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Mapping and Analysis of Sirevirus Elements / MASiVE

Transposable Elements (TEs) are highly active and mobile genetic elements that can be found within the genomes of virtually all living organisms. Initially considered as junk or selfish DNA due to their ability to replicate independently of their hosts, their profound influence in shaping eukaryotic genomes is now widely accepted. TEs can amplify in vast numbers, especially in plant genomes. For example, they occupy nearly 85% of the 2,300 Mb maize genome, the majority of which belong to a certain class called LTR retrotransposons.

Our team has delved into the lifestyle and histories of the ancient Sirevirus genus of the Copia LTR retrotransposon superfamily. Due to their envelope gene, Sireviruses may have retroviral properties, which differentiates them from the other Copia genera. They have exclusively proliferated within plant genomes, comprising a large proportion of the available TE populations. It appears that their host specificity is supported by a unique genome structure among LTR retrotransposons [Bousios et al. 2010]. Sireviruses represent the only TE genus whose members contain a variety of highly conserved short (20-40bp) sequence motifs, regardless of the evolutionary distance of their hosts. The motifs are located in key non-coding domains known to decisively participate in the life cycle of LTR retrotransposons and thus may confer novel features in the Sirevirus regulation, replication and integration processes.

We integrated some of these motifs into the development of an expertly-built algorithm [Darzentas et al. 2010], MASiVE (i.e. Mapping and Analysis of Sirevirus Elements), that enables the precise annotation of Sirevirus populations in complex plant genomes - the first and most troublesome step towards deciphering their role in shaping plant genomes. We applied MASiVE in the maize genome and discovered >10,600 intact Sireviruses and ~28,000 degenerate ones that form a plethora of families with distinct genome characteristics [Bousios et al. 2011]. They occupy ~21% of the maize genome, with the majority of copies accumulating the last 600,000 years, while it is the only Copia genus that has successfully proliferated in maize, as they take up 90% of the maize Copia population. Our summarizing conclusion is that Sireviruses have been a crucial force in the current make-up of the maize genome.

We have used MASiVE to scan a collection of fully sequenced plant genomes and generate MASiVEdb, a comprehensive and highly curated resource of the Sirevirus complement of each species.