Unequal recombination and other rearrangements in plant nuclear and chloroplast genomes
Frailey, Daniel Christopher
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Plant genomes vary tremendously in terms of size and chromosome structure. One factor that plays a major role in genome evolution is homologous recombination. Both meiotic and mitotic recombination increase genetic diversity by rearranging combinations of alleles, creating new alleles and altering the copy numbers of genes by unequal recombination. Previous studies identified unequal recombination events between two disease resistance gene homologues from sorghum, Pc A and Pc C. Interestingly, most of the recombination events occurred in the least conserved part of the gene, which was the domain responsible for pathogen recognition. Changes here have the potential to allow evolution of new resistance specificities. We created transgenic maize lines containing tandem Pc A and Pc C genes, and then used a PCR assay to screen maize pollen for unequal recombination. We identified 23 unequal recombination events, yielding a rate of 1 per ~7700 pollen grains. DNA sequence analysis indicated that, unlike in sorghum, all unequal recombined Pc products had crossovers occurring in the conserved regions of the genes. Transposons are responsible for most plant genome variation. For instance, LTR retrotransposon amplification can rapidly increase a species’ genome size. This increase can be partially counteracted by unequal recombination between LTRs, deleting the internal sequence and leaving behind a solo LTR. We used the same techniques as for the Pc locus to identify a total of 23 unequal recombination events from 10 LTR retrotransposons. We found a positive correlation between recombination and LTR sequence identity and a negative correlation with DNA methylation. We also assembled and analyzed the chloroplast genomes from five species of parasitic plants. In most angiosperms, the chloroplast genome, or plastome, is highly conserved. We found several rearrangements and gene deletions in four of the five species. We also found large increases in plastome size. Plastomes contain two virtually identical inverted repeats separating a large and small single copy region. The plastome size increase was due to expansion of these repeats into the single copy regions.