Tri- and tetranucleotide microsatellite markers developed based on the genome of the common vampire bat (Desmodus rotundus)

This data resource contains information on tri- and tetranucleotide microsatellite markers that have been developed based on the whole genome of the common vampire bat, Desmodus rotundus. 1. Software for screening genome resource We downloaded v.2 of the common vampire bat (Desmodus rotundus) reference genome from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_002940915.1/#/st) to identify a new set of candidate microsatellite loci. We used Msatcommander v.1.0.8-beta (Faircloth 2008) with default parameters and the search parameter settings for tri- and tetranucleotide sites set to 10. The build-in function for primer design (Primer3; Rozen Skaletsky 2000) was then used with mostly default settings and GC-content for primers to vary between 40 and 60%. Overall, this yielded 6080 potential loci (see sheet "All candidate loci" in the Excel file "Markers") and 4309 candidate loci with associated primers (sheet "Candidate loci with primers" in the file "Markers"). We then selected candidates that had a product size of ca. 120-300 bp and 10-15 repeated motifs. Twenty such candidates have been further evaluated in the lab and 18 have successfully been genotyped. Faircloth, B. C. (2008). MSATCOMMANDER: Detection of microsatellite repeat arrays and automated, locus‐specific primer design. Molecular ecology resources, 8(1), 92-94. Rozen, S., Skaletsky, H. (2000). Primer3 on the WWW for general users and for biologist programmers. In Bioinformatics methods and protocols (pp. 365-386). Humana Press, Totowa, NJ. 2. Lab work We conducted uniplex PCRs using a three-primer system (Schuelke 2000) with an M13-tailed forward primer and a fluorescent-labeled M13 primer to amplify the target fragments. Primer sequences and information on fragment length and the sequence of the repeating motif can be found in the sheet "overview markers" in the Excel file "Markers". Details on preparation and cycling conditions are described in the sheet "PCR" in the Excel file "Markers". Fragments were analyzed on a SeqStudio™ Genetic Analyzer and genotyping was done in the software GeneMapper 6. All details are described in the sheet "Seq Studio" in the Excel file "Markers". Schuelke, M. (2000). An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18(2), 233-234. 3. Allele frequencies and deviance from Hardy-Weinberg Equilibrium We calculated allele frequencies for 18 markers based on 42 adult female vampire bats. We used the R library 'genetics' to test for deviance from Hardy Weinberg Equilibrium. Results are summarized in the sheet "overview markers" in the Excel file "Markers".