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Nomenclature for endogenous retrovirus (ERV) loci
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 inf...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114882/ https://www.ncbi.nlm.nih.gov/pubmed/30153831 http://dx.doi.org/10.1186/s12977-018-0442-1 |
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author | Gifford, Robert J. Blomberg, Jonas Coffin, John M. Fan, Hung Heidmann, Thierry Mayer, Jens Stoye, Jonathan Tristem, Michael Johnson, Welkin E. |
author_facet | Gifford, Robert J. Blomberg, Jonas Coffin, John M. Fan, Hung Heidmann, Thierry Mayer, Jens Stoye, Jonathan Tristem, Michael Johnson, Welkin E. |
author_sort | Gifford, Robert J. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6114882 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-61148822018-09-04 Nomenclature for endogenous retrovirus (ERV) loci Gifford, Robert J. Blomberg, Jonas Coffin, John M. Fan, Hung Heidmann, Thierry Mayer, Jens Stoye, Jonathan Tristem, Michael Johnson, Welkin E. Retrovirology Review 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. BioMed Central 2018-08-28 /pmc/articles/PMC6114882/ /pubmed/30153831 http://dx.doi.org/10.1186/s12977-018-0442-1 Text en © The Author(s) 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Review Gifford, Robert J. Blomberg, Jonas Coffin, John M. Fan, Hung Heidmann, Thierry Mayer, Jens Stoye, Jonathan Tristem, Michael Johnson, Welkin E. Nomenclature for endogenous retrovirus (ERV) loci |
title | Nomenclature for endogenous retrovirus (ERV) loci |
title_full | Nomenclature for endogenous retrovirus (ERV) loci |
title_fullStr | Nomenclature for endogenous retrovirus (ERV) loci |
title_full_unstemmed | Nomenclature for endogenous retrovirus (ERV) loci |
title_short | Nomenclature for endogenous retrovirus (ERV) loci |
title_sort | nomenclature for endogenous retrovirus (erv) loci |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6114882/ https://www.ncbi.nlm.nih.gov/pubmed/30153831 http://dx.doi.org/10.1186/s12977-018-0442-1 |
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