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This Week in Nature: Jun 28, 2013

Researchers led by the University of Copenhagen's Eske Willerslev report in Nature that they have sequenced an ancient horse — the oldest creature to be sequenced — along with a number of other, related species. The ancient horse, between 560,000 years and 780,000 years old, was sequenced to 1.12 times using the Illumina and Helicos platforms. Their analyses of that genome in combination with those from a 43,000-year-old horse, five modern domestic horse breeds, a Przewalski's horse, and a donkey indicated that they split from their most recent common ancestor about 4.0 million to 4.5 million years ago, much earlier than was previously thought. In addition, they found that Przewalski's and domestic horses populations diverged between 38,000 and 72,000 years ago. "Our study has pushed the timeframe of palaeogenomics back by almost an order of magnitude, the researchers noted."This enabled us to readdress a range of questions related to the evolution of Equus—a group representing textbook examples of evolutionary processes."

GenomeWeb Daily News has more on this study here.

A team of Japanese researchers report in Nature Genetics on their analysis of clear-cell renal cell carcinoma using whole-genome and/or whole-exome and RNA sequencing in addition to array-based gene expression, copy number, and/or methylation analyses. Such an integrated approach, they say, allowed them to identify a number of genetic lesions, gene expression changes, and methylation signatures in the tumors. For example, they note that defective VHL-mediated proteolysis in clear-cell renal cell carcinoma is due to both VHL inactivation and hotspot TCEB1 mutations. "By integrating multiple layers of different comprehensive analyses, we unmasked unique correlations between somatic mutations, DNA methylation, gene expression, and copy number alterations, which were also linked to the clinical behaviors of tumors," the researchers say.

Genome Web Daily News also covers this study here.

Magnus Nordborg from the Austrian Academy of Sciences and the University of Southern California and his team sequenced 180 Arabidopsis thaliana lines from Sweden to characterize the genetic variation in that population. As they write in Nature Genetics, they were able to estimate SNP and indel variation in those lines, though they note that much may have been missed. Still, they uncovered a large structural variant that appeared to have been under strong selection, especially in northern Swedish populations. "Even in an organism as well studied as A. thaliana, the genome is full of surprises," they note.