Skip to main content
SpringerLink
Log in

Development of a set of SNP markers for population genetics of the sea rose, Pentapora fascialis

  • Technical Note
  • Published:
Conservation Genetics Resources Aims and scope Submit manuscript

Abstract

A set of single nucleotide polymorphisms (SNP) was developed from the transcriptome of 10 individuals of the sea rose Pentapora fascialis (Cheilostomata) collected in Banyuls-sur-Mer Bay (NW Mediterranean sea). 53,042 putative SNPs were identified and mapped on a de novo assembled transcriptome. A selected set of 320 SNPs with highest coverage and uniquely mapped in the assembled transcriptome was tested using a MassARRAY System on 95 individuals sampled in natural rocks and artificial reefs distributed over a hundred kilometers in the NW Mediterranean (outisde Banyuls-sur-Mer Bay). A total of 177 SNPs were successfully genotyped and found to be polymorphic. Among these, 154 SNPs were in Hardy-Weinberg equilibrium over all samples, with significant linkage disequilibrium in only 21 pairs of SNPs. The newly developed loci will be a valuable tool for population genetics studies of this calcifying bryozoan species whose erect structure makes it an engineering species and a target for conservation plans.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Data availability

The RNA seq data will be released publicly through National Center for Biotechnology Information portal in March 2024 (https://submit.ncbi.nlm.nih.gov).

References

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

  • Blouet S, Bramanti L, Guizien K (2022) Artificial reefs geographical location matters more than shape, age and depth for sessile invertebrate colonization in the Gulf of Lion (NorthWestern Mediterranean Sea). Peer Community Journal 2(article no e24). https://doi.org/10.24072/pcjournal.107

  • 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 

  • Cocito S, Sgorbini S, Bianchi C (1998a) Aspects of the biology of the bryozoan Pentapora fascialis in the northwestern Mediterranean. Mar Biol 131:73–82. https://doi.org/10.1007/s002270050298

    Article  Google Scholar 

  • Cocito S, Ferdeghini F, Sgorbini S (1998b) Pentapora fascialis (Pallas) [Cheilostomata: Ascophora] colonization of one sublittoral rocky site after sea-storm in the northwest Mediterranean. Hydrobiologia 375/376:59–66

    Article  Google Scholar 

  • Fortunato H (2015) Bryozoans in climate and ocean acidification research: a reappraisal of an under-used tool. Reg Stud Mar Sci 2:32–44 ISSN 2352–4855. https://doi.org/10.1016/j.rsma.2015.08.010

    Article  Google Scholar 

  • Gautier YV (1962) Recherches écologiques sur les bryozoaires cheilostomes en Méditerranée occidentale. Thèse de l’Université d’Aix-Marseille

  • 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, Regev A (2011) Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol 2011 May 15(7):644–652. https://doi.org/10.1038/nbt.1883

    Google Scholar 

  • Hayward PJ, Ryland JS (1999) Synopses of the British Fauna (new series): Cheilostomatous Bryozoa Part II: Hippothoidea-Celleporoidea. The Linnean Society of London and Estuarine and Coastal Sciences Association, London

    Google Scholar 

  • Keough MJ, Chernoff H (1987) Dispersal and population variation in the bryozoan Bugula neritina. Ecology 68:199–210

    Article  Google Scholar 

  • Lombardi C, Cocito S, Occhipinti-Ambrogi A, Porter J (2008) Distribution and morphological variation of colonies of the bryozoan Pentapora fascialis (Bryozoa: Cheilostomata) along the western coast of Italy. J Mar Biol Association United Kingd 88(4):711–717. https://doi.org/10.1017/S0025315408001525

    Article  Google Scholar 

  • Lombardi C, Taylor PD, Cocito S (2010) Systematics of the Miocene–Recent bryozoan genus Pentapora (Cheilostomata) (2010) Zool J Linn Soc 160:17?39.

  • Lombardi C, Taylor PD, Cocito S (2014) Bryozoan constructions in a changing Mediterranean Sea. In: Godofredo S, Dubinsky (eds) The Mediterranean Sea: its history and Present challenges. Springer, Dordrecht, pp 373–384

    Chapter  Google Scholar 

  • Pagès-Escolà M, Hereu B, Garrabou J, Montero‐Serra I, Gori A, Gómez‐Gras D, Figuerola B, Linares C (2018) Divergent responses to warming of two common co‐occurring Mediterranean bryozoans. Sci Rep 8:17455. https://doi.org/10.1038/s41598-018-36094-9

    Article  PubMed  PubMed Central  Google Scholar 

  • Pagès-Escolà M, Linares C, Gómez‐Gras D, Medrano A, Hereu B (2020) Assessing the effectiveness of restoration actions for bryozoans: the case of the Mediterranean Pentapora fascialis. Aquat Conserv: Mar Freshw Ecosyst 30:8–19. https://doi.org/10.1002/aqc.3236

    Article  Google Scholar 

  • Rousset F (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Article  PubMed  Google Scholar 

  • Sala E, Garrabou J, Zabala M (1996) Effects of diver frequentation on Mediterranean sublittoral populations of the bryozoan Pentapora fascialis. Mar Biol 126:451–459. https://doi.org/10.1007/BF00354627

    Article  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. doi:https://doi.org/10.1093/nar/gku1187

  • Wood ACL, Probert PK, Rowden AA, Smith AM (2012) Complex habitat generated by marine bryozoans: a review of its distribution, structure, diversity, threats and conservation. Aquat Conserv 22:547–563. https://doi.org/10.1002/aqc.2236

    Article  Google Scholar 

  • Zabala M (1986) Fauna dels briozous dels Països catalans. Institut d’Estudis Catalans, pp. 883.

Download references

Acknowledgements

The authors gratefully acknowledge the helpful assistance during sampling of S. Blouet and the staff of the Aire Marine Protégée Agatoise. We also thank the scuba divers, JC Roca and B Hesse, for their technical assistance for field sampling in Banyuls sur Mer. We are grateful to the Bio2Mar core facility (http://bio2mar.obs-banyuls.fr) for providing access to instrumentation for RNA extractions. RNAseq was performed at the GeT-PlaGe core facility, INRAE Toulouse. SNP genotyping was performed at the Genome Transcriptome Facility of Bordeaux (grants from ANR-10-EQPX-16) with the help of Laure Dubois.

Funding

This work was funded by the Agence de l’Eau Rhône-Méditerranée-Corse under project ICONE - Impacts actuels et potentiels de la CONnectivité Ecologique ajoutée par les récifs artificiels sur la biodiversité fixée des substrats durs du Golfe du Lion (2017 7267 / 2017 7268 / 2018 0697, PI K. Guizien, AAP 2016).

Author information

Authors and Affiliations

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

    M Padrón & Guizien K.

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

    M. Milhes

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

    M. Massot & E. Guichoux

Authors
  1. M Padrón
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. Milhes
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. M. Massot
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. E. Guichoux
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Guizien K.
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

MP and KG designed the study. MM, AD, and EG, performed the sequencing and genotyping. MP analyzed the data. KG wrote the manuscript. All authors reviewed the manuscript.

Corresponding author

Correspondence to Guizien K..

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Material 1

Supplementary Material 2

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Padrón, M., Milhes, M., Massot, M. et al. Development of a set of SNP markers for population genetics of the sea rose, Pentapora fascialis. Conservation Genet Resour (2024). https://doi.org/10.1007/s12686-024-01348-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12686-024-01348-4

Keywords

Search

Navigation