Maintenance of multiple lineages of R1 and R2 retrotransposable elements in the ribosomal RNA gene loci of Nasonia

Abstract

Abstracti mb_949 37..48Sequencing reads from the Nasonia genome project were used to study the ribosomal RNA gene loci and the retrotransposons R1 and R2 that insert specifically into the 28S genes. Five highly divergent R1 and five highly divergent R2 families were identified in the three sequenced species, as well as a nonautonomous element that appears to use the retrotransposition machinery of R1. A duplication of the R1 target site within the spacer region of the rDNA units was also found to be extensively utilized by R1 elements. We document numerous instances where the R1 and R2 families appropriated parts of the retrotransposition machinery of other lineages and speculate that this enables rapid adaptation and the maintenance of multiple R1 and R2 families.

Impact of a selfish B chromosome on chromatin dynamics and nuclear organization in Nasonia

“…We also generated probes that specifically recognize two different normal chromosomes. One of these probes is directed against a satellite DNA repeat located in the rDNA spacer region (Stage and Eickbush, 2010). This probe highlights a single locus that overlaps with a chromosomal constriction that we interpret to be the Nuclear Organizer Region (NOR; Fig.…”

“…The following sequences were used for fluorescence in situ hybridization probes: 59-TCAAAAGTCTTGACTTTGGCTTACACGCTT-39 and 59-TATAATCAAA-AGTCTCGACTTATGATTGGA-39 are regions of two unique satellite DNA repeats on PSR (Eickbush et al, 1992); 59-TTTTTAAGACGTTTTATTGT-TACTGGTAGT-39 is a region of a satellite DNA repeat that is found on a single autosome (Eickbush et al, 1992); and 59-GTATGTGTTCATATGATTTTGG-CAATTATA-39 is a 240-bp spacer repeat of the rDNA locus (Stage and Eickbush, 2010). Additionally, three sequences corresponding to regions of the 28S rDNA gene also were used for probes: 59-TGGTTGCAAAGCTGAAACTTA-AAGGAATT-39, 59-ATTTAGAGGAAGTAAAAGTCGTAACAAGG-39, 59-AT-GTTTTCATTAATCAAGAACGAAAGTTAG-39.…”

Integration, Regulation, and Long-Term Stability of R2 Retrotransposons

“…Interestingly, variation in the ability of an organism to transcribe a region of the rDNA locus free of R2 insertions can explain why species have very different percentages of their rDNA units inserted with R2 (10,27,31,121,122). If an organism is less capable at differentiating between inserted and uninserted rDNA units, than all R2 inserts are potentially harmful and will be selected against.…”

“…Unfortunately, because the R2 protein sequence eventually reaches maximal divergence, this dating can only be done with confidence for a time frame of less then 200 - 300 million years. Remarkably, multiple lineages of R2 have propagated in some animal lineages for the entire 200-300 million year time estimate (10,12,30,31). Why some animals are able to maintain multiple R2 lineages and other animals only one R2 lineage is unknown.…”

“…However, the original findings leading to this conclusion have been challenged (35). The many species containing either multiple lineages of R2 or multiple classes of non-LTR retrotransposons inserted into the rDNA locus (10,12,28,31) are more consistent with the propagation of selfish genetic elements than a means used by animals to regulate gene expression. Finally, the frequently suggested argument that mobile elements provide useful genetic diversity seems unlikely for R2; comparisons of species with or without R2 elements reveal no sequence differences in 28S rRNA genes near the insertion site and no detectable difference in the mechanism of rRNA regulation.…”