Dispersed repetitive sequences in the chloroplast genome of Douglas-fir

Summary Restriction mapping and DNA sequencing were used to characterize dispersed repetitive DNA in the chloroplast genome of Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco]. To map repeat families, chloroplast DNA (cpDNA) clones were hybridized at high stringency to one another and to cpDNA cut with restriction enzymes. Repeats are clustered in four regions of the genome and comprise at least six families. Sequence analysis of one repeat family shared among three XbaI fragments indicated the presence of a 633 by inverted repeat which contains a complete tRNA-Serine (GCU) gene and a highly conserved open reading frame (ORF 3.6). Both ends of this 633 bp dispersed repeat have a transposon-like combination of short direct and inverted repeats. One copy of the repeat flanks one of the endpoints of a major inversion which differentiates Douglas-fir from tobacco cpDNA. Dispersion of repetitive DNA by transposition, coupled with loss of the large inverted repeat, appears to have predisposed conifer cpDNA to a number of inversions. An 8 by (CATCTTTT) direct repeat in tobacco is located between two inverted sections in Douglas-fir; it may be a target sequence for homologous recombination.