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Genomics in the Journals Aug 28, 2014

NEW YORK (GenomeWeb) – In Nature Genetics, researchers from the US and the UK reported on results from a population genomic study of the black cottonwood poplar, Populus trichocarpa.

The team did whole-genome sequencing on 544 black cottonwood trees, representing populations adapted to three environments spanning its range across California, Oregon, Washington, and British Columbia, Canada.

A comparison with the P. trichocarpa reference genome revealed almost 18 million SNPs in the re-sequenced genomes. Using these variants and other genomic features, the researchers looked at the relationships between the poplar populations and looked for signs of selection associated with specific traits from trees adapted to various locales.

The latter search led to 397 sites in the black cottonwood genome showing hints of recent positive selection or divergent selection — a set of regions that often overlapped with genomic sites containing genes involved in adaptive black cottonwood traits such as drought resistance and stress response.

Along with insights into the plant's biology, the study's authors argued that an enhanced understanding of such adaptations may help in identifying genes behind black cottonwood traits that are desirable in a biofuel research context.

"Our approach is particularly powerful because we are mining standing natural variation resulting from tens of thousands of years of evolution and selection such that the alleles or gene variants that we have identified have great promise to provide robust, long-term improvements to biofuel feedstocks," the study's senior author Stephen DiFazio, a biology researcher based at West Virginia University, said in a statement.


An mBio study suggests that forms of methicillin-resistant Staphylococcus aureus, or MRSA, currently implicated in most community-acquired MRSA infections in Europe, the Middle East, and Northern Africa likely originated in sub-Saharan Africa prior to the mid-1980s.

Researchers from France, Denmark, the US, and elsewhere used whole-genome sequencing to assess a global collection of methicillin-sensitive and -resistant S. aureus isolates falling in clonal complex 80, or CC80, a group that includes most of the community-acquired forms of MRSA found in Europe. In general, CA-MRSA strains from CC80 also tend to be resistant to other antibiotics, they noted, including kanamycin, tetracyclin, and fusidic acid.

With genome sequences generated for 74 MRSA isolates and 23 methicillin-sensitive S. aureus isolates, the team produced a phylogenetic tree that appeared to have its roots in sub-Saharan Africa. In particular, it pointed to the advent of methicillin resistance in a previously sensitive strain with the ability to produce the so-called Panton-Valentine leukocidin toxin.

Descendants of that ancestor, which share four canonical SNPs, seem to have spread extensively during the mid- to late 1990s. On the other hand, a methicillin-sensitive version of S. aureus is still found in sub-Saharan Africa, the study authors noted, and remains sensitive to several antibiotics.

"Our study determined that a single descendant of a methicillin-sensitive ancestor circulating in sub-Saharan Africa rose to become the dominant CA-MRSA clone in Europe, the Middle East, and North Africa," the study's first author Marc Stegger, a microbiology and infection control researcher with the Statens Serum Institute, said in a statement.


A Paleo-Eskimo population unrelated to present-day Native American and Inuit populations appears to have peopled the Arctic for roughly 4,000 years before disappearing just over 700 years ago, according to a new Science study.

Researchers from the University of Copenhagen and elsewhere did mitochondrial sequencing on DNA from 154 ancient bone, teeth, or hair samples collected in Arctic Siberia, Alaska, Canada, and Greenland, along with low-coverage whole-genome sequencing on more than two-dozen such samples.

From there, they compared the genetic profiles in these ancient Arctic individuals with high-coverage genome sequence data for two individuals from a present-day Native American population in British Columbia, two Inuit individuals from Greenland, an Aleutian Islander, and two individuals from Siberia's Nivkh population.

Based on the genetic patterns and radiocarbon dating profiles generated for the ancient samples, the team argued in favor of an ancient Paleo-Eskimo migration to the Arctic around 5,000 years ago.

Although subsequent migration by the ancestors of Inuit individuals led to some mixing between the populations, the Paleo-Eskimo group's arrival appears to have been independent from migrations made by the Native American and Inuit ancestral groups, the study's authors explained.

"The genetics reveal that there must have been at least three separate pulses of migration from Siberia into the Americas and the Arctic," corresponding author Eske Willerslev, with the University of Copenhagen's Centre for GeoGenetics, said in a statement. "First came the ancestors of today's Native Americans, then came the Paleo-Eskimos, and finally the ancestors of today's Inuit."


In another Science paper, a team from the University of Chicago, Argonne National Laboratory, and elsewhere provided evidence of pronounced variation in the microbial communities found in homes inhabited by different families.

As part of the Home Microbiome Project, the researchers used 16S ribosomal RNA sequencing to follow microbial community patterns in 18 individuals, three dogs, one cat, and seven corresponding family homes over six weeks. During that time, three of the families moved, providing the opportunity to look at whether their presence altered existing microbial communities in their new residences.

The team saw substantial differences in the microbial communities that had taken up residence in one home to the next. These microbiomes seemed to be rapidly seeded by those living in each home, producing family-specific indoor microbial signatures.

The analysis indicated that individuals living in the same home carried microbial communities that were more similar than usual to one another than to those living in different places, for instance. And diverse sampling sites within any one home were more microbially similar to one another than were matched locations from different people's homes.

For a subset of samples from one home, investigators used shallow metagenomic sequencing to track the transfer of microbes between humans, pets, and surfaces in the home. With deeper metagenomic sequencing, they also put together draft genome assemblies for several potential pathogens passed between hand samples and a kitchen counter in that home.

All told, the study's authors saw signs of "substantial interaction among human, home, and pet microbiota."

"[W]e suggest that homes harbor a distinct microbial fingerprint that can be predicted by their occupants and that supersedes intersurface differentiation within the home," they wrote.

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