Comprehensive profiling of retroviral integration sites using enrichment methods from historical koala samples without a reference genome

Pin Cui; Ulrike Lober; Yasuko Ishida; David Alquezar-Planas; Alexandre Courtiol; Peter Timms; Rebecca Johnson; Dorina Lenz; Kristofer Helgen; Alfred L Roca; Stefanie Hartmann; Alex D Greenwood

doi:10.7717/peerj.1847

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Comprehensive profiling of retroviral integration sites using enrichment methods from historical koala samples without a reference genome

Journal article

Open access

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Comprehensive profiling of retroviral integration sites using enrichment methods from historical koala samples without a reference genome

Pin Cui, Ulrike Lober, Yasuko Ishida, David Alquezar-Planas, Alexandre Courtiol, Peter Timms, Rebecca Johnson, Dorina Lenz, Kristofer Helgen, Alfred L Roca, …

PeerJ, Vol.4, e1847

2016

DOI: https://doi.org/10.7717/peerj.1847

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Abstract

integration sites

retroviral endogenization

KoRV

target enrichment

clustering

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.

Details

Title: Comprehensive profiling of retroviral integration sites using enrichment methods from historical koala samples without a reference genome
Authors: Pin Cui (Author) - Leibniz Institute for Zoo and Wildlife Research, Germany
Ulrike Lober (Author) - Leibniz Institute for Zoo and Wildlife Research, Germany
Yasuko Ishida (Author) - Leibniz Institute for Zoo and Wildlife Research, Germany
David Alquezar-Planas (Author) - University of Illinois at Urbana-Champaign, United States
Alexandre Courtiol (Author) - Leibniz Institute for Zoo and Wildlife Research, Germany
Peter Timms (Author) - University of the Sunshine Coast - Faculty of Science, Health, Education and Engineering
Rebecca Johnson (Author) - Australian Museum
Dorina Lenz (Author) - Leibniz Institute for Zoo and Wildlife Research, Germany
Kristofer Helgen (Author) - Smithsonian Institute, United States
Alfred L Roca (Author) - University of Illinois at Urbana-Champaign, United States
Stefanie Hartmann (Author) - University of Potsdam, Germany
Alex D Greenwood (Author) - Leibniz Institute for Zoo and Wildlife Research, Germany
Publication details: PeerJ, Vol.4, e1847; 29
Publisher: PeerJ, Ltd.
Date published: 2016
DOI: 10.7717/peerj.1847
ISSN: 2167-8359
Copyright note: Copyright © 2016 Cui et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
Organisation Unit: University of the Sunshine Coast, Queensland; Centre for Bioinnovation
Language: English
Record Identifier: 99449256902621
Output Type: Journal article

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