CACTA Transposons in Triticeae. A Diverse Family of High-Copy Repetitive Elements

Abstract

In comparison with retrotransposons, which comprise the majority of the Triticeae genomes, very few class 2 transposons have been described in these genomes. Based on the recent discovery of a local accumulation of CACTA elements at the Glu-A3 loci in the two wheat species Triticum monococcum and Triticum durum, we performed a database search for additional such elements in Triticeae spp. A combination of BLAST search and dot-plot analysis of publicly available Triticeae sequences led to the identification of 41 CACTA elements. Only seven of them encode a protein similar to known transposases, whereas the other 34 are considered to be deletion derivatives. A detailed characterization of the identified elements allowed a further classification into seven subgroups. The major subgroup, designated the "Caspar " family, was shown by hybridization to be present in at least 3,000 copies in the T. monococcum genome. The close association of numerous CACTA elements with genes and the identification of several similar elements in sorghum (Sorghum bicolor) and rice (Oryza sativa) led to the conclusion that CACTA elements contribute significantly to genome size and to organization and evolution of grass genomes.

Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea

“…High copy number CACTA-like families were recently reported in a few species of grasses with large genomes. For example, there are Ϸ5,000 Tpo1 elements in ryegrass (Lolium perenne, 5,000 Mb) (39) and Ϸ3,000 Caspar elements in wheat (Triticum monococcum, Ϸ5,000 Mb) (40).…”

A Helitron-Like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

“…1, and functional domains predicted B. mori Helitron-like RepHel protein (BMHEL1p) encoded by the autonomous Helitron1_BM element are described with the text OnMINE-1 (GAAA) n and 5 0 SIR regions, but were only 30 bp in length (E-values = 0.08) and consisted of a [(GAAA) 4 T-CATTTATTCGCCA] sequence. Although this represents a motif that could be encountered by chance within the genome, similarly short regions of homology were used to define DINE-1-like elements in Drosophila (Wilder and Hollocher 2001;Yang and Barbash 2008) and the highly variable CACTA TE family from the plant species Triticeae (Wicker et al 2003). The subsequent database search #3 that queried the B. mori genome sequence build 2 with the [(GAAA) 4 T-CATTTATTCGCCA] sequence identified 316 unique positions that share C89.7% similarity, and are distributed within the genome at an average of 0.65 ± 0.24 per Mb (11.29 ± 3.93 per chromosome; Table 1; supplementary Table T1).…”

Rapid Genome Divergence at Orthologous Low Molecular Weight Glutenin Loci of the A and Am Genomes of Wheat[W]

“…The sixth transposon is similar to Mutator elements (Joseph_107G22-1). A detailed characterization of the identified class-II elements is provided by Wicker et al (2003).…”

“…The large genome size of wheat is attributable partially to the presence of a large amount of nested long terminal repeat (LTR) retrotransposons, very similar to the situation in maize (SanMiguel et al, 1996;Wicker et al, 2001;Ramakrishna et al, 2002a). The increase of genome size caused by retrotransposons as well as transposons (Wicker et al, 2003) is counteracted by mechanisms that reduce genome size. These include unequal inter-or intraretroelement recombination events and deletions of apparently random fragments of repetitive elements (reviewed by Bennetzen, 2002).…”