Microsatellites and microhaplotypes are genetic markers that, through DNA amplicon sequencing, generate genotypes to distinguish between individuals from wildlife populations. Here, these markers were sequenced in caribou (Rangifer tarandus) specimens using Oxford Nanopore's MinION DNA sequencer for the first time. Microsatellite loci previously sequenced with an Illumina MiSeq were compared to MinION Mk1B sequencing data for the same samples/loci, revealing highly consistent microsatellite characterization across platforms. Additionally, a novel panel of caribou microhaplotype loci was developed and sequenced on the MinION Mk1B and Illumina MiSeq. Microhaplotype characterization of the same samples revealed that ambiguous read distributions for the top 3 reads per locus is a key challenge, particularly for the MinION, that hinders concordant haplotype calls across platforms. Potential reasons for this ambiguity include duplicated gene regions and PCR errors. Removing suspected duplicated gene regions and reducing the number of PCR cycles during target DNA amplification may mitigate this problem.
Author Keywords: Conservation Genomics, DNA Profiling, Microhaplotypes, Microsatellites, Nanopore Sequencing, Wildlife Monitoring