Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA

Microsatellite markers have played a major role in ecological,
evolutionary and conservation research during the past 20 years. However,
technical constrains related to the use of capillary electrophoresis and a
recent technological revolution that has impacted other marker types have
brought to question the continued use of microsatellites for certain
applications. We present a study for improving microsatellite genotyping
in ecology using high-throughput sequencing (HTS). This approach entails
selection of short markers suitable for HTS, sequencing PCR-amplified
microsatellites on an Illumina platform and bioinformatic treatment of the
sequence data to obtain multilocus genotypes. It takes advantage of the
fact that HTS gives direct access to microsatellite sequences, allowing
unambiguous allele identification and enabling automation of the
genotyping process through bioinformatics. In addition, the massive
parallel sequencing abilities expand the information content of single
experimental runs far beyond capillary electrophoresis. We illustrated the
method by genotyping brown bear samples amplified with a multiplex PCR of
13 new microsatellite markers and a sex marker. HTS of microsatellites
provided accurate individual identification and parentage assignment and
resulted in a significant improvement of genotyping success (84%) of
faecal degraded DNA and costs reduction compared to capillary
electrophoresis. The HTS approach holds vast potential for improving
success, accuracy, efficiency and standardization of microsatellite
genotyping in ecological and conservation applications, especially those
that rely on profiling of low-quantity/quality DNA and on the construction
of genetic databases. We discuss and give perspectives for the
implementation of the method in the light of the challenges encountered in
wildlife studies.