Targeted capture of phylogenetically informative ves SINE insertions in genus Myotis

Platt, Roy N., Zhang, Yuhua, Witherspoon, David J., Xing, Jinchuan, Suh, Alexander ORCID: https://orcid.org/0000-0002-8979-9992, Keith, Megan S., Jorde, Lynn B., Stevens, Richard D. and Ray, David A. (2015) Targeted capture of phylogenetically informative ves SINE insertions in genus Myotis. Genome Biology and Evolution, 7 (6). pp. 1664-1675. ISSN 1759-6653

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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.

Item Type: Article
Additional Information: Publisher Copyright: © The Author(s) 2015.
Uncontrolled Keywords: dollo parsimony,myotis lucifugus,phylogenetics,rare genomic events,retrotransposon,medicine(all) ,/dk/atira/pure/subjectarea/asjc/2700
Faculty \ School: Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 16 Sep 2022 15:35
Last Modified: 24 Sep 2022 07:16
URI: https://ueaeprints.uea.ac.uk/id/eprint/88413
DOI: 10.1093/gbe/evv099

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