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This Week in Genome Research: Jun 26, 2014

An international team led by investigators at the University of California, San Francisco, introduces a computational scheme for quickly identifying viral and bacterial pathogens using high-throughput sequences generated from patient samples. The bioinformatics method, known as "sequence-based ultrarapid pathogen identification" (SURPI), is designed to be compatible with cloud or standalone servers, the study authors note, identifying potential pathogens within a short enough timeframe to be clinically useful. As they demonstrated using more than a billion bases of sequence data generated from hundreds of clinical samples, the tool can provide rapid pathogen identification in fast mode or be used in a comprehensive mode that offers a more complete tally of new and known microbes present in a sample. GenomeWeb Daily News covers how this tool was used to determine the cause of a teenaged boy's encephalitis here.

A US Department of Energy Joint Genome Institute-led team used metagenomic and metatranscriptomic sequencing to take a look at sheep rumen microbiome changes associated with enhanced methane production. Based on the microbial genes and transcripts found in rumen samples from 22 sheep with known methane yields, the team determined that methane-related microbial gene repertories tend to be similar in rumen samples from sheep with variable methane emissions. In contrast, though, the analysis revealed a rise in the expression of methanogenesis-related microbial genes in the rumens of sheep emitting more methane than usual.

Researchers at the University of Michigan at Ann Arbor and the Chinese Academy of Sciences present evidence supporting the notion that gene duplications can spur new functional adaptations. The team systematically compared the consequences of knocking out individual genes in the fission yeast Schizosaccharomyces pombe or homologous pairs of duplicated genes in the budding yeast Saccharomyces cerevisiae. According to that analysis, the duplicated gene knockouts had more marked fitness effects than losses of comparable singleton genes, suggesting that duplicates have adapted to take on new and additional functions. "These results provide genomic evidence for the role of gene duplication in organismal adaptation," the study authors write, "and are important for understanding the genetic mechanisms of evolutionary innovation."