Organization of repetitive DNAs and the genomic regions carrying ribosomal RNA, cob, and atp9 genes in the cucurbit mitochondrial genomes

Abstract

Plants in the genus Cucumis (cucumber and melon) have the largest mitochondrial genomes known among all plants, due in part to the accumulation of repetitive DNAs of varying complexities. Recombination among these repetitive DNAs should produce highly rearranged mitochondrial genomes relative to the smaller mitochondrial genomes of related plants. We cloned and sequenced mitochondrial genomic regions near the rRNA, atp9 and cob genes from cucumber, melon, squash and watermelon (all members of the Cucurbitaceae family), and compared to the previously sequenced mitochondrial genomes of Arabidopsis thaliana and sugar beet to study the distribution and arrangement of coding and repetitive DNAs. Cucumber and melon had regions of concentrated repetitive DNAs spread throughout the sequenced regions; few repetitive DNAs were revealed in the mitochondrial genomes of A. thaliana, sugar beet, squash and watermelon. Recombination among these repetitive DNAs most likely produced unique arrangements of the rrn18 and rrn5 genes in the genus Cucumis. Cucumber mitochondrial DNA had more pockets of dispersed direct and inverted repeats than melon and the other plants, and we did not reveal repetitive sequences significantly contributing to mitochondrial genome expansion in both cucumber and melon.

Next generation sequencing and omics in cucumber ( Cucumis sativus L.) breeding directed research

“…Cucumber mtDNA is characterized by accumulation of repetitive DNA in which inter-and intramolecular recombination results in mtDNA rearrangements [112,114,115]. Accumulation of short and degenerated repetitive DNA is particular for cucumber mtDNA [114,116]. Further sequencing of mitochondrial genomes of different cucumber accessions will provide insights about structural dynamics of cucumber mitochondrial genome.…”

Organization and variation of angiosperm mitochondrial genome

“…Local gene arrangement can be evolutionarily conserved (examples are listed in Ogihara et al 2005, Sugiyama et al 2005), but the selective pressure to maintain such gene arrangements seems to be weak compared to that in the mitochondrial genomes of vertebrates or the chloroplast genome. For example, rrn18‐rrn5 linkage was thought to be conserved among angiosperms, however, exceptions are found in the genus Cucumis , where the linkage is broken or the two genes are linked in an opposite orientation (Bartoszewski et al 2004).…”

The selection of mosaic (MSC) phenotype after passage of cucumber (Cucumis sativus L.) through cell culture — a method to obtain plant mitochondrial mutants

“…These huge mitochondrial genomes in plants are due in part to the transfer of DNA from the chloroplast or nucleus, and the accumulation of short repetitive DNAs (Unseld et al 1997;Kubo et al 2000;Notsu et al 2002;Clifton et al 2004;Ogihara et al 2005). Recombination among these repetitive sequences produces rearrangements in the mitochondrial DNAs, shifting the linear order of genes even among relatively closely related species (Palmer and Hebron 1988;Fauron et al 1995;Bartoszewski et al 2004a).…”