Development of a set of SNP markers for population genetics of the red gorgonian ( Paramuricea clavata ), an emblematic
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TECHNICAL NOTE
Development of a set of SNP markers for population genetics of the red gorgonian (Paramuricea clavata), an emblematic species of the Mediterranean coralligenous M. Padrón1 · M. Milhes2 · M. Massot3 · E. Guichoux3 Received: 31 January 2020 / Accepted: 28 February 2020 © Springer Nature B.V. 2020
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. Keywords Paramuricea clavata · Single nucleotide polymorphism · MassARRAY
Introduction The gorgonian Paramuricea clavata is one of the most emblematic and conspicuous coralligenous species in the Mediterranean Sea. A species of great interest for conservation given its role in the persistence and stability of several associated species (Ballesteros 2006). However, given its slow dynamics, P. clavata is particularly vulnerable to disturbances. The red gorgonian has suffered the most drastic reductions in density and biomass over a broad spatial scale, as a consequence of sea temperature anomalies in the NW Mediterranean (Cupido et al. 2009; Santangelo et al. 2015). It is, therefore, essential to provide an understanding of the natural genetic variability of P. clavata populations, as well as their ability to withstand perturbations.
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12686-020-01139-7) contains supplementary material, which is available to authorized users. * M. Padrón padron@obs‑banyuls.fr 1
Laboratoire d’Ecogeochimie des Environnements Benthique, CNRS, Sorbonne Université, UMR 8222, 66650 Banyuls‑sur‑Mer, France
2
INRA, GeT-PlaGe, Genotoul, 31326 Castanet‑Tolosan, France
3
Univ. Bordeaux, INRAE, BIOGECO, 33610 Cestas, France
The genetic structure of P. clavata populations has usually been studied with the use of a few microsatellite markers, sometimes resulting in conflicting results (Pilczynska et al. 2016; Padrón et al. 2018), and thus motivating the development of SNP markers for the species. Here, we describe a set of 118 SNP markers developed for population genetics of P. clavata, that were analyzed using iPLEX Gold technology on a MassARRAY System (Agena Bioscience, San Diego, USA).
Material and methods Transcriptome sequencing Total RNA from ten individuals was used to sequence the transcriptome of P. clavata, using paired-end Illumina HiSeq 3000. RNAseq was performed at the GeT-PlaGe core facility, INRA Toulouse. RNA-seq libraries were prepared according to Illumina’s protocols using the Illumina TruSeq Stranded mRNA sample prep kit to analyze mRNA. Briefly, mRNA was selected using poly-T beads. Then, RNA were fragmented to generate double stranded cDNA and adaptators were ligate
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