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Broad-scale phylogenomics provides insights into retrovirus–host evolution
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
2013 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, no 50, 20146-20151 p.Article in journal (Refereed) Published
Abstract [en]

Genomic data provide an excellent resource to improve understanding of retrovirus evolution and the complex relationships among viruses and their hosts. In conjunction with broad-scale in silico screening of vertebrate genomes, this resource offers an opportunity to complement data on the evolution and frequency of past retroviral spread and so evaluate future risks and limitations for horizontal transmission between different host species. Here, we develop a methodology for extracting phylogenetic signal from large endogenous retrovirus (ERV) datasets by collapsing information to facilitate broad-scale phylogenomics across a wide sample of hosts. Starting with nearly 90,000 ERVs from 60 vertebrate host genomes, we construct phylogenetic hypotheses and draw inferences regarding the designation, host distribution, origin, and transmission of the Gammaretrovirus genus and associated class I ERVs. Our results uncover remarkable depths in retroviral sequence diversity, supported within a phylogenetic context. This finding suggests that current infectious exogenous retrovirus diversity may be underestimated, adding credence to the possibility that many additional exogenous retroviruses may remain to be discovered in vertebrate taxa. We demonstrate a history of frequent horizontal interorder transmissions from a rodent reservoir and suggest that rats may have acted as important overlooked facilitators of gammaretrovirus spread across diverse mammalian hosts. Together, these results demonstrate the promise of the methodology used here to analyze large ERV datasets and improve understanding of retroviral evolution and diversity for utilization in wider applications.

Place, publisher, year, edition, pages
2013. Vol. 110, no 50, 20146-20151 p.
National Category
Medical and Health Sciences Bioinformatics and Systems Biology
Research subject
Biology with specialization in Evolutionary Genetics; Biology with specialization in Evolutionary Organismal Biology; Biology with specialization in Microbiology; Bioinformatics
Identifiers
URN: urn:nbn:se:uu:diva-211542DOI: 10.1073/pnas.1315419110ISI: 000328061700050OAI: oai:DiVA.org:uu-211542DiVA: diva2:667361
Available from: 2013-11-26 Created: 2013-11-26 Last updated: 2017-12-06Bibliographically approved

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Publisher's full texthttp://www.ncbi.nlm.nih.gov/pubmed/24277832

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Hayward, AlexanderGrabherr, ManfredJern, Patric

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