A mutation hotspot in the chloroplast genome of a conifer (Douglas fir: Pseudotsuga) is caused by variability in the number of direct repeats derived from a partially duplicated tRNA gene
1995
Hipkins, V.D. | Marshall, K.A. | Neale, D.B. | Rottmann, W.H. | Strauss, S.H. (United States Dept. of Agriculture, Forest Service, Camino (USA). National Forest Genetic Electrophoresis Lab.)
The DNA sequence of a 2.7-kb cpDNA XbaI fragment from douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) was determined. RFLPs revealed by the 2.7-kb XbaI clone were observed to vary up to 1 kb among species within the genus Pseudotsuga and up to 200 bp among trees of P. menziesii. The polymerase chain reaction (PCR) allowed the locus of polymorphism to be identified, and the variable region was then sequenced in a second Douglas-fir tree, a single tree of a related species, Japanese Douglas-fir (P. japonica), and in a species lacking a mutation hotspot in the region, Pinus radiata (Monterey pine). The locus of polymorphism is characterized by hundreds of base pairs of imperfect, tandem direct repeats flanked by a partially duplicated and an intact trnY-GUA gene. The duplication is direct in orientation and consists of 43 bp of the 3' end of trnY and 25 bp of its 3' flanking sequence. Tandem repeats show high sequence similarity to a 27-bp region of the trnY gene that overlaps one end of the duplication. The 2 trees of Douglas-fir sequenced differed by a single tandem repeat unit, whereas these trees differed from the Japanese Douglas-fir sequenced by approximately 34 repeat units. Repetitive DNA in the Pseudotsuga cpDNA hotspot was most likely generated at the time of the partial trnY gene duplication and these sequences expanded by slipped-strand mispairing and unequal crossingover.
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