Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

Drouin, Guy; Daoud, Hanane; Xia, Junnan

doi:10.1016/j.ympev.2008.09.009

Cited by 381 publications

(311 citation statements)

References 25 publications

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“…Despite the fact that plant organelle genomes are constantly exposed to reactive by-products of the electron transport machineries, they are surprisingly more stable than the nuclear genome at the nucleotide level (Wolfe et al, 1987;Drouin et al, 2008). Contrasting with their slow rate of nucleotide substitution, plant organelle genome organization is complex and highly dynamic.…”

Section: Introductionmentioning

confidence: 99%

Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair

et al. 2010

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DNA double-strand breaks are highly detrimental to all organisms and need to be quickly and accurately repaired. Although several proteins are known to maintain plastid and mitochondrial genome stability in plants, little is known about the mechanisms of DNA repair in these organelles and the roles of specific proteins. Here, using ciprofloxacin as a DNA damaging agent specific to the organelles, we show that plastids and mitochondria can repair DNA double-strand breaks through an error-prone pathway similar to the microhomology-mediated break-induced replication observed in humans, yeast, and bacteria. This pathway is negatively regulated by the single-stranded DNA (ssDNA) binding proteins from the Whirly family, thus indicating that these proteins could contribute to the accurate repair of plant organelle genomes. To understand the role of Whirly proteins in this process, we solved the crystal structures of several Whirly-DNA complexes. These reveal a nonsequence-specific ssDNA binding mechanism in which DNA is stabilized between domains of adjacent subunits and rendered unavailable for duplex formation and/or protein interactions. Our results suggest a model in which the binding of Whirly proteins to ssDNA would favor accurate repair of DNA double-strand breaks over an error-prone microhomology-mediated break-induced replication repair pathway.

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Section: Introductionmentioning

confidence: 99%

Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair

et al. 2010

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“…Plant mitochondria tend to have very slow point mutation rates as evidenced by their low rate of synonymous substitution (Wolfe et al 1987;Palmer and Herbon 1988;Mower et al 2007;Drouin et al 2008). Lynch et al (2006) have argued that high mutation rates intensify selection against RNA editing because of the increased probability of disrupting sequences necessary for editing site recognition [the mutational burden hypothesis (Lynch 2006)].…”

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confidence: 99%

Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selectionvs. Retroprocessing as the Driving Force

et al. 2010

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Theoretical arguments suggest that mutation rates influence the proliferation and maintenance of RNA editing. We identified RNA editing sites in five species within the angiosperm genus Silene that exhibit highly divergent mitochondrial mutation rates. We found that mutational acceleration has been associated with rapid loss of mitochondrial editing sites. In contrast, we did not find a significant difference in the frequency of editing in chloroplast genes, which lack the mutation rate variation observed in the mitochondrial genome. As found in other angiosperms, the rate of substitution at RNA editing sites in Silene greatly exceeds the rate at synonymous sites, a pattern that has previously been interpreted as evidence for selection against RNA editing. Alternatively, we suggest that editing sites may experience higher rates of C-to-T mutation than other portions of the genome. Such a pattern could be caused by gene conversion with reverse-transcribed mRNA (i.e., retroprocessing). If so, the genomic distribution of RNA editing site losses in Silene suggests that such conversions must be occurring at a local scale such that only one or two editing sites are affected at a time. Because preferential substitution at editing sites appears to occur in angiosperms regardless of the mutation rate, we conclude that mitochondrial rate accelerations within Silene have ''fast-forwarded'' a preexisting pattern but have not fundamentally changed the evolutionary forces acting on RNA editing sites.

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“…The phylogenetic distance (i.e., genetic divergence) between the two proposed Eutrema lineages was estimated using two methods. The first method employed Nei's equation, T = D A /2λ (Nei, 1987) /synonymous site per year (Chase et al, 1993;Zurawski and Clegg, 1987), based on the rbcL region, and an adjusted Ks ratio (0.528 for matK vs. 0.372 for rbcL) (Drouin et al, 2008). Using this method, the estimated time since the Eutrema species in Japan diverged from E. yunnanense was estimated to be 4.7 million years ago (Mya), in the Late Tertiary.…”

Section: Resultsmentioning

confidence: 99%

Genetic Differentiation, Molecular Phylogenetic Analysis, and Ethnobotanical Study of Eutrema japonicum and E. tenue in Japan and E. yunnanense in China

Yamane

Sugiyama

et al. 2016

Hortic J

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This paper reports the level of genetic differentiation between two Japanese and one Chinese species of Eutrema: E. japonicum, "wasabi"; its wild relative in Japan, E. tenue; and their wild relative in China, E. yunnanense. Phylogenetic analyses were based on the DNA sequence of the chloroplast trnK/matK region of 16 Brassicaceae and an outgroup species. Neighbor joining (NJ) and maximum parsimony (MP) trees were constructed, revealing that the three Eutrema species form a single clade clearly separated from other Brassicaceae species. The two Japanese Eutrema species are highly differentiated from Chinese E. yunnanense, and it is estimated that they diverged from E. yunnanense approximately 5 million years ago. An ethnobotanical survey was conducted among ethnic Chinese in Yunnan Province, and the results indicate that E. yunnanense is not perceived as "hot" in taste, while a pungent flavor is associated with wasabi; in addition, no evidence was found for the domestication of E. yunnanense. On the basis of the present molecular phylogenetic study and the ethnobotanical survey, we conclude that wasabi acquired its specific pungent flavor during its long botanical history in Japan, and that its subsequent domestication in Japan was because of this acquired pungent flavor. The culinary habit of using wasabi with raw fish has since become an important feature of Japanese cuisine and culture.

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Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

Cited by 381 publications

References 25 publications

Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair

Crystal Structures of DNA-Whirly Complexes and Their Role in Arabidopsis Organelle Genome Repair

Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selectionvs. Retroprocessing as the Driving Force

Genetic Differentiation, Molecular Phylogenetic Analysis, and Ethnobotanical Study of <i>Eutrema japonicum</i> and <i>E. tenue</i> in Japan and <i>E. yunnanense</i> in China

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