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Title: ORGANIZATION OF RIBOSOMAL RNA CODING AND REPETITIVE DNAS IN THE CUCURBIT MITOCHONDRIAL GENOMES

Author
item BARTTOSZEWSKI, GRZEFORZ - WARSAW AG UNIV POLAND
item KATZIR, NURIT - VOLCANI INSTITUTE ISRAEL
item Havey, Michael

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/12/2003
Publication Date: 3/21/2004
Citation: Barttoszewski, G., Katzir, N., Havey, M.J. 2004. Organization of ribosomal RNA coding and repetitive DNAs in the cucurbit mitochondrial genomes. Theoretical and Applied Genetics. 108(6):982-992.

Interpretive Summary: Cucumber and melon have the largest amount of DNA carried in the mitochondrion among all plants. In order to understand how this huge amount of DNA accumulated, we cloned and sequenced specific mitochondrial DNAs from cucumber and melon, comparing with closely related squash and watermelon (all members of the Cucurbitaceae), and the previously sequenced mitochondrial genomes of Arabidopsis thaliana and sugarbeet. Cucumis species possessed unique arrangements of the ribosomal genes. Cucumber and melon also had regions of concentrated repetitive DNAs spread through out the sequenced regions; few repetitive DNAs were revealed in the mitochondrial DNAs of A. thaliana, sugarbeet, squash, and watermelon. Cucumber mitochondrial DNA had many more pockets of dispersed direct and inverted repeats than similarly sized regions in melon and other plants. Although the mitochondrial DNA of melon is 35% larger than cucumber, it possessed fewer concentrated regions of repetitive DNAs than cucumber and essentially none of the inverted repeat sequences. We did not reveal repetitive sequences significantly contributing to mitochondrial DNA expansion in both cucumber and melon. Therefore, accumulation of short repetitive DNAs contributed more to mitochondrial DNA expansion in cucumber than melon, at least across the sequenced regions. This research will be of interest to scientists studying the underlying factors contributing to large amounts of DNA in plants. It will also be of interest to geneticists because the large numbers of inverted repeat DNA in the cucumber mitochondrion will allow for rearrangements that may alter mitochondrial gene expression.

Technical Abstract: Cucumber and melon have the largest known mitochondrial genomes among all plants. We cloned and sequenced mitochondrial genomic regions carrying the rDNA, atp9, and cob genes from cucumber, melon, squash, and watermelon (all members of the Cucurbitaceae), comparing to the previously sequenced mitochondrial genomes of Arabidopsis thaliana and sugarbeet, to study the distribution and arrangement of coding and repetitive DNAs. Cucumis species possessed unique arrangements of the rrn18 and rrn5 genes. Cucumber and melon had regions of concentrated repetitive DNAs spread through out the sequenced regions; few repetitive DNAs were revealed in the mitochondrial genomes of A. thaliana, sugarbeet, squash, and watermelon. Cucumber mitochondrial DNA had many more pockets of dispersed direct and inverted repeats than similarly sized regions in melon and other plants. Cucumber possessed 294 regions across 29.3 kb with inverted repeats of 11 bp, short direct di to tetranucleotide repeats, and lengths of 700 bp or less. In comparison, the sequenced mitochondrial regions of the melon and Arabidopsis possessed only four and two sequences, respectively, with these characteristics. Although these sequences resembled miniature inverted-repeat transposable elements (MITEs), there was little conservation of internal sequences among sequences with the same inverted and direct repeats and none were homologous to previously described MITE superfamilies. Although the mitochondrial genome of melon is 35% larger than cucumber, it possessed fewer concentrated regions of repetitive DNAs than cucumber and essentially none of the inverted repeat sequences. We did not reveal repetitive sequences significantly contributing to mitochondrial genome expansion in both cucumber and melon. Accumulation of short repetitive DNAs contributed more to mitochondrial genome expansion in cucumber than melon, at least across the sequenced regions.