Exact(1)
The parameters of TE (e.g., ignition temperature, reaction times, etc).
Similar(59)
The other abundant TEs (e.g., mariner DNA transposons and copia retrotransposons) were in contrast scattered in the genomes.
First, to our knowledge, this is the first example of a predominantly eukaryotic canonical Class II TE (i.e. a Tc1/ mariner) colonizing a giant virus, although other TEs (e.g. IS sequences of the bacterial and archaeal IS 607 family) have previously been reported in giant virus genomes [ 17, 30, 31, 46].
Some, however, are reverse transcribed and retroposed in a highly efficient manner by the machinery of autonomous TEs (e.g., LINEs) and hence give rise to thousands, up to a million copies in a genome.
These detrimental effects exert selective pressures to remove the TEs (e.g., by recombination between LTR sequences), and to evolve mechanisms that prevent TEs from invading, or, once established, to prevent these TEs from expressing their functions and enhanced replication and movement.
In addition to the typical and highly abundant plant TEs (e.g. LTR retrotransposons), the barley (or any plant) genome contains a multitude of TE-derived sequences that do not contain typical and easily identifiable structural features or coding regions [ 25, 29].
In many cases, two closely related species were missing one well-conserved TE family, further exemplifying the highly dynamic gain and loss patterns of TEs (e.g. DTT_ Finwe absent from Lbt, but present in other members of the species complex, or DTA_ Kami absent from C. sativus, but present in C. heterostrophus (Additional file 13: Supplementary Data 2)).
In eukaryotes, this has been shown in the case of genes (for review, see Anderson 2005; Keeling and Palmer 2008) and, more recently, with transposable elements (TEs) (e.g., Silva et al. 2004; Casse et al. 2006; Diao et al. 2006; de Boer et al. 2007; Loreto et al. 2008; Pace et al. 2008; Bartolome et al. 2009; Roulin et al. 2009).
Our results corroborate their finding that none of these superfamilies is disproportionately excised from the soma; however, other TEs (e.g. DNA-hAT, DNA-MuDR, LINE-L1), as well as unknown repeats, not represented in McKinnon and Drouin's dataset but represented in our shotgun data are disproportionately excised.
In addition to the annotation of gene space, a detailed annotation of repeated sequences and transposable elements (TEs) (e.g. presence/absence, types, and location) is critical for understanding the biology of a genome, as well as an important tool for the improvement of high-quality genome assemblies.
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