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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.
Highlights
There are two main classification systems that include LTR retrotransposons (LTR-RTNs) in their taxonomies: (1) the International Committee on the Taxonomy of Viruses (ICTV), which categorizes the plethora of viruses into a single scheme that reflects their evolutionary relationships [1]; and (2) the unified classification system for eukaryotic transposable elements (TEs), which was proposed in a seminal 2007 Nature Review paper [2], and provides standardized nomenclature rules and simple classification strategies for the efficient identification of
To better capture the diversity of the Pseudoviridae family, we used a large set of elements (Additional file 1) including all ICTV exemplars of the three genera, LTRRTNs used in previous similar studies [15,16,19], and Sirevirus representatives from all plant hosts that are present in MASiVEdb
The ICTV, and especially the TE-based system proposed by Wicker et al [2], are indispensable resources for the challenging identification and annotation of TEs in eukaryotic genomes
Summary
There are two main classification systems that include LTR retrotransposons (LTR-RTNs) in their taxonomies: (1) the International Committee on the Taxonomy of Viruses (ICTV), which categorizes the plethora of viruses into a single scheme that reflects their evolutionary relationships [1]; and (2) the unified classification system for eukaryotic transposable elements (TEs), which was proposed in a seminal 2007 Nature Review paper [2], and provides standardized nomenclature rules and simple classification strategies for the efficient identification of. The most plausible scenario suggests that retroviruses evolved from Gypsy LTR-RTNs after the acquisition of an envelope gene [6], which permitted an infectious extracellular stage Due to this relationship, and a limited number of LTR-RTNs contain a putative envelope-like gene, of which only the Gypsy element in Drosophila has been found to be infectious [7], ICTV has incorporated LTR-RTNs in its virus-based scheme and classified them as Pseudoviridae (that is, Copia) and Metaviridae (that is, Gypsy). A limited number of LTR-RTNs contain a putative envelope-like gene, of which only the Gypsy element in Drosophila has been found to be infectious [7], ICTV has incorporated LTR-RTNs in its virus-based scheme and classified them as Pseudoviridae (that is, Copia) and Metaviridae (that is, Gypsy) Both families are divided in three genera: for Pseudoviridae these are the Sirevirus, Pseudovirus, and Hemivirus genera. We indicate that only Sireviruses form a monophyletic group within the Pseudoviridae and that the phylogenetic basis for the division of Pseudoviruses and Hemiviruses is unclear
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