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This Week in Genome Biology: Aug 14, 2014

A study in Genome Biology outlines the impacts that human health and lifestyle can have on the dynamics of the gut and salivary microbiomes over time. Researchers from the Massachusetts Institute of Technology and elsewhere used 16S ribosomal RNA gene sequencing to tally up microbial community members in stool and saliva samples collected daily from two healthy men over a year. By folding in information on almost 350 health and lifestyle variables that included everything from fitness levels and exercise to diet and mood, they followed individuals' microbiomes and took a peek at factors affecting them. The analysis suggest that these microbial communities remain relatively stable over time, though factors such as host infection or international travel led to marked shifts in the microbes present in the communities tested. GenomeWeb Daily News has more on this study here.

A BGI-Shenzhen-led team used population resequencing and comparative genomics to look at the roots of domestication in the peach plant Prunus persica, a cultivated perennial in which relatively few genetic polymorphisms had been identified previously. By sequencing plants from 74 cultivated peach varieties and 10 wild counterpart plants, the researchers identified SNPs in the wild, ornamental, and edible peach varieties and narrowed in on hundreds of genes showing signs of selection in either edible or ornamental peaches. Their analysis pointed to one main transition from wild peach plants to domesticated peach varieties several thousand years ago, followed by a split between ornamental and edible peach plants.

An international group led by investigators in Hong Kong used a combination of RNA sequencing, whole-genome bisulfite sequencing, and chromatin immunoprecipitation sequencing to quantify expression, methylation, and histone modification patterns in samples and cell lines from members of a Chinese parent-child trio affected by type 2 diabetes. Generally speaking, the researchers found that high levels of DNA methylation in the promoter region a gene correspond with lower-than-usual expression of the gene. But methylation across the gene body appeared to have a similar effect, prompting the study's authors to argue that "[f]uture studies on gene regulatory mechanisms and disease-associated differential methylation should pay more attention to DNA methylation at gene bodies and other non-promoter regions."