Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats

Previously conducted sequence analysis of Arabidopsis thaliana (ecotype Col umbia-0) reported an insertion of 270-kb mtDNA into the pericentric region on the short arm of chromosome 2. DNA fiber-based fluorescence in situ hybr idization analyses reveal that the mtDNA insert is 618 +/- 42 kb, approxima te to2.3 times greater than that determined by contig assembly and sequenci ng analysis. Portions of the mitochondrial genome previously believed to be absent were identified within the insert. Sections of the mtDNA are repeat ed throughout the insert. The cytological data illustrate that DNA contig a ssembly by using bacterial artificial chromosomes tends to produce a minima l clone path by skipping over duplicated regions, thereby resulting in sequ encing errors. We demonstrate that fiber-fluorescence in situ hybridization is a powerful technique to analyze large repetitive regions in the higher eukaryotic genomes and is a valuable complement to ongoing large genome seq uencing projects.