Abstract
The structural and functional organization of the ribosomal RNA gene cluster and the full-length R2 non-LTR retrotransposon (integrated into a specific site of 28S ribosomal RNA genes) of the German cockroach, Blattella germanica, is described. A partial sequence of the R2 retrotransposon of the cockroach Rhyparobia maderae is also analyzed. The analysis of previously published next-generation sequencing data from the B. germanica genome reveals a new type of retrotransposon closely related to R2 retrotransposons but with a random distribution in the genome. Phylogenetic analysis reveals that these newly described retrotransposons form a separate clade. It is shown that proteins corresponding to the open reading frames of newly described retrotransposons exhibit unequal structural domains. Within these retrotransposons, a recombination event is described. New mechanism of transposition activity is discussed. The essential structural features of R2 retrotransposons are conserved in cockroaches and are typical of previously described R2 retrotransposons. However, the investigation of the number and frequency of 5′-truncated R2 retrotransposon insertion variants in eight B. germanica populations suggests recent mobile element activity. It is shown that the pattern of 5′-truncated R2 retrotransposon copies can be an informative molecular genetic marker for revealing genetic distances between insect populations.
Highlights
Transposable elements (TEs) are ubiquitous components of eukaryotic genomes that are important for shaping genetic material and genome evolution.TEs can be divided into two classes: retrotransposons (Class I) and DNA transposons (Class II)
Messenger RNA from retrotransposons is expressed in host cells, and after reverse transcription by reverse transcriptases (RTs) that are encoded by TEs, new DNA copies of the elements are integrated into new sites within the host genome
The cluster of the ribosomal RNA genes of B. germanica has been the subject of our research for a long time
Summary
Transposable elements (TEs) are ubiquitous components of eukaryotic genomes that are important for shaping genetic material and genome evolution (for review, see [1,2,3,4,5,6,7]). TEs can be divided into two classes: retrotransposons (Class I) and DNA transposons (Class II). All retrotransposons are transposed through an RNA intermediate. Messenger RNA from retrotransposons is expressed in host cells, and after reverse transcription by reverse transcriptases (RTs) that are encoded by TEs, new DNA copies of the elements are integrated into new sites within the host genome. DNA transposons are transposed from one genome site to another via the movement of DNA copies through the activity of DNA transposases encoded by TEs [8,9,10]. Retrotransposons can be divided into four types: non-long terminal repeat (non-LTR)
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