Isolation and characterization of 21 polymorphic microsatellite loci for the rockpool shrimp Palaemon elegans using Illumina MiSeq sequencing

Abstract

The rockpool shrimp Palaemon elegans is considered an important crustacean species within the European coastline fauna. This species is experiencing an ongoing geographical expansion beyond its native distribution range due to unintentional human introductions. A better knowledge of the genetic diversity, geographic structure and connectivity of its populations is necessary. In the present study, microsatellite loci were isolated using the Illumina MiSeq platform. The microsatellite-enriched library sequencing produced 3.9 million raw reads. Reads were processed and primer pairs were designed for microsatellite sequences amplification. Ninety-six microsatellite loci were preliminary screened in individuals from Atlantic and Mediterranean localities. From them, 21 loci exhibited reliable polymorphism and were thoroughly characterized in 30 individuals from a Cantabrian locality (Spain). No linkage disequilibrium between pairs of loci was detected. Number of alleles per locus ranged from 2 to 12. Observed and expected heterozygosities ranged from 0.033 to 0.833 and from 0.033 to 0.869 respectively. No significant departure from the Hardy-Weinberg equilibrium was detected in most of loci. This is the first time that microsatellite markers have been developed for P. elegans. This characterized microsatellite suite provides new suitable tools for further analyses, facilitating the understanding of population genetics both in natural and introduced populations.

Mitogenome phylogenetics in the genus Palaemon (Crustacea: Decapoda) sheds light on species crypticism in the rockpool shrimp P. elegans

“…This genetic pattern was supported in later phylogeographic studies in the Mediterranean Sea also using mtDNA data [21,22]. Very recently, we have developed polymorphic microsatellite loci for this species [23] and accomplished a large analysis along its native distribution range that corroborated two clearly genetically distinct groups within P. elegans [13]. Our work strongly supported the existence of a cryptic and sympatric species within P. elegans in the Mediterranean Sea, providing nuclear evidence for the divergence signatures previously detected at mitochondrial level.…”

Development and characterization of a duplex PCR assay in Chinese sturgeon (Acipenser sinensis) for genetic analysis

“…The polyploidy nature of Chinese sturgeon is extremely complicated and more investigation should be taken to study the tetraploid nature of the genome of Chinese sturgeon. All of the 10 loci showed low null allele frequencies, <0.2 according to previously reported 33 . The null alleles were found in the AS078 and ZHX43 (11% and 15%), suggesting high amplification mispriming due to its genetic divergence from the sample.…”

Genetic diversity and population structure of the rockpool shrimp Palaemon elegans based on microsatellites: evidence for a cryptic species and differentiation across the Atlantic–Mediterranean transition

“…Thanks to the advent of high-throughput sequencing technologies, the development of microsatellite markers in non-model species has become a rapid and cost-effective process 26 . Precisely, we isolated and characterized 21 novel polymorphic microsatellite loci for Palaemon elegans using Illumina MiSeq sequencing 27 .…”