Abstract
A set of single nucleotide polymorphism (SNP) markers was developed from the transcriptome of the solitary ascidian Halocynthia papillosa. 1399 putative SNPs with coverage larger than 100 reads were identified, and a selected set of 320 SNPs was tested using a MassARRAY System on 95 samples from the NW Mediterranean. A total of 175 SNPs were successfully genotyped, polymorphic and in Hardy-Weinberg equilibrium over all samples, with significant linkage desequilibrium in only 8 pairs of SNPs. The newly developed loci will be a valuable tool for population genetics studies of this endemic ascidian species of the Mediterranean Sea.
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Data Availability
The RNA seq data will be released publicly through National Center for Biotechnology Information portal (https://submit.ncbi.nlm.nih.gov).
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Acknowledgements
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 (PI, K. Guizien, AAP 2016). 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, and the NEREIS crew of the Observatoire Océanologique de Banyuls-sur-Mer 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 PGTB (https://doi.org/10.15454/1.5572396583599417E12) 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 (PI, K. Guizien,
AAP 2016,grant numbers : 2017 7267 / 2017 7268 / 2018 0697).
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MP and KG designed the study. MM, AD, and EG, performed the sequencing and genotyping. MP analyzed the data. KG wrote the main manuscript text. All authors reviewed the manuscript.
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Padrón, M., Milhes, M., Delcamp, A. et al. Development of a set of SNP markers for population genetics of the sea peach (Halocynthia papillosa). Conservation Genet Resour 15, 145–147 (2023). https://doi.org/10.1007/s12686-023-01313-7
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DOI: https://doi.org/10.1007/s12686-023-01313-7