Optimization of an amplicon sequencing‐based microsatellite panel and protocol for stock identification and kinship inference of lake trout (<i>Salvelinus namaycush</i>)

Marcy‐Quay, Benjamin; Wilson, Chris C.; Osborne, Christopher; Marsden, J. Ellen

doi:10.1002/ece3.10020

Cited by 2 publications

(1 citation statement)

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“…NGS techniques have simplified the identification and characterization of microsatellites, establishing them as valuable markers in ecology and evolution for non-model species [64,65]. NGS techniques enabled the reliable discovery of microsatellite markers, a usual method for the description of de novo microsatellites applied in recent studies [66][67][68][69][70]. In this study, we successfully characterized new loci and mitochondrial genomes while performing optimization and cross-species validation of multiplex assays in four species of supralittoral Ochthebius.…”

Section: Discussionmentioning

confidence: 99%

Novel Microsatellite Loci, Cross-Species Validation of Multiplex Assays, and By-Catch Mitochondrial Genomes on Ochthebius Beetles from Supratidal Rockpools

García-Meseguer,

Villastrigo,

Mirón-Gatón

et al. 2023

Insects

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Here we focus on designing, for the first time, microsatellite markers for evolutionary and ecological research on aquatic beetles from the genus Ochthebius (Coleoptera, Hydraenidae). Some of these non-model species, with high cryptic diversity, exclusively inhabit supratidal rockpools, extreme and highly dynamic habitats with important anthropogenic threats. We analysed 15 individuals of four species (O. lejolisii, O. subinteger, O. celatus, and O. quadricollis) across 10 localities from the Mediterranean coasts of Spain and Malta. Using next-generation sequencing technology, two libraries were constructed to interpret the species of the two subgenera present consistently (Ochthebius s. str., O. quadricollis; and Cobalius, the rest of the species). Finally, 20 markers (10 for each subgenus) were obtained and successfully tested by cross-validation in the four species under study. As a by-catch, we could retrieve the complete mitochondrial genomes of O. lejolisii, O. quadricollis, and O. subinteger. Interestingly, the mitochondrial genome of O. quadricollis exhibited high genetic variability compared to already published data. The novel SSR panels and mitochondrial genomes for Ochthebius will be valuable in future research on species identification, diversity, genetic structure, and population connectivity in highly dynamic and threatened habitats such as supratidal coastal rockpools.

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