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We identified BAC clones which harbor DNAs derived from the B. rapa organelle genomes by in silico mapping of 80,292 B. rapa BAC end sequences on the Arabidopsis organelle genomes and subsequent insert size estimation and fingerprinting. A total of 1,048 putative chloroplast genome-derived BAC clones (2.6%) were identified. Fingerprinting and sequencing revealed that many of them represented the entire chloroplast genome (about 150 kb). Meanwhile, only 59 putative mitochondrial genome-derived BACs (0.15%) were identified and most of them showed rare agreement between the in silico map and fingerprinting. We sequenced BAC clone KBrB042G11 (42G11) and compared it to the mitochondrial genome of B. napus and A. thaliana which showed dynamic rearrangement events. The order of 33 orthologous genes was collinear between the 42G11 BAC and its counterpart in B. napus. Five distinctive rearrangements and two InDels were identified between these two closely related species and the rearrangements were related to the occurrence of small tandem repeat sequences. Sequences of the 33 orthologous genes in the homoeologous regions of B. napus and B. rapa were almost 100% identical. Gene orders showed no colinearity between Arabidopsis and Brassica even though 31 orthologous genes shared high sequence similarity with p-values over 1E-32. FISH analysis using the identified BAC revealed a large chloroplast genome insertion in the pericentromeric region of chromosome (chr.) 4 of B. rapa.