Data from: "Genome-wide microsatellite marker development from next-generation sequencing of two non-model bat species impacted by wind turbine mortality: Lasiurus borealis and L. cinereus (Vespertilionidae)" in Genomic Resources Notes accepted 1 October 2013 to 30 November 2013

Tree-roosting bats in the genus Lasiurus are widespread, migratory species that have not been well characterized for population genetic diversity and structure due to a lack of genetic resources. Generating genetic resources in Lasiurus is made pressing by the need for conservation genetic assessments of demographic trends in this genus, which comprise a large percentage of bat mortalities at wind turbine sites across North America. We report on marker development from whole-genome Illumina sequencing of the red bat (Lasirus borealis) and the hoary bat (L. cinereus). We generated paired-end libraries for a single individual of each species, sequenced on the Illumina HiSeq platform. We mapped a total of 46.6 million reads to the Myotis lucifigus reference genome, and used bioinformatics searches to identify tends of thousands of simple sequence repeats (SSRs) distributed across the bat genome. We selected 48 candidate microsatellite loci to develop cross-species primer sequences for Lasiurus, assembled these into multiplex combinations, and tested for amplification and polymorphism levels in a sample of 23 individuals from each of L. borealis and L. cinereus. In total, we identified 42 highly polymorphic loci that could be robustly amplified and scored, the majority of which (39) were also combinable into highly multiplexed assays of 4-8 loci each. The combination of new genomic sequence assemblies, a large set of highly polymorphic microsatellite loci, and the ability to efficiently multiplex represents a significant contribution to the genetic resources available for population and comparative genetic studies of bats