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, , is described. A partial sequence of the R2 retrotransposon of the cockroach is also analyzed. The analysis of previously published next-generation sequencing data from the 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 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.
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