New polymorphic microsatellite loci revealed for the dusky shark Carcharhinus obscurus through Ion Proton double-digest RAD sequencing

Abstract

The non-model shark species, dusky shark Carcharhinus obscurus, is a bio-economically and recreationally important shark in many areas of its range. Despite of the fishery importance of C. obscurus few genetic resources are currently available for the species. Here, we report on the isolation of eight novel microsatellite loci from C. obscurus using a double-digest restriction site associated DNA (RAD) sequencing approach on the Ion Proton semiconductor platform (ddRADseq-ion). We characterised the loci in 26 individuals and all loci were polymorphic, exhibiting 5-10 alleles (average 6.6), and observed and expected heterozygosities of 0.385-0.962 and 0.479-0.847, respectively. We found that all pairs of loci were in linkage equilibrium and conformed to Hardy-Weinberg expectations. The loci reported in this study are only the second set of microsatellite loci ever characterized for C. obscurus and will be valuable for molecular ecology studies for this vulnerable species.

Taking Advantage of the Genomics Revolution for Monitoring and Conservation of Chondrichthyan Populations

“…Double digest RAD-seq (ddRAD-seq) was used to identify 8 novel microsatellite loci to assist molecular ecology research in the dusky shark (Carcharhinus melanopterus), an economically and recreationally important species [76]. Hybridization-based gene capture determined the evolutionary history of Carcharhinus melanopterus metapopulations by sampling many loci from few individuals [74].…”

Microsatellite development and detection of admixture among three sympatric Haploblepharus species (Carcharhiniformes: Scyliorhinidae)

“…However, recent advances in high‐throughput sequencing technologies have allowed for the recovery of a larger number of molecular markers (e.g. microsatellites) from non‐model organisms (Maduna et al, 2018; Maduna, Rossouw, da Silva, Soekoe, & Bester‐van der Merwe, 2017; Pirog, Blaison, Jaquemet, Soria, & Magalon, 2015). Furthermore, owing to highly conserved microsatellite flanking sequences (Martin, Pardini, Noble, & Jones, 2002), cross‐species amplification has been demonstrated in chondrichthyans with relatively high success rates (Blower, Corley, Hereward, Riginos, & Ovenden, 2015; Griffiths et al, 2011).…”