TY  - JOUR
A1  - Cui, Pin
A1  - Löber, Ulrike
A1  - Alquezar-Planas, David E.
A1  - Ishida, Yasuko
A1  - Courtiol, Alexandre
A1  - Timms, Peter
A1  - Johnson, Rebecca N.
A1  - Lenz, Dorina
A1  - Helgen, Kristofer M.
A1  - Roca, Alfred L.
A1  - Hartman, Stefanie
A1  - Greenwood, Alex D.
T1  - Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome
JF  - PeerJ
N2  - 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.
KW  - Integration sites
KW  - Retroviral endogenization
KW  - KoRV
KW  - Target enrichment
KW  - Clustering
Y1  - 2016
U6  - https://doi.org/10.7717/peerj.1847
SN  - 2167-8359
VL  - 4
PB  - PeerJ Inc.
CY  - London
ER  -