Population genetic variation of microsatellite markers developed for Siberian fir (Abies sibirica Ledeb.) and European silver fir (Abies alba Mill.) using whole genome sequencing data

Abstract

The article presents the results of the search for microsatellite or simple sequence repeat (SSR) loci with tri-, tetra-, penta- and hexanucleotide tandem repeat motifs in the draft de novo assembly of the Siberian fir (Abies sibirica Ledeb.) genome and the development of convenient relatively highly and moderately polymorphic markers that can be easily genotyped even by simple gel electrophoresis. In total, 64 pairs of oligonucleotide polymerase chain reaction (PCR) primers for 32 detected microsatellite loci were designed and tested. Based on the testing results, 10 most promising polymorphic loci were selected and genotyped in eight natural populations of Siberian fir. Homologous microsatellite loci in the genome of European silver fir (Abies alba Mill.) were also identified by mapping Siberian fir contigs, containing SSR loci to the European silver fir genome assembly. A multiplex panel of 14 universal microsatellite loci was developed and genotyped in samples from four natural populations of A. alba and a small sample of eight Nordmann fir (Abies nordmanniana (Steven) Spach) trees.

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

“…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.…”