Repeated sequences associated with inversions and length mutations in the chloroplast genomes of Pseudotsuga and Pinus Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/z603r047g

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  • To help understand the mechanisms of conifer chloroplast genome evolution, we characterized the nucleotide sequences of Douglas-fir (Pseudotsuga menziesiz) and Monterey pine (Pinus radiata) chioroplast DNA that are associated with a length mutation hotspot and inversion. The chloroplast DNA ofthese two conifers are characterized by shared large inversions that are not found in angiosperms or nonconiferous gymnosperms, and are distinguished from each other by an additional 40-50 kb inversion. We cloned and sequenced common endpoints of the 40-50 kb inversion from Monterey pine and Douglas-&, and a hypervariable chloroplast DNA region from two individuals of Douglas-fir and one individual of its relative, Pseudotsugajaponica. We found repeated sequences to be associated with all the observed structural changes in these genomes. The locus of polymorphism in the Pseudotsuga hotspot is characterized by hundreds of base pairs of imperfect, tandem direct repeats flanked by a partially duplicated and intact trnY-GUA gene in direct orientation. Repetitive DNA was likely generated at the time of the partial IrnY gene duplication by slipped-strand mispairing and these sequences expanded further by unequal crossing-over. At inversion borders, we observed the presence of inverted repeats that were hundreds of base pairs in length, adjacent tRNA genes, and pseudo-tRNA genes. We propose that homologous recombination between tRNA genes, with the concomitant pseudo-tRNA gene formation, inversion, and creation of repeated sequences at inversion borders, was the cause of this rearrangement.
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