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This Week in PNAS: Jun 26, 2013

Korean researchers sequenced the genome of a bacteria-infecting marine virus that could be cultured in the lab and used the genome data to help interpret metagenomic sequence data for phages found in the ocean in general — work they describe the early, online edition of the Proceedings of the National Academy of Sciences. The team sequenced the 55,000 or so bases of the HMO-2001 genome, representing a bacteriophage from a widespread marine phage clade called SAR116. The sequence housed novel genes, But it also helped in classifying metagenomic sequence data from uncultured marine viruses, study authors say, noting that the "genomic uniqueness of the SAR116 clade contributed to the remarkable power of the HMO-2011 genome in the binning of marine viromes."

A team from the US and Argentina takes a look contributions that the gut microbiome makes to the success of a plant pest known as western corn rootworm. Using 16S ribosomal RNA gene sequencing, researchers assessed microbial communities in the guts of field-grown western corn rootworms that were sensitive or resistant to crop-planting rotations designed to stem the pest's survival in its host corn plant. They found that gut microbiomes differed in rotation-resistant and -sensitive rootworm strains — microbial community changes that apparently bolster the resistant rootworms' ability to survive on a non-host plant such as soybean, often grown in rotation with corn.

Positive selection acting on dozens of genes, along with extensive gene expression changes, have contributed to tomato domestication, according to an RNA-sequencing study by investigators in the US, Germany, Japan, and Spain. Through deep trancriptome sequencing on tissues from a domestic tomato accession and five wild relative species, the group began to tease apart sequence and expression changes at play during tomato domestication. For instance, the analysis unearthed domestication-associated signs of positive selection involving at least 50 genes, along with expression shifts at thousands of genes. "Taken together," they write, "our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.

For more on the study, check out a story from our sister publication GenomeWeb Daily News.