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Genomics in the Journals: Jun 12, 2014

NEW YORK (GenomeWeb News) – In Nature Genetics, researchers from the US Department of Energy's Joint Genome Institute, the HudsonAlpha Institute for Biotechnology, and elsewhere reported on results from an effort to sequence and analyze the common bean genome.

The team used a combination of Sanger, Roche 454, and Illumina sequencing to generate genome sequences from an inbred landrace line of the common bean species Phaseolus vulgaris, which belong to the Andean gene pool as opposed to the geographically and genetically distinct group of Mesoamerican common beans.

After generating a 473 million base genome assembly for the plant, which spanned more than 80 percent of the common bean's total genome, the researchers went on to compare it to that of the related soybean plant, first sequenced in 2010. They also re-sequenced another 60 wild beans as well as representatives from 100 Mesoamerican and Andean landraces of common bean.

The team's analysis indicated that ancestral Mesoamerican and Andean common beans diverged from one another prior to independent domestications of plants from each pool. Those domestication events appear to have affected some 74 million bases of sequence in the common bean genome, but less than one-tenth of those proposed domestication contributors overlapped in both gene pools.

The study's authors also identified genes suspected of influencing several important common bean traits such as nitrogen fixation, leaf size, seed weight, disease resistance, and more.

"We're trying to understand what the common bean looked like before human intervention, to identify what occurred during early domestication and to apply that to modern bean breeding," co-corresponding author Jeremy Schmutz, a plant program leader at JGI and co-director of HudsonAlpha's Genome Sequencing Center, said in a statement. "Studies such as this are necessary to identify genes that could be used to improve traits such as ease of harvest, flavor, yield and disease resistance."


A PLOS One study by researchers in the US and France suggests that individuals with sepsis — potentially life-threatening bloodstream infections — are prone to reactivation of long-dormant viruses in their bodies.

The team used quantitative PCR to screen for the Epstein-Barr virus, herpes simplex virus, human herpes virus-6, and other types of viruses in whole blood and plasma samples collected from more than 700 critically ill patients with or without sepsis and 164 healthy age-matched controls.

Findings from the blood and urine analyses indicated that almost 43 percent of patients with sepsis carried two or more detectable viruses. This sepsis-related viremia often coincided with infections by fungi and opportunistic pathogen bacteria, researchers reported. They also found that sepsis patients with cytomegalovirus (CMV) in their bloodstream were more likely to experience poor outcomes and high mortality compared to their CMV-free counterparts.

"We stumbled onto more viruses than we expected, and we don't know yet whether some of these viruses are causing problems in their own right," co-author Gregory Storch, a pediatrics researcher at Washington University, said in a statement. "We think this paper will stimulate others to carry out further investigations of the role of latent viruses in sepsis."


Members of the SIGMA Type 2 Diabetes Consortium described a rare missense variant in the hepatocyte nuclear factor 1-a gene HNF1A that's associated with type 2 diabetes risk in individuals with Latino ancestry.

As they reported in the Journal of the American Medical Association, the researchers did exome sequencing on 1,794 Latino individuals with type 2 diabetes and 1,962 unaffected controls. The study participants included individuals of Latino descent from the US as well as individuals from Mexico.

When the team compared protein-coding sequences from individuals with or without diabetes, it detected an apparent association involving a low-frequency variant in HNF1A, a gene that's been implicated in a condition called maturity onset diabetes of the young type 3, or MODY3.

Follow up experiments involving another 14,276 individuals from multiple populations indicated that ties to type 2 diabetes risk may be specific to individuals with Latino ancestry. In that population, the study's authors found the HNF1A variant in more than 2 percent of individuals with type 2 diabetes and only 0.36 percent of those without.

They noted that this apparent association "may have implications for screening and therapeutic modification in this population, but additional studies are required."


Flu viruses circulating in present-day wild bird populations contain sequences that are sometimes very similar to those found in the virus that caused the 1918 Spanish flu pandemic, according to a study in Cell Host & Microbe.

Using sequences for the 1918 pandemic strain and for avian influenza A viruses found in the Influenza Research Database, a team from the US, Japan, and the UK performed a phylogenetic analysis that pointed to the presence of circulating avian flu virus gene segments that are only subtly different from the Spanish flu strain.

Indeed, when they put eight such segments together in an order expected to have homology to the 1918 strain, the researchers found that the resulting virus was infectious to ferrets, a model for human flu infections.

Based on such findings, the study's authors argued that ongoing avian flu virus surveillance is warranted to watch for the emergence of bird flu strains with enhanced pathogenicity that are capable of infecting humans.

"Because avian influenza viruses in nature require only a few changes to adapt to humans and cause a pandemic, it is important to understand the mechanisms involved in adaptation and identify the key mutations so we can be better prepared," the University of Wisconsin at Madison's Yoshihiro Kawaoka, senior author on the study, said in a statement. "Research findings like this help us assess the risk of outbreaks and could contribute to routine surveillance of influenza viruses."

The Scan

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The Wall Street Journal reports that Paul Stoffels will be stepping down as chief scientific officer at Johnson & Johnson by the end of the year.

Science Papers Present Proteo-Genomic Map of Human Health, Brain Tumor Target, Tool to Infer CNVs

In Science this week: gene-protein-disease map, epigenomic and transcriptomic approach highlights potential therapeutic target for gliomas, and more