Nomenclature for endogenous retrovirus (ERV) loci

Gifford, R. J. , Blomberg, J., Coffin, J. M., Fan, H., Heidmann, T., Mayer, J., Stoye, J., Tristem, M. and Johnson, W. E. (2018) Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology, 15, 59. (doi:10.1186/s12977-018-0442-1) (PMID:30153831) (PMCID:PMC6114882)

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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 unifed 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 identifers for individual loci, but also denote orthologous relationships between ERVs in diferent 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

Item Type:Articles
Additional Information:RJG was supported by a grant from the UK Medical Research Council (No. MC_UU_12014/10).
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Gifford, Dr Robert
Authors: Gifford, R. J., Blomberg, J., Coffin, J. M., Fan, H., Heidmann, T., Mayer, J., Stoye, J., Tristem, M., and Johnson, W. E.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Retrovirology
Publisher:BioMed Central
ISSN:1742-4690
ISSN (Online):1742-4690
Copyright Holders:Copyright © 2018 The Authors
First Published:First published in Retrovirology 15: 59
Publisher Policy:Reproduced under a Creative Commons License

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