Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis.
Bottom Line: Dollo parsimony analysis of more than 85,000 phylogenetically informative insertions recovered strongly supported, monophyletic clades that correspond with the biogeography of each taxa.This phylogeny is similar to previously published mitochondrial phylogenies, with the exception of the placement of M. vivesi.These results support the utility of our variation on ME-Scan to identify polymorphic retrotransposon insertions in taxa without a reference genome and for large-scale retrotransposon-based phylogenetics.
Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.Show MeSH
Related in: MedlinePlus
Mentions: A summary of the biochemical pipeline is shown in figure 1A–H. Genomic DNA (gDNA) was extracted from tissue samples using a standard phenol–chloroform/ethanol precipitation protocol. For each sample, 10 µg of gDNA was fragmented to an average size of 1 kb on a Covaris S220 Focused-ultrasonicator using the following parameters: Peak incident power, 105 W; duty factor, 5.0%; cycles per burst, 200; time, 40 s; temperature, 7 °C (fig. 1A). Fragmented gDNA was purified and concentrated using Qiagen QIAquick PCR purification columns (Qiagen, Germantown, MD) using the recommended protocol.Fig. 1.—
Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.