In the PNAS Early Edition this week, a team led by researchers at the University of Nebraska-Lincoln shows that "individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors." Namely, using quantitative pyrosequencing of the microbiota in 645 intercross line mice, the team found a core measurable microbiota of 64 taxonomic groups, within which they identified "co-segregation with 530 fully informative SNP markers" and "18 host quantitative trait loci that show significant or suggestive genome-wide linkage with relative abundances of specific microbial taxa," the authors write. The team suggests that their work demonstrates "clear evidence for the importance of host genetic control in shaping individual microbiome diversity in mammals."
MIT's Maureen Coleman and Sallie Chisholm used comparative population genomics to deduce ecosystem-specific selection pressures in Prochlorococcus and Pelagibacter, two model marine microbes. Coleman and Chisholm found many rare genes in each population, which they say reflects "continual gene transfer and loss" between the two populations, which occur in biogeochemically distinct environments, "only a few genes significantly differ ... nearly all of these are related to phosphorus acquisition," the pair writes, adding that the findings "implicate phosphorus availability as the dominant selective force driving divergence between these populations."
Investigators at the University of California, Berkeley, show in PNAS this week that rice endosperm DNA is hypomethylated across all sequence contexts. Specifically, they report that "non-CG methylation is reduced evenly across the genome" and "CG hypomethylation is localized." In embryos, the team found an increased in CHH methylation of small transposable elements, which they suggest demonstrates that "DNA methylation is a crucial regulator of rice endosperm biogenesis."
A National Institute of Allergy and Infectious Diseases-led team describes in a PNAS paper published online this week a "method to recover recombinant viruses in which independent selection strategies are used to engineer single-gene replacements" in a rotavirus genome. By combining "a mutant SA11 RV encoding a temperature-sensitive defect in the NSP2 protein with RNAi-mediated degradation of NSP2 mRNAs," the team was able to "isolate a virus containing a single recombinant gene." Subsequently, they used reverse genetics to "generate a panel of viruses with chimeric NSP2 genes," to demonstrate their so-called "'two-hit' reverse genetics methodology," they write.