Bousios et al. BMC Genomics 2010, 11:89 http://www.biomedcentral.com/1471-2164/11/89 R E S E A R C H A R T I C L E Open Access Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants? Alexandros Bousios1*, Nikos Darzentas2, Athanasios Tsaftaris2,3, Stephen R Pearce1 Abstract Background: Retrotransposons are key players in the evolution of eukaryotic genomes. Moreover, it is now known that some retrotransposon classes, like the abundant and plant-specific Sireviruses, have intriguingly distinctive host preferences. Yet, it is largely unknown if this bias is supported by different genome structures. Results: We performed sensitive comparative analysis of the genomes of a large set of Ty1/copia retrotransposons. We discovered that Sireviruses are unique among Pseudoviridae in that they constitute an ancient genus characterized by vastly divergent members, which however contain highly conserved motifs in key non-coding regions: multiple polypurine tract (PPT) copies cluster upstream of the 3’ long terminal repeat (3’LTR), of which the terminal PPT tethers to a distinctive attachment site and is flanked by a precisely positioned inverted repeat. Their LTRs possess a novel type of repeated motif (RM) defined by its exceptionally high copy number, symmetry and core CGG-CCG signature. These RM boxes form CpG islands and lie a short distance upstream of a conserved promoter region thus hinting towards regulatory functions. Intriguingly, in the envelope-containing Sireviruses additional boxes cluster at the 5’ vicinity of the envelope. The 5’LTR/internal domain junction and a polyC-rich integrase signal are also highly conserved domains of the Sirevirus genome. Conclusions: Our comparative analysis of retrotransposon genomes using advanced in silico methods highlighted the unique genome organization of Sireviruses. Their structure may dictate a life cycle with different regulation and transmission strategy compared to other Pseudoviridae, which may contribute towards their pattern of distribution within and across plants. Background Retrotransposons and retroviruses (collectively referred as retroelements) can replicate their genomes via an RNA intermediate and insert the copies into new chro- mosomal locations of the host organism [1,2]. This ‘copy and paste’ process has the potential to greatly amplify their abundance, even over short evolutionary timescales, enabling them to become a major compo- nent of genomes [3-5]. Unlike retrotransposons, retro- viruses have additional coding capacity in the form of an envelope (ENV) gene that allows them to enter the extracellular space and infect other individuals. Retro- transposons lack the ENV gene and cannot escape the cell, however they are free to reinfect their host genome. * Correspondence: alexandros.bousios@gmail.com 1Department of Biology and Environmental Science, School of Life Sciences, University of Sussex, Brighton, UK Long Terminal Repeat (LTR) retrotransposons form the most abundant transposable element type in plants, lar- gely accounting for the vast differences in genome sizes [6]. Small genome plants like Arabidopsis (121 Mbp) and rice (389 Mbp) are sparsely populated by LTR ret- rotransposons, 5.6% [7] and 17% [8] respectively. In con- trast, the LTR retrotransposon-derived fraction of medium/large genomes may reach up to 75% in maize (2.300 Mbp) [9,10] and 70% in barley (5439 Mbp) [11]. The two main superfamilies of LTR retrotransposons are the Ty1/copia (Pseudoviridae) and Ty3/gypsy (Meta- viridae) [12], which differ in the order they package their genes in the coding domains. Both typically con- tain the gag gene and the pol gene region. gag encodes a capsid protein that forms the virus-like particle (VLP), which houses one or two RNA genomes and the enzymes for the cytoplasmic step of reverse © 2010 Bousios et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.