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Triboush, S. O.; Даниленко, Н. Г.; Давыденко, О. Г.

doi:10.1023/a:1007487806583

Cited by 70 publications

(11 citation statements)

References 6 publications

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“…After centrifugation, the mitochondria formed a white-yellow colour band toward the bottom of the gradient, which was carefully recovered with a syringe, transferred to a new 50-ml Nalgene tube with 1× wash buffer and concentrated in a pellet with 3 wash centrifugation steps at 13,600 rpm for 15 min. After organelle isolation, mitochondrial DNA was lysed and purified as described [62]. …”

Section: Methodsmentioning

confidence: 99%

Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

et al. 2011

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BackgroundThe melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurbits show great variation when their mitochondrial genomes are compared. The melon possesses the largest plant mitochondrial genome, as much as eight times larger than that of other cucurbits.ResultsThe nucleotide sequences of the melon chloroplast and mitochondrial genomes were determined. The chloroplast genome (156,017 bp) included 132 genes, with 98 single-copy genes dispersed between the small (SSC) and large (LSC) single-copy regions and 17 duplicated genes in the inverted repeat regions (IRa and IRb). A comparison of the cucumber and melon chloroplast genomes showed differences in only approximately 5% of nucleotides, mainly due to short indels and SNPs. Additionally, 2.74 Mb of mitochondrial sequence, accounting for 95% of the estimated mitochondrial genome size, were assembled into five scaffolds and four additional unscaffolded contigs. An 84% of the mitochondrial genome is contained in a single scaffold. The gene-coding region accounted for 1.7% (45,926 bp) of the total sequence, including 51 protein-coding genes, 4 conserved ORFs, 3 rRNA genes and 24 tRNA genes. Despite the differences observed in the mitochondrial genome sizes of cucurbit species, Citrullus lanatus (379 kb), Cucurbita pepo (983 kb) and Cucumis melo (2,740 kb) share 120 kb of sequence, including the predicted protein-coding regions. Nevertheless, melon contained a high number of repetitive sequences and a high content of DNA of nuclear origin, which represented 42% and 47% of the total sequence, respectively.ConclusionsWhereas the size and gene organisation of chloroplast genomes are similar among the cucurbit species, mitochondrial genomes show a wide variety of sizes, with a non-conserved structure both in gene number and organisation, as well as in the features of the noncoding DNA. The transfer of nuclear DNA to the melon mitochondrial genome and the high proportion of repetitive DNA appear to explain the size of the largest mitochondrial genome reported so far.

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Section: Methodsmentioning

confidence: 99%

Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

et al. 2011

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“…The purification method [35] provided mitochondrial DNA free from nuclear DNA contamination which was confirmed by quantitative real time PCR. Based on sequencing read counts, 3 to 9% of overall reads were chloroplastic DNA and no nuclear DNA was detected.…”

Section: Resultsmentioning

confidence: 99%

“…Mitochondria isolation was conducted according to the protocol developed by Triboush et al [35] with minor modifications. Before mitochondrial isolation leaf tissues were rinsed with 4°C distilled water and transferred to the cold room (4°C).…”

Section: Methodsmentioning

confidence: 99%

Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat

et al. 2014

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BackgroundWheat is an excellent plant species for nuclear mitochondrial interaction studies due to availability of large collection of alloplasmic lines. These lines exhibit different vegetative and physiological properties than their parents. To investigate the level of sequence changes introduced into the mitochondrial genome under the alloplasmic condition, three mitochondrial genomes of the Triticum-Aegilops species were sequenced: 1) durum alloplasmic line with the Ae. longissima cytoplasm that carries the T. turgidum nucleus designated as (lo) durum, 2) the cytoplasmic donor line, and 3) the nuclear donor line.ResultsThe mitochondrial genome of the T. turgidum was 451,678 bp in length with high structural and nucleotide identity to the previously characterized T. aestivum genome. The assembled mitochondrial genome of the (lo) durum and the Ae. longissima were 431,959 bp and 399,005 bp in size, respectively. The high sequence coverage for all three genomes allowed analysis of heteroplasmy within each genome. The mitochondrial genome structure in the alloplasmic line was genetically distant from both maternal and paternal genomes. The alloplasmic durum and the Ae. longissima carry the same versions of atp6, nad6, rps19-p, cob and cox2 exon 2 which are different from the T. turgidum parent. Evidence of paternal leakage was also observed by analyzing nad9 and orf359 among all three lines. Nucleotide search identified a number of open reading frames, of which 27 were specific to the (lo) durum line.ConclusionsSeveral heteroplasmic regions were observed within genes and intergenic regions of the mitochondrial genomes of all three lines. The number of rearrangements and nucleotide changes in the mitochondrial genome of the alloplasmic line that have occurred in less than half a century was significant considering the high sequence conservation between the T. turgidum and the T. aestivum that diverged from each other 10,000 years ago. We showed that the changes in genes were not limited to paternal leakage but were sufficiently significant to suggest that other mechanisms, such as recombination and mutation, were responsible. The newly formed ORFs, differences in gene sequences and copy numbers, heteroplasmy, and substoichiometric changes show the potential of the alloplasmic condition to accelerate evolution towards forming new mitochondrial genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-67) contains supplementary material, which is available to authorized users.

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“…Before performing DNA extraction, chloroplast and mitochondrial fractions were isolated from 10 day sunflower seedlings according to the method of Triboush et al (1998) with our modifications. Briefly, 1 g of leaves was homogenized by mortar and pestle in STE buffer (0,4M sucrose, 50 mMTris pH 7.8, 20 mM EDTA-Na2, 0.2% bovine serum albumin, 0.2% bmercaptoethanol) and then centrifuged.…”

Section: Mitochondrial and Chloroplast Dna Isolationmentioning

confidence: 99%

Comparative Genomics of Domesticated and Wild Sunflower: Complete Chloroplast and Mitochondrial Genomes

Makarenko¹,

Усатов²,

Markin³

et al. 2016

OnLine Journal of Biological Sciences

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Abstract:The entire chloroplast and mitochondrial genomes of domesticated and wild type sunflower were sequenced. The comparative analysis of chloroplast genomes revealed 43 variant sites, including 21 polymorphic SSR loci and 22 SNPs. About 14 variant sites were found by collation of mitochondrial DNA (mtDNA), among them 4 SSRs, 8 SNPs and 2 deletions. About 9 SNPs were located in coding region of chloroplast DNA (cpDNA) and single SNP was mapped in mitochondrial gene. Only three SNPs caused amino acid changes: Two SNPs in cpDNA and one mtDNA SNP. Despite the fact that sunflower mitochondrial genome sequence is twice as long as chloroplast genome sequence, mtDNA has one third as much variant sites than cpDNA.

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Untitled

Cited by 70 publications

References 6 publications

Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin

Accelerated evolution of the mitochondrial genome in an alloplasmic line of durum wheat

Comparative Genomics of Domesticated and Wild Sunflower: Complete Chloroplast and Mitochondrial Genomes

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