BOUSIOS, Alexandros and Nikos DARZENTAS. Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world. Mobile DNA. London: BioMed Central, 2013, vol. 4, Mar, p. "nestránkováno", 5 pp. ISSN 1759-8753. doi:10.1186/1759-8753-4-9.
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Basic information
Original name Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world
Authors BOUSIOS, Alexandros and Nikos DARZENTAS.
Edition Mobile DNA, London, BioMed Central, 2013, 1759-8753.
Other information
Original language English
Type of outcome Article in a journal
Field of Study 30200 3.2 Clinical medicine
Country of publisher United Kingdom of Great Britain and Northern Ireland
Confidentiality degree is not subject to a state or trade secret
WWW URL
Impact factor Impact factor: 2.429
Organization unit Central European Institute of Technology
Doi http://dx.doi.org/10.1186/1759-8753-4-9
UT WoS 000318309600001
Keywords in English sirevirus; transposable elements; LTR retrotransposons ICTV; Phylogenetic analysis; Pseudoviridae; Copia; Plant genomes; Maize
Tags EDITORIAL, OA, podil
Tags International impact, Reviewed
Changed by Changed by: Olga Křížová, učo 56639. Changed: 28. 4. 2014 16:17.
Abstract
Sireviruses are an ancient and plant-specific LTR retrotransposon genus. They possess a unique genome structure that is characterized by a plethora of highly conserved sequence motifs in key domains of the non-coding genome, and often, by the presence of an envelope-like gene. Recently, their crucial role in the organization of the maize genome, where Sireviruses occupy approximately 21% of its nuclear content, was revealed, followed by an analysis of their distribution across the plant kingdom. It is now suggested that Sireviruses have been a major mediator of the evolution of many plant genomes. However, the name 'Sirevirus' has caused confusion in the scientific community in regards to their classification within the LTR retrotransposon order and their relationship with viruses - a situation that is not unique to Sireviruses, but also affects other LTR retrotransposon genera. Here, we clarify the phylogenetic position of Sireviruses as typical LTR retrotransposons of the Copia superfamily and explain that the confusion stems from the discrepancy in the categorization of LTR retrotransposons by the two main classification systems: the International Committee on the Taxonomy of Viruses (ICTV) system and the unified classification system for eukaryotic transposable elements. While the name 'Sirevirus' has been given by ICTV, we show that the transposable element system, which is more suitable for eukaryotic genome studies, lacks an appropriate taxonomic level for describing them. We urge for this inconsistency to be addressed. Finally, we provide data suggesting that of the three ICTV-proposed genera of the Pseudoviridae (that is, Copia) family, only Sireviruses form a monophyletic group, while the phylogenetic distinction between Pseudoviruses and Hemiviruses is unclear. We conclude that because of their ongoing important contribution to the classification of transposable elements, these schemes need to be frequently revisited and revised - as shown by the example of the Sirevirus LTR retrotransposon genus.
Links
ED1.1.00/02.0068, research and development projectName: CEITEC - central european institute of technology
EE2.3.20.0045, research and development projectName: Podpora profesního růstu a mezinárodní integrace výzkumných týmů v oblasti molekulární medicíny
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