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Nomenclature for endogenous retrovirus (ERV) loci
Univ Glasgow, MRC, Ctr Virus Res, Glasgow, Lanark, Scotland.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology.ORCID iD: 0000-0001-6492-2491
Tufts Univ, Dept Mol Biol & Microbiol, Boston, MA 02111 USA.
Univ Calif Irvine, Dept Mol Biol & Biochem, Irvine, CA 92697 USA;Univ Calif Irvine, Canc Res Inst, Irvine, CA 92697 USA.
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2018 (English)In: Retrovirology, ISSN 1742-4690, E-ISSN 1742-4690, Vol. 15, article id 59Article, review/survey (Refereed) Published
Abstract [en]

Retroviral integration into germline DNA can result in the formation of a vertically inherited proviral sequence called an endogenous retrovirus (ERV). Over the course of their evolution, vertebrate genomes have accumulated many thousands of ERV loci. These sequences provide useful retrospective information about ancient retroviruses, and have also played an important role in shaping the evolution of vertebrate genomes. There is an immediate need for a unified system of nomenclature for ERV loci, not only to assist genome annotation, but also to facilitate research on ERVs and their impact on genome biology and evolution. In this review, we examine how ERV nomenclatures have developed, and consider the possibilities for the implementation of a systematic approach for naming ERV loci. We propose that such a nomenclature should not only provide unique identifiers for individual loci, but also denote orthologous relationships between ERVs in different species. In addition, we propose that-where possible-mnemonic links to previous, well-established names for ERV loci and groups should be retained. We show how this approach can be applied and integrated into existing taxonomic and nomenclature schemes for retroviruses, ERVs and transposable elements.

Place, publisher, year, edition, pages
BMC , 2018. Vol. 15, article id 59
Keywords [en]
Retrovirus, Nomenclature, Endogenous, Taxonomy, Classification
National Category
Genetics
Identifiers
URN: urn:nbn:se:uu:diva-364730DOI: 10.1186/s12977-018-0442-1ISI: 000443648700001PubMedID: 30153831OAI: oai:DiVA.org:uu-364730DiVA, id: diva2:1260131
Available from: 2018-11-01 Created: 2018-11-01 Last updated: 2018-11-01Bibliographically approved

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Blomberg, Jonas

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