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Whole-genome comparison of endogenous retrovirus segregation across wild and domestic host species populations
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.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 43, p. 11012-11017, article id 201815056Article in journal (Refereed) Published
Abstract [en]

Although recent advances in sequencing and computational analyses have facilitated use of endogenous retroviruses (ERVs) for deciphering coevolution among retroviruses and their hosts, sampling effects from different host populations present major challenges. Here we utilize available whole-genome data from wild and domesticated European rabbit (Oryctolagus cuniculus sp.) populations, sequenced as DNA pools by paired-end Illumina technology, for identifying segregating reference as well as nonreference ERV loci, to reveal their variation along the host phylogeny and domestication history. To produce new viruses, retroviruses must insert a proviral DNA copy into the host nuclear DNA. Occasional proviral insertions into the host germline have been passed down through generations as inherited ERVs during millions of years. These ERVs represent retroviruses that were active at the time of infection and thus present a remarkable record of historical virus–host associations. To examine segregating ERVs in host populations, we apply a reference library search strategy for anchoring ERV-associated short-sequence read pairs from pooled whole-genome sequences to reference genome assembly positions. We show that most ERVs segregate along host phylogeny but also uncover radiation of some ERVs, identified as segregating loci among wild and domestic rabbits. The study targets pertinent issues regarding genome sampling when examining virus–host evolution from the genomic ERV record and offers improved scope regarding common strategies for single-nucleotide variant analyses in host population comparative genomics.

Place, publisher, year, edition, pages
2018. Vol. 115, no 43, p. 11012-11017, article id 201815056
Keywords [en]
endogenous, retrovirus, host population, segregation, comparative genomics, evolution
National Category
Evolutionary Biology
Identifiers
URN: urn:nbn:se:uu:diva-362814DOI: 10.1073/pnas.1815056115ISI: 000448040500066PubMedID: 30297425OAI: oai:DiVA.org:uu-362814DiVA, id: diva2:1254911
Funder
Swedish Research Council, VR-M 2015-02429
Note

Correction in: PNAS, vol. 115, issue 52, pages E12465. DOI: 10.1073/pnas.1820237116

Available from: 2018-10-10 Created: 2018-10-10 Last updated: 2019-01-14Bibliographically approved

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Rivas-Carrillo, Salvador DanielPettersson, MatsRubin, Carl-JohanJern, Patric

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