Junctions between repetitive DNAs on the PSR chromosome of Nasonia vitripennis: Association of palindromes with recombination

Abstract

The Paternal-Sex-Ratio (PSR) chromosome of Nasonia vitripennis contains several families of repetitive DNAs that show significant sequence divergence but share two palindromic regions. This study reports on the analysis of junctions between two of these repetitive DNA families (psr2 and psr18). Three lambda clones that hybridized to both repeat families were isolated from PSR-genomic DNA libraries through multiple screenings and analyzed by Southern blots. Analysis of clones showed a region in which the two repeat types are interspersed, flanked by uniform blocks of each repeat type. PCR amplification of genomic DNA confirmed the contiguous arrangement of psr2 and psr18 on PSR and identified an additional junction region between these repeats that was not present in the lambda inserts. We isolated and sequenced 41 clones from the lambda inserts and genomic PCR products containing junction sequences. Sequence analysis showed that all transitions between psr2 and psr18 repeats occurred near one of the two palindromes. Based on the inheritance pattern of PSR, recombination between repeats on this chromosome must be mitotic (rather than meiotic) in origin. The occurrence of exchanges near the palindromes suggests that these sequences enhance recombination between repeat units. Rapid amplification of repetitive DNA may have been an important factor in the evolution of the PSR chromosome.

Evolution of Tandemly Repeated Sequences: What Happens at the End of an Array?

“…Analyses of junction sites at the ends of repetitive arrays provide an opportunity to characterize repetitive sequences with a unique level of resolution. Several studies of junctions between different tandemly repeated se- quences reveal that these junctions are generally complex and not defined by a specific site of transition (Maresca and Singer 1983;Lohe and Brutlag 1987;Reed et al 1994). This complexity arises because the different repeated sequences interdigitate throughout a junction region, suggesting that multiple recombination events have occurred between established repetitive arrays.…”

“…Clones were isolated from a genomic library (EMBL 3) constructed from Sau3AI partially digested DNA from a standard PSR lab strain (PSR A) crossed to the high fertilizing MI strain of N. vitripennis (Reed et al 1994). Regions of the -clones were subcloned into plasmid (Bluescript) vectors for use as probes in Southern blots and as sequencing template.…”

“…Resolution of the configuration presumably led to a break between A and B, with recombination between NATE and PSR2 at this site causing truncation of the NATE element. It is also interesting to note that this region of the PSR2 sequence has been involved in recombination with another tandemly repetitive sequence (Reed et al 1994) and is adjacent to a 14-bp palindromic region (palin I) present in the PSR2 repeat ( Fig. 2A).…”

“…2A). Palindromes are known to facilitate DNA melting (Chalker et al 1993) and to be associated with recombination events (Bigot et al 1990;Reed et al 1994).…”

“…The three repeated sequences are approximately 171-214 bp in length (Eickbush et al 1992) and are present in large localized arrays on the PSR chromosome (Beukeboom and Werren 1993). Overall sequence similarity is evident and two palindromes are highly conserved among the sequences, thus it appears that these repetitive sequences are evolutionarily related (Eickbush et al 1992;Reed et al 1994). In this study, junction regions between tandem arrays and regions of nonarray DNA are analyzed to evaluate mechanisms of tandem array evolution.…”