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Wenne R, Zbawicka M, Prądzińska A, Kotta J, Herkül K, Gardner JPA, Apostolidis AP, Poćwierz-Kotus A, Rouane-Hacene O, Korrida A, Dondero F, Baptista M, Reizopoulou S, Hamer B, Sundsaasen KK, Árnyasi M, Kent MP. Molecular genetic differentiation of native populations of Mediterranean blue mussels, Mytilus galloprovincialis Lamarck, 1819, and the relationship with environmental variables. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2086306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- R. Wenne
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - M. Zbawicka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - A. Prądzińska
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - J. Kotta
- Department of Marine Systems, Estonian Marine Institute, University of Tartu, 12619 Tallinn, Estonia
| | - K. Herkül
- Department of Marine Systems, Estonian Marine Institute, University of Tartu, 12619 Tallinn, Estonia
| | - J. P. A. Gardner
- School of Biological Sciences, Victoria University of Wellington, Wellington, 6140, New Zealand
| | - A. P. Apostolidis
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - A. Poćwierz-Kotus
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, 81-712 Sopot, Poland
| | - O. Rouane-Hacene
- Department of Biology, Faculty of Nature and Life Sciences, University of Oran 1 - Ahmed Ben Bella, Algeria
| | - A. Korrida
- High Institute of Nursing Professions and Health Techniques, ISPITS-Agadir, Moroccan Ministry of Health and Social Protection, Kingdom of Morocco
| | - F. Dondero
- Department of Science and Technological Innovation (DISIT), Ecotoxicology and Ecology, Università del Piemonte Orientale “Amedeo Avogadro”, Novara, 15121, Italy
| | - M. Baptista
- Marine and Environmental Sciences Centre, University of Lisbon, Portugal
| | - S. Reizopoulou
- Department of Biological Oceanography, Institute of Oceanography, Hellenic Centre for Marine Research, Athens Sounio, 19013 Anavyssos, Greece
| | - B. Hamer
- Ruđer Bošković Institute, Center for Marine Research Rovinj, Rovinj, Croatia
| | - K. K. Sundsaasen
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (Cigene), Faculty of Biosciences, Norwegian University of Life Sciences, No-1432 Ås, Norway
| | - M. Árnyasi
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (Cigene), Faculty of Biosciences, Norwegian University of Life Sciences, No-1432 Ås, Norway
| | - M. P. Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (Cigene), Faculty of Biosciences, Norwegian University of Life Sciences, No-1432 Ås, Norway
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2
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Dimond JL, Crim RN, Unsell E, Barry V, Toft JE. Population genomics of the basket cockle Clinocardium nuttallii in the southern Salish Sea: Assessing genetic risks of stock enhancement for a culturally important marine bivalve. Evol Appl 2022; 15:459-470. [PMID: 35386400 PMCID: PMC8965374 DOI: 10.1111/eva.13359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/18/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
Coastal Indigenous communities that rely on subsistence harvests are uniquely vulnerable to declines in nearshore species. The basket cockle Clinocardium nuttallii is among the favored foods of Indigenous people along the northwest Pacific coast of North America, yet localized declines in their abundance have led to interest in stock enhancement efforts. We used a population genomics approach to examine potential risks associated with stock enhancement of C. nuttallii in the southern Salish Sea, a large inland estuary that includes Puget Sound. More than 8000 single nucleotide polymorphisms across 349 individuals at 12 locations were assembled de novo using restriction site-associated DNA sequencing. Results indicated that C. nuttallii within the southern Salish Sea were distinct from those along the outer Pacific coast (F ST = 0.021-0.025). Within the southern Salish Sea, C. nuttallii populations appear to be well-connected despite numerous potential impediments to gene flow; Hood Canal, which experiences the lowest flushing rates of all Puget Sound sub-basins, was a minor exception to this strong connectivity. We found evidence of isolation by distance within the southern Salish Sea, but the slope of this relationship was shallow, and F ST values were low (F ST = 0.001-0.004). Meanwhile, outlier analyses did not support the hypothesis that southern Salish Sea sub-populations are locally adapted. Estimates of effective population size had no upper bound, suggesting potentially very high adaptive capacity in C. nuttallii, but also making it difficult to assess potential reductions in effective population size resulting from stock enhancement. We present several strategies to augment cockle populations for subsistence harvest that would limit risk to the genetic diversity of wild cockle populations.
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Affiliation(s)
- James L. Dimond
- Puget Sound Restoration FundBainbridge IslandWashingtonUSA
- Shannon Point Marine CenterWestern Washington UniversityAnacortesWashingtonUSA
| | - Ryan N. Crim
- Puget Sound Restoration FundBainbridge IslandWashingtonUSA
| | | | - Viviane Barry
- Fisheries DepartmentSuquamish TribeSuquamishWashingtonUSA
| | - Jodie E. Toft
- Puget Sound Restoration FundBainbridge IslandWashingtonUSA
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3
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Vera M, Maroso F, Wilmes SB, Hermida M, Blanco A, Fernández C, Groves E, Malham SK, Bouza C, Robins PE, Martínez P. Genomic survey of edible cockle ( Cerastoderma edule) in the Northeast Atlantic: A baseline for sustainable management of its wild resources. Evol Appl 2022; 15:262-285. [PMID: 35233247 PMCID: PMC8867702 DOI: 10.1111/eva.13340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 11/12/2022] Open
Abstract
Knowledge on correlations between environmental factors and genome divergence between populations of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9309 SNPs localized in the cockle's genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic Ocean to analyse the genetic structure with regard to environmental variables. Larval dispersal modelling considering species behaviour and interannual/interseasonal variation in ocean conditions was carried out as an essential background to which compare genetic information. Cockle populations in the Northeast Atlantic displayed low but significant geographical differentiation between populations (F ST = 0.0240; p < 0.001), albeit not across generations. We identified 742 and 36 outlier SNPs related to divergent and balancing selection in all the geographical scenarios inspected, and sea temperature and salinity were the main environmental correlates suggested. Highly significant linkage disequilibrium was detected at specific genomic regions against the very low values observed across the whole genome. Two main genetic groups were identified, northwards and southwards of French Brittany. Larval dispersal modelling suggested a barrier for larval dispersal linked to the Ushant front that could explain these two genetic clusters. Further genetic subdivision was observed using outlier loci and considering larval advection. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for the management of cockles, designing conservation strategies, founding broodstock for depleted beds and producing suitable seed for aquaculture production.
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Affiliation(s)
- Manuel Vera
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Francesco Maroso
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Department of Life Sciences and BiotechnologiesUniversity of FerraraFerraraItaly
| | - Sophie B. Wilmes
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Miguel Hermida
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Andrés Blanco
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
| | - Carlos Fernández
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | - Emily Groves
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Shelagh K. Malham
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Carmen Bouza
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
| | | | - Peter E. Robins
- School of Ocean SciencesMarine Centre WalesBangor UniversityMenai BridgeUK
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical AnthropologyACUIGEN GroupFaculty of VeterinaryUniversidade de Santiago de Compostela, Campus of LugoLugoSpain
- Institute of AquacultureUniversidade de Santiago de CompostelaSantiago de CompostelaSpain
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4
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Ma M, Wang T, Lu B. Assessment of genetic diversity in Amomum tsao-ko Crevost & Lemarié, an important medicine food homologous crop from Southwest China using SRAP and ISSR markers. GENETIC RESOURCES AND CROP EVOLUTION 2021; 68:2655-2667. [PMID: 34031623 PMCID: PMC8134809 DOI: 10.1007/s10722-021-01204-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 05/05/2021] [Indexed: 05/27/2023]
Abstract
Amomum tsao-ko Crevost & Lemarié is an important crop that has been widely used in traditional Chinese medicine and daily diets for a long time. In this study, the genetic diversity and relationships of eight cultivated populations of A. tsao-ko grown in Southwest China were examined using sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers. The results showed that 139 (99.29%) of 140 and 185 (99.46%) of 186 bands were polymorphic by SRAP and ISSR primers amplification, respectively. The polymorphic information content of detected bands were 0.270 (SRAP) and 0.232 (ISSR), respectively. The average Nei's gene diversity (H = 0.217) and Shannon's information index (I = 0.348) at the species level generated by SRAP primer were higher than those by ISSR analysis (H = 0.158, I = 0.272). Genetic differentiation coefficients and molecular variance analysis (AMOVA) indicated that the genetic variance of A. tsao-ko mainly occurred within populations rather than among populations. The high genetic identity among populations was revealed by SRAP (0.937) and ISSR (0.963). Using UPGMA cluster analysis, principal coordinate analysis, and population structure analysis, the accessions were categorized into two major groups. Overall, results obtained here will be useful for A. tsao-ko germplasm characterization, conservation, and utilization.
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Affiliation(s)
- Mengli Ma
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan People’s Republic of China
| | - Tiantao Wang
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan People’s Republic of China
| | - Bingyue Lu
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, College of Biological and Agricultural Sciences, Honghe University, Mengzi, Yunnan People’s Republic of China
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5
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Lucentini L, Plazzi F, Sfriso AA, Pizzirani C, Sfriso A, Chiesa S. Additional taxonomic coverage of the doubly uniparental inheritance in bivalves: Evidence of sex‐linked heteroplasmy in the razor clam
Solen marginatus
Pulteney, 1799, but not in the lagoon cockle
Cerastoderma glaucum
(Bruguière, 1789). J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12386] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Livia Lucentini
- Department of Chemistry, Biology and Biotechnologies University of Perugia Perugia Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences University of Bologna Bologna Italy
| | - Andrea Augusto Sfriso
- Department of Chemical and Pharmaceuticals Sciences University of Ferrara Ferrara Italy
| | - Claudia Pizzirani
- Department of Chemistry, Biology and Biotechnologies University of Perugia Perugia Italy
| | - Adriano Sfriso
- Department of Environmental Sciences, Informatics and Statistics Ca' Foscari University of Venice Venice Italy
| | - Stefania Chiesa
- Department of Molecular Sciences and Nanosystems Ca' Foscari University of Venice Venice Italy
- ISPRA Institute for Environmental Protection and Research Rome Italy
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Maroso F, Pérez de Gracia C, Iglesias D, Cao A, Díaz S, Villalba A, Vera M, Martínez P. A Useful SNP Panel to Distinguish Two Cockle Species, Cerastoderma edule and C. glaucum, Co-Occurring in Some European Beds, and Their Putative Hybrids. Genes (Basel) 2019; 10:genes10100760. [PMID: 31569787 PMCID: PMC6826453 DOI: 10.3390/genes10100760] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 11/16/2022] Open
Abstract
Cockles are highly appreciated mollusks and provide important services in coastal areas. The two European species, edible (Cerastoderma edule) and lagoon (Cerastoderma glaucum) cockles, are not easily distinguishable, especially when young. Interestingly, the species show different resistance to Marteilia cochillia, the parasite responsible for marteiliosis outbreaks, which is devastating cockle production in some areas. C. edule is severely affected by the parasite, while C. glaucum seems to be resistant, although underlying reasons are still unknown. Hybrids between both species might be interesting to introgress allelic variants responsible for tolerance, either naturally or through artificial selection, from lagoon into edible cockle. Here, we used 2b restriction site-associated DNA sequencing (2b–RAD) to identify single nucleotide polymorphisms (SNP) diagnostic for cockle discrimination (fixed for alternative allelic variants). Among the nine diagnostic SNPs selected, seven were validated using a SNaPshot assay in samples covering most of the distribution range of both species. The validated SNPs were used to check cockles that were suggested to be hybrids by a claimed diagnostic tool based on the internal transcribed spacers of the ribosomal RNA. Although these were shown to be false positives, we cannot rule out the fact that hybrids can occur and be viable. The SNP tool here developed will be valuable for their identification and management.
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Affiliation(s)
- Francesco Maroso
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002 Lugo, Spain; (F.M.); (C.P.d.G.); (P.M.)
| | - Celia Pérez de Gracia
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002 Lugo, Spain; (F.M.); (C.P.d.G.); (P.M.)
| | - David Iglesias
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain; (D.I.); (A.C.); (A.V.)
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain; (D.I.); (A.C.); (A.V.)
| | - Seila Díaz
- Department of Zoology, Genetics and Physical Anthropology, Mobile Genomes and Disease Group, CIMUS, Universidade de Santiago de Compostela, Campus of Santiago de Compostela, 15706 Santiago de Compostela, Spain;
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain; (D.I.); (A.C.); (A.V.)
- Department of Life Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620 Plentzia, Basque Country, Spain
| | - Manuel Vera
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002 Lugo, Spain; (F.M.); (C.P.d.G.); (P.M.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
- Correspondence: ; Tel.: +34-982-82-24-26
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002 Lugo, Spain; (F.M.); (C.P.d.G.); (P.M.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
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7
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Porro B, Mallien C, Hume BCC, Pey A, Aubin E, Christen R, Voolstra CR, Furla P, Forcioli D. The many faced symbiotic snakelocks anemone (Anemonia viridis, Anthozoa): host and symbiont genetic differentiation among colour morphs. Heredity (Edinb) 2019; 124:351-366. [PMID: 31527783 DOI: 10.1038/s41437-019-0266-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 07/30/2019] [Accepted: 08/15/2019] [Indexed: 11/09/2022] Open
Abstract
How can we explain morphological variations in a holobiont? The genetic determinism of phenotypes is not always obvious and could be circumstantial in complex organisms. In symbiotic cnidarians, it is known that morphology or colour can misrepresent a complex genetic and symbiotic diversity. Anemonia viridis is a symbiotic sea anemone from temperate seas. This species displays different colour morphs based on pigment content and lives in a wide geographical range. Here, we investigated whether colour morph differentiation correlated with host genetic diversity or associated symbiotic genetic diversity by using RAD sequencing and symbiotic dinoflagellate typing of 140 sea anemones from the English Channel and the Mediterranean Sea. We did not observe genetic differentiation among colour morphs of A. viridis at the animal host or symbiont level, rejecting the hypothesis that A. viridis colour morphs correspond to species level differences. Interestingly, we however identified at least four independent animal host genetic lineages in A. viridis that differed in their associated symbiont populations. In conclusion, although the functional role of the different morphotypes of A. viridis remains to be determined, our approach provides new insights on the existence of cryptic species within A. viridis.
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Affiliation(s)
- Barbara Porro
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France. .,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France.
| | - Cédric Mallien
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France
| | - Benjamin C C Hume
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Alexis Pey
- THALASSA Marine research & Environmental awareness, 17 rue Gutenberg, 06000, Nice, France
| | - Emilie Aubin
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France.,Laboratoire Génome et Développement des Plantes-UMR CNRS/UPVD 5096, Université de Perpignan, 66860, Perpignan, France
| | - Richard Christen
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Paola Furla
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France.,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France
| | - Didier Forcioli
- UPMC Univ Paris 06, Univ Antilles, Univ Nice Sophia Antipolis, CNRS, Symbiose Marine, Evolution Paris Seine-Institut de Biologie Paris Seine (EPS-IBPS), Sorbonne Universités, 75005, Paris, France. .,Institute for Research on Cancer and Aging, Nice (IRCAN), Université Côte d'Azur, CNRS, INSERM, 06107, Nice, France.
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