Large-scale identification of microsatellite loci from multiple otter (Mammalia, Carnivora, Lutrinae) species using whole genome sequence data

Abstract

The development of molecular studies on elusive, rare, and/or poorly known species faces challenges due to the lack of suitable markers. Species-specific microsatellite markers minimize bias, offer better performance, and are cost-effective, aiding the development of population genetic studies. The use of whole-genome sequences allows for the development of species-specific microsatellite markers and their survey in closely related species, enabling the discovery of shared markers that can facilitate comparative studies. Lutrinae includes 14 extant species of otters. Despite their worrisome conservation status, due to inherent characteristics of these species that make their study difficult by traditional methods, many of them lack reliable population genetic data, limiting conservation efforts. In this study, we employed a multi-taxon approach to identify a large number of novel microsatellite loci for 11 of the 14 otter species, assessing whether the identified loci were shared among different taxa. We identified a total of 23,320 microsatellite loci across 11 species, which were reduced to 12,573 after stringent filtering criteria. Primer design was completed successfully for 420 and 259 unique loci, considering two minimum melting temperatures. We validated marker efficiency by testing the 81 loci designed for two Asian species. Of these, 51 loci yielded reliable microsatellite genotypes in both species, with 34 showing allelic variation in at least one of them. These results demonstrate that these markers are applicable in empirical genotyping for both their target and closely related ones.