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Cucumber (Cucumis sativus) has one of the largest mitochondrial genomes known among all eukaryotes, due in part to the accumulation of short 20 to 60 by repetitive DNA motifs. Recombination among these repetitive DNAs produces rearrangements affecting organization and expression of mitochondrial genes. To more efficiently identify rearrangements in the cucumber mitochondrial DNA, we built two nonoverlapping 800 and 220 kb BAC contigs and assigned major mitochondrial genes to these BACs. Polymorphism carried on the largest BAC contig was used to confirm paternal transmission. Mitochondrial genes were distributed across BACs and physically distant, although occasional clustering was observed. Introns in the nad1, nad4, and nad7 genes were larger than those reported in other plants, due in part to accumulation of short repetitive DNAs and indicating that increased intron sizes contributed to mitochondrial genome expansion in cucumber. Mitochondrial genes atp6 and atp9 are physically close to each other and cotranscribed. These physical contigs will be useful for eventual sequencing of the cucumber mitochondrial DNA, which can be exploited to more efficiently screen for unique rearrangements affecting mitochondrial gene expression. Key words: Cucumis sativus, bacterial artificial chromosome, FPC, organellar genome. Le concombre (Cucumis sativus) possede fun des plus grands genomms mitochondriaux chez les eucaryotes en raison, en partie, dune accumulation de courts motifs repetitifs d'ADN de 20 a 60 pb. La recombinaison entre ces sequences repetees produit des rearrangements qui affectent l'organisation et (expression des genes mitochondriaux. Afin d'identifier plus efficacement les rearrangements au sein de l'ADN mitochondrial du concombre, les auteurs ont assemble deux contigs totalisant 800 et 220 kb de clones BAC sans chevauchements et ont assigne les principaux genes mitochondriaux a ces BAC. Le polymorphisme present sur le plus grand contig BAC a ete employe pour en confirmer la transmission paternelle. Les genes mitochondriaux etaient distrbbues sur les BAC et separes dune grande distance physique, bien que quelques groupements aient ete observes. Les Introns dens les genes nad1, nad4 et nad7 etaient plus grands que leurs homologues chez d'autres plantes en raison, en partie, de l'accumulation de courts motifs repetes d'ADN, ce qui indique que des Introns de taille accrue ont contribue a l'expansion du genome mitochondrial chez le concombre. Les genes mitochondriaux atp6 et atp9 sont physiquement proches l'un de l'autre et co-transcrits. Ces contigs physiques seront utiles en vue du sequencage de l'ADN mitochondrial du concombre qu'il serait possible d'exploiter pour identifier efficacement des rearrangements uniques affectent (expression de genes mitochondriaux. Mots-cles : Cucumis sativus, chromosome bacterien artifcial, FBC, genome d'organite. [Traduit par la Redaction], Introduction Plant mitochondrial genomes are larger than those of most other eukaryotes, even though the numbers of mitochondrially encoded genes are similar (Unseld et al. 1997; Kubo et al. 2000; [...]

Abstract Background Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. Results Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. Conclusions This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.