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Retrovirology. 2018 Aug 28;15(1):59. doi: 10.1186/s12977-018-0442-1.

Nomenclature for endogenous retrovirus (ERV) loci.

Author information

1
MRC-University of Glasgow Centre for Virus Research, Glasgow, UK. robert.gifford@glasgow.ac.uk.
2
Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
3
Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA.
4
Department of Molecular Biology and Biochemistry and Cancer Research Institute, University of California, Irvine, CA, 92697, USA.
5
Department of Molecular Physiology and Pathology of Infectious and Endogenous Retroviruses, CNRS UMR 9196, Institut Gustave Roussy, 94805, Villejuif, France.
6
Department of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, Homburg, Germany.
7
The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, UK.
8
Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK.
9
Biology Department, Boston College, Chestnut Hill, Massachusetts, 02467, USA. welkin.johnson@bc.edu.

Abstract

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.

KEYWORDS:

Classification; Endogenous; Nomenclature; Retrovirus; Taxonomy

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