dc.contributor.author
Cui, Pin
dc.contributor.author
Löber, Ulrike
dc.contributor.author
Alquezar-Planas, David E.
dc.contributor.author
Ishida, Yasuko
dc.contributor.author
Courtiol, Alexandre
dc.contributor.author
Timms, Peter
dc.contributor.author
Johnson, Rebecca N.
dc.contributor.author
Lenz, Dorina
dc.contributor.author
Helgen, Kristofer M.
dc.contributor.author
Roca, Alfred L.
dc.contributor.author
Hartman, Stefanie
dc.contributor.author
Greenwood, Alex D.
dc.date.accessioned
2018-06-08T03:24:51Z
dc.date.available
2016-05-18T10:05:05.059Z
dc.identifier.uri
https://refubium.fu-berlin.de/handle/fub188/15124
dc.identifier.uri
http://dx.doi.org/10.17169/refubium-19312
dc.description.abstract
Background. Retroviral integration into the host germline results in permanent
viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is
currently invading the germline of the koala (Phascolarctos cinereus) and
provides a unique opportunity for studying retroviral endogenization. Previous
analysis of KoRV integration patterns in modern koalas demonstrate that they
share integration sites primarily if they are related, indicating that the
process is currently driven by vertical transmission rather than infection.
However, due to methodological challenges, KoRV integrations have not been
comprehensively characterized. Results. To overcome these challenges, we
applied and compared three target enrichment techniques coupled with next
generation sequencing (NGS) and a newly customized sequence-clustering based
computational pipeline to determine the integration sites for 10 museum
Queensland and New South Wales (NSW) koala samples collected between the 1870s
and late 1980s. A secondary aim of this study sought to identify common
integration sites across modern and historical specimens by comparing our
dataset to previously published studies. Several million sequences were
processed, and the KoRV integration sites in each koala were characterized.
Conclusions. Although the three enrichment methods each exhibited bias in
integration site retrieval, a combination of two methods, Primer Extension
Capture and hybridization capture is recommended for future studies on
historical samples. Moreover, identification of integration sites shows that
the proportion of integration sites shared between any two koalas is quite
small.
en
dc.format.extent
29 Seiten
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject.ddc
600 Technik, Medizin, angewandte Wissenschaften::630 Landwirtschaft
dc.title
Comprehensive profiling of retroviral integration sites using target
enrichment methods from historical koala samples without an assembled
reference genome
dc.type
Wissenschaftlicher Artikel
dcterms.bibliographicCitation
Peer J. - 4 (2016), Artikel Nr. e1847
dcterms.bibliographicCitation.doi
10.7717/peerj.1847
dcterms.bibliographicCitation.url
http://doi.org/10.7717/peerj.1847
refubium.affiliation
Veterinärmedizin
de
refubium.mycore.fudocsId
FUDOCS_document_000000024565
refubium.note.author
Der Artikel wurde in einer Open-Access-Zeitschrift publiziert.
refubium.resourceType.isindependentpub
no
refubium.mycore.derivateId
FUDOCS_derivate_000000006430
dcterms.accessRights.openaire
open access