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Development of a set of SNP markers for population genetics of the red gorgonian (Paramuricea clavata), an emblematic species of the Mediterranean coralligenous

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Abstract

Transcriptome sequencing was used for the development of single nucleotide polymorphisms (SNP) for the red gorgonian (Paramuricea clavata). A total of 20,736 SNPs were identified, and 1718 had a coverage of over 100 reads. Of the 480 SNPs tested, 347 SNPs were successfully genotyped at 95 samples from the NW Mediterranean using a MassARRAY System. This set of markers will be of great value for population genetics and phylogeography.

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References

  • Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc

  • Ballesteros E (2006) Mediterranean coralligenous assemblages: a synthesis of present knowledge. Oceanogr Mar Biol 44:1–74

    Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina Sequence Data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cupido R, Cocito S, Barsanti M, Sgorbini S, Peirano A, Santangelo G (2009) Unexpected long-term population dynamics in a canopy-forming gorgonian coral following mass mortality. Mar Ecol Prog Ser 394:195–200

    Article  Google Scholar 

  • Gabriel S, Ziaugra L, Tabbaa D (2009) SNP genotyping using Sequenom MassARRAY iPLEX platform. Curr Protoc Hum Genet 42:2–12

    Google Scholar 

  • Grabherr M, Haas B, Yassour M, Levin J, Thompson D, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N (2011) Regev A (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 29(7):644–652. https://doi.org/10.1038/nbt.1883

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meirmans P, van Tienderen P (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Resour 4(4):792–794

    Article  Google Scholar 

  • Padrón M, Costantini F, Bramanti L, Guizien K, Abbiati M (2018) Genetic connectivity supports recovery of gorgonian populations affected by climate change. Aquat Conserv. https://doi.org/10.1002/aqc.2912

    Article  Google Scholar 

  • Pilczynska J, Cocito S, Boavida J, Serrão E, Queiroga H (2016) Genetic diversity and local connectivity in the Mediterranean red gorgonian coral after mass mortality events. PLoS ONE 11(3):1–16

    Article  Google Scholar 

  • Santangelo G, Cupido R, Cocito S, Bramanti L, Priori C, Erra F, Iannelli M (2015) Effects of increased mortality on gorgonian corals (Cnidaria, Octocorallia): different demographic features may lead affected populations to unexpected recovery and new equilibrium points. Hydrobiologia 759:171–187

    Article  CAS  Google Scholar 

  • Uricaru R, Rizk G, Lacroix V, Quillery E, Plantard O, Chikhi R, Lemaitre C, Peterlongo P (2014) Reference-free detection of isolated SNPs. Nucleic Acids Res. https://doi.org/10.1093/nar/gku1187

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was funded by EC Interreg Marittimo program under Project IMPACT - IMpatto Portuale su aree marine protette: Azioni Cooperative Transfrontaliere (PI, M. Magaldi; Ecology Task Leader, K. Guizien; CUP B12F17000370005). We thank the scuba divers, JC Roca and B Hesse, for their technical assistance for field sampling. RNA extractions were performed using instruments and facilities of the Marine Biodiversity and Biotechnology (Bio2Mar) platform of the OOB. SNP genotyping were performed at the Genome Transcriptome Facility of Bordeaux (Grants from ANR-10-EQPX-16) with the help of Adline Delcamp and Christophe Boury.

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Authors and Affiliations

  1. Laboratoire d’Ecogeochimie des Environnements Benthique, CNRS, Sorbonne Université, UMR 8222, 66650, Banyuls-sur-Mer, France

    M. Padrón

  2. INRA, GeT-PlaGe, Genotoul, 31326, Castanet-Tolosan, France

    M. Milhes

  3. Univ. Bordeaux, INRAE, BIOGECO, 33610, Cestas, France

    M. Massot & E. Guichoux

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  1. M. Padrón
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  2. M. Milhes
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  3. M. Massot
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  4. E. Guichoux
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Correspondence to M. Padrón.

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Padrón, M., Milhes, M., Massot, M. et al. Development of a set of SNP markers for population genetics of the red gorgonian (Paramuricea clavata), an emblematic species of the Mediterranean coralligenous. Conservation Genet Resour 12, 521–523 (2020). https://doi.org/10.1007/s12686-020-01139-7

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  • DOI: https://doi.org/10.1007/s12686-020-01139-7

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