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Genetics, Vol. 168, 2207-2215, December 2004, Copyright © 2004
doi:10.1534/genetics.104.032896
The Effect of Sequence Divergence on Recombination Between Direct Repeats in Arabidopsis
Roy Opperman1, Eyal Emmanuel and Avraham A. Levy2
Plant Sciences Department, Weizmann Institute of Science, Rehovot, 76100 Israel
2 Corresponding author: Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel.
E-mail: avi.levy{at}weizmann.ac.il
It is well established that sequence divergence has an inhibitory effect on homologous recombination. However, a detailed analysis of this relationship is missing for most higher eukaryotes. We have measured the rate of somatic recombination between direct repeats as a function of the number, type, and position of divergent nucleotides in Arabidopsis. We show that a minor divergence level of 0.16% (one mutation in otherwise identical 618 bp) has a profound effect, decreasing the recombination rate approximately threefold. A further increase in the divergence level affects the recombination rate to a smaller extent until a "divergence saturation" effect is reached at relatively low levels of divergence (
0.5%). The type of mismatched nucleotide does not affect recombination rates. The decrease in the rate of recombination caused by a single mismatch was not affected by the position of the mismatch along the repeat. This suggests that most recombination intermediate tracts contain a mismatch and thus are as long as the full length of the 618-bp repeats. Finally, we could deduce an antirecombination efficiency of 66% for the first mismatch in the repeat. Altogether, this work shows some degree of conservation across kingdoms when compared to previous reports in yeast; it also provides new insight into the effect of sequence divergence on homologous recombination.
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