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This Week in Nature: Nov 18, 2011

In a paper published online in advance in Nature this week, a large international team led by investigators at the University of Minnesota presents a draft sequence of Medicago truncatula "euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing [about] 94 percent of all M. truncatula genes." The team says a whole-genome duplication that occurred approximately 58 million years ago played "a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation." Our sister publication GenomeWeb Daily News has more on this study.

In another Nature advance online publication, MIT's Howard Chang, Jennifer Paek, and Dennis Kim report their molecular characterization of coding polymorphisms in Caenorhabditis elegans HECW-1, which encodes a conserved HECT domain-containing E3 ubiquitin ligase. "We show that two distinct polymorphisms in neighboring residues of HECW-1 each affect C. elegans behavioral avoidance of a lawn of Pseudomonas aeruginosa," Chang, Paek, and Kim write, adding that their "data establish a molecular basis for natural variation in a C. elegans behavior that may undergo adaptive changes in response to microbial pathogens."

Over in Nature Genetics, researchers at the Centre for Genomic Regulation in Barcelona report their use of "conservation-based methods to predict the impact of protein-coding variation within genes on protein function" in 19 Saccharomyces cerevisiae strains. The team also presents evaluations of those predictions "by comparing them with the observed growth rate and efficiency of 15 strains tested across 20 conditions in quantitative experiments." Overall, the CRG groups says its S. cerevisiae "predictions were more accurate when the genes reported to influence a trait were highly connected in a functional gene network."

Researchers at Harvard Medical School and elsewhere describe in Nature Genetics this week their identification of "bacterial genes under adaptive evolution by tracking recurrent patterns of mutations in the same pathogenic strain during the infection of multiple individuals." GenomeWeb Daily News has more on this study.

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.