Targeted capture of phylogenetically informative ves SINE insertions in genus Myotis

Roy N. Platt, Yuhua Zhang, David J. Witherspoon, Jinchuan Xing, Alexander Suh, Megan S. Keith, Lynn B. Jorde, Richard D. Stevens, David A. Ray

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

Identification of retrotransposon insertions in nonmodel taxa can be technically challenging and costly. This has inhibited progress in understanding retrotransposon insertion dynamics outside of a fewwell-studied species. To address this problem,wehave extended a retrotransposon-based capture and sequence method (ME-Scan [mobile element scanning]) to identify insertions belonging to the Ves family of short interspersed elements (SINEs) across seven species of the bat genus Myotis. We identified between 120,000 and 143,000 SINE insertions in six taxa lacking a draft genomeby comparing to the M. lucifugus reference genome.Onaverage, eachVes insertion was sequenced to 129.6 × coverage. When mapped back to the M. lucifugus reference genome, all insertions were confidently assigned within a 10-bp window. Polymorphic Ves insertions were identified in each taxon based on their mapped locations. Using cross-species comparisons and the identified insertion positions, a presence-absence matrix was created for approximately 796,000 insertions. 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.

Original languageEnglish
Pages (from-to)1664-1675
Number of pages12
JournalGenome Biology and Evolution
Volume7
Issue number6
DOIs
StatePublished - Jun 2015

Keywords

  • Dollo parsimony
  • Myotis lucifugus
  • Phylogenetics
  • Rare genomic events
  • Retrotransposon

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