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 the notable exception of the budding yeast, Saccharomyces cerevisiae , one of the most prominent organisms used in the study of molecular biology. Indeed, RNAi has been thought to be missing from all budding yeast. Drinnenberg et al. (p. 544 , published online 10 September; see the Perspective by Moazed ) now show that several species of budding yeast do possess RNAi, which seems to act primarily on transposable elements and subtelomeric repeats. A noncanonical Dicer protein generates siRNAs that are loaded onto Ago1 protein in S. castellii . Introduction of these two genes into S. cerevisiae was sufficient to reconstitute RNAi, where it also acted to dampen the activity of transposons.

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. Systematic studies have experimentally identified sites of RNA editing in organellar transcriptomes from several species, but these analyses have not kept pace with rate of genome sequencing. The PREP (predictive RNA editors for plants) suite was developed to computationally predict sites of RNA editing based on the well-known principle that editing in plant organelles increases the conservation of proteins across species. The PREP suite provides predictive RNA editors for plant mitochondrial genes (PREP-Mt), for chloroplast genes (PREP-Cp), and for alignments submitted by the user (PREP-Aln). These servers require minimal input, are very fast, and are highly accurate on all seed plants examined to date. PREP-Mt has proved useful in several research studies and the newly developed PREP-Cp and PREP-Aln servers should be of further assistance for analyses that require knowledge of the location of sites of RNA editing. The PREP suite is freely available at http://prep.unl.edu/.

Background: It 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 pattern have recently been reported, it is unclear how often major increases in substitution rates occur during plant mitochondrial evolution and what the overall magnitude of substitution rate variation is across plants.Results: A broad survey was undertaken to evaluate synonymous substitution rates in mitochondrial genes of angiosperms and gymnosperms. Although most taxa conform to the generality that plant mitochondrial sequences evolve slowly, additional cases of highly accelerated rates were found. We explore in detail one of these new cases, within the genusSilene. A roughly 100-fold increase in synonymous substitution rate is estimated to have taken place within the last 5 million years and involves only one of ten species ofSilenesampled in this study. Examples of unusually slow sequence evolution were also identified. Comparison of the fastest and slowest lineages shows that synonymous substitution rates vary by four orders of magnitude across seed plants. In other words, some plant mitochondrial lineages accumulate more synonymous change in 10,000 years than do others in 100 million years. Several perplexing cases of gene-to-gene variation in sequence divergence within a plant were uncovered. Some of these probably reflect interesting biological phenomena, such as horizontal gene transfer, mitochondrial-to-nucleus transfer, and intragenomic variation in mitochondrial substitution rates, whereas others are likely the result of various kinds of errors.Conclusion: The extremes of synonymous substitution rates measured here constitute by far the largest known range of rate variation for any group of organisms. These results highlight the utility of examining absolute substitution rates in a phylogenetic context rather than by traditional pairwise methods. Why substitution rates are generally so low in plant mitochondrial genomes yet occasionally increase dramatically remains mysterious.

Mitochondrial genomes (mitogenomes) of flowering plants are well known for their extreme diversity in size, structure, gene content, and rates of sequence evolution and recombination. In contrast, little is known about mitogenomic diversity and evolution within gymnosperms. Only a single complete genome sequence is available, from the cycad Cycas taitungensis, while limited information is available for the one draft sequence, from Norway spruce (Picea abies). To examine mitogenomic evolution in gymnosperms, we generated complete genome sequences for the ginkgo tree (Ginkgo biloba) and a gnetophyte (Welwitschia mirabilis). There is great disparity in size, sequence conservation, levels of shared DNA, and functional content among gymnosperm mitogenomes. The Cycas and Ginkgo mitogenomes are relatively small, have low substitution rates, and possess numerous genes, introns, and edit sites; we infer that these properties were present in the ancestral seed plant. By contrast, the Welwitschia mitogenome has an expanded size coupled with accelerated substitution rates and extensive loss of these functional features. The Picea genome has expanded further, to more than 4 Mb. With regard to structural evolution, the Cycas and Ginkgo mitogenomes share a remarkable amount of intergenic DNA, which may be related to the limited recombinational activity detected at repeats in Ginkgo. Conversely, the Welwitschia mitogenome shares almost no intergenic DNA with any other seed plant. By conducting the first measurements of rates of DNA turnover in seed plant mitogenomes, we discovered that turnover rates vary by orders of magnitude among species.