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This Week in PNAS: Jul 30, 2013

In the early, online edition of the Proceedings of the National Academy of Sciences, a team from the US and China report on the identification of quantitative trait loci in soybean that coincide with resistance to a pesky pest known as the southern root-knot nematode. The group sifted through shallow genome sequence data for 246 inbred paleopolyploid soybean lines generated by crossing sensitive and resistant soybeans to tally up SNPs and assign them to their original parental line. That phased variant information, together with recombination profiles and linkage maps, eventually led the researchers to a trio of southern root-knot nematode resistance QTLs, including one chromosome 10 locus that they have begun to characterize in more detail.

A coding mutation not expected to alter the amino acid sequence of the resulting protein turns up recurrently in melanoma, according to another study set to appear online in PNAS this week. Researchers from Israel, the US, and Australia unearthed the change — a cytosine to thymine swap at position 51 in the BCL2L12 gene — using genome sequence data for 11 matched tumor normal samples, together with exome sequence data for 14 tumor-normal pairs and four melanomas missing matched normal control samples. In addition to the two melanomas containing the synonymous mutation in the discovery stage of the study, the team tracked down another 10 cases involving the change through targeted screening in 256 more melanomas. "Our data indicate that silent alterations have a role to play in human cancer," the study's authors say, "emphasizing the importance of their investigation in future cancer genome studies."

Hannover Medical School's Sebastian Suerbaum and colleagues performed genome sequencing on 97 Helicobacter pylori isolates from members of two large families from rural South Africa in an effort to understand how the stomach ulcer-causing bacteria evolve and are passed from one individual to another. By comparing the genomes of different H. pylori isolates from the same person, for instance, they were able to both retrace the bug's evolution within individual hosts and detect instance of co-infection by different H. pylori strains. Meanwhile, H. pylori sequences from across the families revealed transmission patterns and recombination events in the bacterial genomes.