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Targeted Capture of...
Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis
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Platt, Roy N., II (författare)
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Zhang, Yuhua (författare)
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Witherspoon, David J. (författare)
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Xing, Jinchuan (författare)
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- Suh, Alexander (författare)
- Uppsala universitet,Evolutionsbiologi
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Keith, Megan S. (författare)
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Jorde, Lynn B. (författare)
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Stevens, Richard D. (författare)
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Ray, David A. (författare)
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(creator_code:org_t)
- 2015-05-25
- 2015
- Engelska.
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 7:6, s. 1664-1675
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://academic.oup...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- 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 few well-studied species. To address this problem, we have 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 genome by comparing to the M. lucifugus reference genome. On average, eachVes insertion was sequenced to 129.6 x 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.
Ämnesord
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
Nyckelord
- rare genomic events
- Dollo parsimony
- retrotransposon
- phylogenetics
- Myotis lucifugus
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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- Av författaren/redakt...
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Platt, Roy N., I ...
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Zhang, Yuhua
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Witherspoon, Dav ...
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Xing, Jinchuan
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Suh, Alexander
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Keith, Megan S.
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visa fler...
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Jorde, Lynn B.
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Stevens, Richard ...
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Ray, David A.
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visa färre...
- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Biologi
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Genome Biology a ...
- Av lärosätet
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Uppsala universitet