
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Julie Haguait
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Florian Humily
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Morgane Ratin
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Frances D Pitt
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Martin Ostrowski
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Christophe Six
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Loraine Brillet-Guéguen
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France.,Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Mark Hoebeke
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Antoine Bisch
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Gildas Le Corguillé
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Erwan Corre
- CNRS, FR 2424, ABiMS Platform, Station Biologique de Roscoff (SBR), Roscoff, France
| | - Karine Labadie
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Jean-Marc Aury
- Genoscope, Institut de Biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Évry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Évry, France
| | - Dong Han Choi
- Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea.,Ocean Science and Technology School, Korea Maritime and Ocean University, Busan, South Korea
| | - Jae Hoon Noh
- Marine Ecosystem Research Center, Korea Institute of Ocean Science and Technology, Busan, South Korea.,Department of Marine Biology, Korea University of Science and Technology, Daejeon, South Korea
| | - Damien Eveillard
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France.,Research Federation (FR2022) Tara Océans GO-SEE, Paris, France
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Frédéric Partensky
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Laurence Garczarek
- Sorbonne Université, CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment (AD2M), Station Biologique de Roscoff (SBR), Roscoff, France.,Research Federation (FR2022) Tara Océans GO-SEE, Paris, France
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Guyet U, Nguyen NA, Doré H, Haguait J, Pittera J, Conan M, Ratin M, Corre E, Le Corguillé G, Brillet-Guéguen L, Hoebeke M, Six C, Steglich C, Siegel A, Eveillard D, Partensky F, Garczarek L. Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803. Front Microbiol 2020; 11:1707. [PMID: 32793165 PMCID: PMC7393227 DOI: 10.3389/fmicb.2020.01707] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/29/2020] [Indexed: 11/18/2022] Open
Abstract
Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.
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Affiliation(s)
- Ulysse Guyet
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Ngoc A Nguyen
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Hugo Doré
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Julie Haguait
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Justine Pittera
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Maël Conan
- DYLISS (INRIA-IRISA)-INRIA, CNRS UMR 6074, Université de Rennes 1, Rennes, France
| | - Morgane Ratin
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Erwan Corre
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Gildas Le Corguillé
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Loraine Brillet-Guéguen
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France.,CNRS, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Mark Hoebeke
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Christophe Six
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | | | - Anne Siegel
- DYLISS (INRIA-IRISA)-INRIA, CNRS UMR 6074, Université de Rennes 1, Rennes, France
| | - Damien Eveillard
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Frédéric Partensky
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Laurence Garczarek
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
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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. Unveiling membrane thermoregulation strategies in marine picocyanobacteria. New Phytol 2020; 225:2396-2410. [PMID: 31591719 DOI: 10.1111/nph.16239] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/29/2019] [Indexed: 05/23/2023]
Abstract
The wide latitudinal distribution of marine Synechococcus cyanobacteria partly relies on the differentiation of lineages adapted to distinct thermal environments. Membranes are highly thermosensitive cell components, and the ability to modulate their fluidity can be critical for the fitness of an ecotype in a particular thermal niche. We compared the thermophysiology of Synechococcus strains representative of major temperature ecotypes in the field. We measured growth, photosynthetic capacities and membrane lipidome variations. We carried out a metagenomic analysis of stations of the Tara Oceans expedition to describe the latitudinal distribution of the lipid desaturase genes in the oceans. All strains maintained efficient photosynthetic capacities over their different temperature growth ranges. Subpolar and cold temperate strains showed enhanced capacities for lipid monodesaturation at low temperature thanks to an additional, poorly regiospecific Δ9-desaturase. By contrast, tropical and warm temperate strains displayed moderate monodesaturation capacities but high proportions of double unsaturations in response to cold, thanks to regiospecific Δ12-desaturases. The desaturase genes displayed specific distributions directly related to latitudinal variations in ocean surface temperature. This study highlights the critical importance of membrane fluidity modulation by desaturases in the adaptive strategies of Synechococcus cyanobacteria during the colonization of novel thermal niches.
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Affiliation(s)
- Solène Breton
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144 Adaptation et Diversité en Milieu Marin (AD2M), Ecology of Marine Plankton (ECOMAP) Team, Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixe de recherche 5168 CNRS, CEA, INRA, Université Grenoble Alpes, IRIG, CEA Grenoble, 17, rue des Martyrs, 38000, Grenoble, France
| | - Ulysse Guyet
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144 Adaptation et Diversité en Milieu Marin (AD2M), Ecology of Marine Plankton (ECOMAP) Team, Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Valérie Gros
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixe de recherche 5168 CNRS, CEA, INRA, Université Grenoble Alpes, IRIG, CEA Grenoble, 17, rue des Martyrs, 38000, Grenoble, France
| | - Justine Pittera
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144 Adaptation et Diversité en Milieu Marin (AD2M), Ecology of Marine Plankton (ECOMAP) Team, Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - David Demory
- School of Biology, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Frédéric Partensky
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144 Adaptation et Diversité en Milieu Marin (AD2M), Ecology of Marine Plankton (ECOMAP) Team, Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Hugo Doré
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144 Adaptation et Diversité en Milieu Marin (AD2M), Ecology of Marine Plankton (ECOMAP) Team, Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Morgane Ratin
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144 Adaptation et Diversité en Milieu Marin (AD2M), Ecology of Marine Plankton (ECOMAP) Team, Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire et Végétale, Unité mixe de recherche 5168 CNRS, CEA, INRA, Université Grenoble Alpes, IRIG, CEA Grenoble, 17, rue des Martyrs, 38000, Grenoble, France
| | - Ngoc An Nguyen
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144 Adaptation et Diversité en Milieu Marin (AD2M), Ecology of Marine Plankton (ECOMAP) Team, Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Laurence Garczarek
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144 Adaptation et Diversité en Milieu Marin (AD2M), Ecology of Marine Plankton (ECOMAP) Team, Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Christophe Six
- Sorbonne Université, Centre National de la Recherche Scientifique, UMR 7144 Adaptation et Diversité en Milieu Marin (AD2M), Ecology of Marine Plankton (ECOMAP) Team, Station Biologique de Roscoff (SBR), 29680, Roscoff, France
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Maniangou B, Legrand N, Alizadeh M, Guyet U, Willem C, David G, Charpentier E, Walencik A, Retière C, Gagne K. Killer Immunoglobulin-Like Receptor Allele Determination Using Next-Generation Sequencing Technology. Front Immunol 2017; 8:547. [PMID: 28579987 PMCID: PMC5437120 DOI: 10.3389/fimmu.2017.00547] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/24/2017] [Indexed: 02/05/2023] Open
Abstract
The impact of natural killer (NK) cell alloreactivity on hematopoietic stem cell transplantation (HSCT) outcome is still debated due to the complexity of graft parameters, HLA class I environment, the nature of killer cell immunoglobulin-like receptor (KIR)/KIR ligand genetic combinations studied, and KIR+ NK cell repertoire size. KIR genes are known to be polymorphic in terms of gene content, copy number variation, and number of alleles. These allelic polymorphisms may impact both the phenotype and function of KIR+ NK cells. We, therefore, speculate that polymorphisms may alter donor KIR+ NK cell phenotype/function thus modulating post-HSCT KIR+ NK cell alloreactivity. To investigate KIR allele polymorphisms of all KIR genes, we developed a next-generation sequencing (NGS) technology on a MiSeq platform. To ensure the reliability and specificity of our method, genomic DNA from well-characterized cell lines were used; high-resolution KIR typing results obtained were then compared to those previously reported. Two different bioinformatic pipelines were used allowing the attribution of sequencing reads to specific KIR genes and the assignment of KIR alleles for each KIR gene. Our results demonstrated successful long-range KIR gene amplifications of all reference samples using intergenic KIR primers. The alignment of reads to the human genome reference (hg19) using BiRD pipeline or visualization of data using Profiler software demonstrated that all KIR genes were completely sequenced with a sufficient read depth (mean 317× for all loci) and a high percentage of mapping (mean 93% for all loci). Comparison of high-resolution KIR typing obtained to those published data using exome capture resulted in a reported concordance rate of 95% for centromeric and telomeric KIR genes. Overall, our results suggest that NGS can be used to investigate the broad KIR allelic polymorphism. Hence, these data improve our knowledge, not only on KIR+ NK cell alloreactivity in HSCT but also on the role of KIR+ NK cell populations in control of viral infections and diseases.
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Affiliation(s)
- Bercelin Maniangou
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Nolwenn Legrand
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Mehdi Alizadeh
- Laboratoire de Recherche et Développement, EFS Rennes, Rennes, France
| | - Ulysse Guyet
- L'institut du thorax, INSERM, CNRS, UNIV Nantes, Nantes, France
| | - Catherine Willem
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Gaëlle David
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | | | | | - Christelle Retière
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Katia Gagne
- Etablissement Français du Sang Pays de la Loire, Nantes, France.,CRCINA, INSERM U1232 CNRS, Université d'Angers, Université de Nantes, Nantes, France.,Laboratoire d'Histocompatibilité, EFS Nantes, Nantes, France.,LabeX Transplantex, Université de Strasbourg, Strasbourg, France
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