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Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome

The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across th...

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Autores principales: Tsangaras, Kyriakos, Siracusa, Matthew C., Nikolaidis, Nikolas, Ishida, Yasuko, Cui, Pin, Vielgrader, Hanna, Helgen, Kristofer M., Roca, Alfred L., Greenwood, Alex D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994108/
https://www.ncbi.nlm.nih.gov/pubmed/24752422
http://dx.doi.org/10.1371/journal.pone.0095633
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author Tsangaras, Kyriakos
Siracusa, Matthew C.
Nikolaidis, Nikolas
Ishida, Yasuko
Cui, Pin
Vielgrader, Hanna
Helgen, Kristofer M.
Roca, Alfred L.
Greenwood, Alex D.
author_facet Tsangaras, Kyriakos
Siracusa, Matthew C.
Nikolaidis, Nikolas
Ishida, Yasuko
Cui, Pin
Vielgrader, Hanna
Helgen, Kristofer M.
Roca, Alfred L.
Greenwood, Alex D.
author_sort Tsangaras, Kyriakos
collection PubMed
description The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin.
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spelling pubmed-39941082014-04-25 Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome Tsangaras, Kyriakos Siracusa, Matthew C. Nikolaidis, Nikolas Ishida, Yasuko Cui, Pin Vielgrader, Hanna Helgen, Kristofer M. Roca, Alfred L. Greenwood, Alex D. PLoS One Research Article The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin. Public Library of Science 2014-04-21 /pmc/articles/PMC3994108/ /pubmed/24752422 http://dx.doi.org/10.1371/journal.pone.0095633 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration, which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
spellingShingle Research Article
Tsangaras, Kyriakos
Siracusa, Matthew C.
Nikolaidis, Nikolas
Ishida, Yasuko
Cui, Pin
Vielgrader, Hanna
Helgen, Kristofer M.
Roca, Alfred L.
Greenwood, Alex D.
Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
title Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
title_full Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
title_fullStr Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
title_full_unstemmed Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
title_short Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
title_sort hybridization capture reveals evolution and conservation across the entire koala retrovirus genome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994108/
https://www.ncbi.nlm.nih.gov/pubmed/24752422
http://dx.doi.org/10.1371/journal.pone.0095633
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