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Diverse transposable elements are abundant in genomes of cellular organisms from all three domains of life.
This revealed that the majority of the sRNAs were derived from the abundant and diverse transposable elements that make up over 70% of the P. infestans genome.
The genome of M. lychnidis-dioicae contained diverse transposable elements (TEs), represented by 286 consensus elements, covering 14%% of the total assembly.
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Various transposable elements are found in genomes and the same type of TE can have very different invasive success in diverse species [ 11].
Additional 518 BES that had not been masked by RepeatMasker were identified as homologs of proteins encoded by diverse families of transposable elements using transposonPSI[ 25].
Next, BES homology to proteins encoded by diverse families of transposable elements were searched using TransposonPSI [ 14], a program that performs tBLASTn searches using a set of position specific scoring matrices (PSSMs) specific for different transposon element families.
Additionally, the M. lychnidis-dioicae genome is riddled with a diverse array of transposable elements (TEs), including a higher proportion of Helitron elements than found in the much larger and more highly-repetitive genomes of related rust fungi.
Putative transposon elements were predicted using Transposon-PSI [ 93] which performed PSI-TBLASTN search of our genomes with a collection of (retro- transposon Oretro- transposonles tORFdentify statistically significant alignments encoded by diverse families of transposable elements.
Stramenopiles, in particular oomycetes and the brown alga E. siliculosus, contain a large and diverse repertoire of transposable elements (Jiang et al. 2005; Tyler et al. 2006; Haas et al. 2009; Cock et al. 2010).
To address this issue we used Transposon-PSI, an analysis tool developed in-house to identify sequences homologous to large and diverse families of transposable elements (see Methods) to look for mariner-related sequences in the genomes of E. histolytica and E. dispar.
These studies have revealed that the bulk of repetitive DNA is composed of interspersed repeats that are derived predominantly from the past amplification of diverse forms of mobile or transposable elements (TEs).
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