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The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments
TLDR
RNA editing alters plant mitochondrial and chloroplast transcripts by converting specific cytidines to uridines, which usually results in a change in the amino acid sequence of the translated protein. Expand
RNAi in Budding Yeast
Yeast Joins RNAi Club RNA interference (RNAi) silences gene expression via small interfering (si) RNAs that bind to target sequences. RNAi has been found in almost all eukaryotes examined, with theExpand
Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates.
Rates of nucleotide substitution were previously shown to be several times slower in the plastid inverted repeat (IR) compared with single-copy (SC) regions, suggesting that the IR provides enhancedExpand
The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants.
The chloroplast genome of Pelargonium x hortorum has been completely sequenced. It maps as a circular molecule of 217,942 bp and is both the largest and most rearranged land plant chloroplast genomeExpand
Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants
BackgroundIt has long been known that rates of synonymous substitutions are unusually low in mitochondrial genes of flowering and other land plants. Although two dramatic exceptions to this patternExpand
Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae
BackgroundRates of synonymous nucleotide substitutions are, in general, exceptionally low in plant mitochondrial genomes, several times lower than in chloroplast genomes, 10–20 times lower than inExpand
PREP-Mt: predictive RNA editor for plant mitochondrial genes
TLDR
The PREP-Mt methodology can be used to predict RNA editing sites for any protein-coding gene in plant mitochondria by identifying positions where an RNA editing event would increase protein conservation across species. Expand
Mitochondrial substitution rates are extraordinarily elevated and variable in a genus of flowering plants.
Plant mitochondrial (mt) genomes have long been known to evolve slowly in sequence. Here we show remarkable departure from this pattern of conservative evolution in a genus of flowering plants.Expand
Origin and evolution of the octoploid strawberry genome
Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million yearsExpand
Unprecedented heterogeneity in the synonymous substitution rate within a plant genome.
The synonymous substitution rate varies widely among species, but it is generally quite stable within a genome due to the absence of strong selective pressures. In plants, plastid genes tend toExpand
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