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Genomics in the Journals: 2013.07.25

NEW YORK (GenomeWeb News) – A genome sequencing study in Nature offered hints about genetic strategies organisms may use to maintain species diversity, even in the absence of sexual reproduction.

An international team led by investigators in Belgium and France did whole-genome sequencing on the bdelloid rotifer Adineta vaga, a tiny, asexual aquatic organism that reproduces through the division of unfertilized eggs.

From the resulting 218 million-base genome assembly, researchers determined that the organism has a tetraploid genome housing paired allelic sequences that are rearranged in ways that would make it impossible to separate genetic material into equal parcels during meiosis, the type of cell division that sexually reproducing organisms use to make germs cells.

The sequence contained a lower-than-usual representation of transposable elements, the group noted, along with expansions to gene families involved in defense against transposons and oxidation. The bdelloid rotifer's genome also showed signs of both gene conversion and horizontal gene transfer, with 8 percent or more of the genes in the genome apparently originating in other animals.

"It is plausible that the repeated cycles of desiccation and re-hydration experienced by A. vaga in its natural habitats have had a major role in shaping its genome: Desiccation presumably causes DNA double-strand breaks," the study's authors wrote, "and these breaks that allow integration of horizontally transferred genetic material also promote gene conversion when they are repaired."

Also in Nature, a look at the evolution of genome sequences in populations of Saccharomyces cerevisiae. Researchers at Princeton University, Harvard University, and elsewhere performed whole-genome and whole-population sequencing on 14 large and 26 small yeast populations started from replicate, haploid S. cerevisiae cells.

By sequencing samples from populations grown for 1,000 generations in rich growth medium, the team saw signs of rampant genetic hitchhiking — a phenomenon whereby sets of mutations arise together and spread through the population as a group, or 'clonal cohort.'

"Multiple clonal cohorts are often present simultaneously, competing with each other in the same population," senior author Michael Desai, an organismic and evolutionary biology researcher at Harvard University, and his co-authors wrote.

"Our results show that patterns of sequence evolution are driven by a balance between these chance effects of hitchhiking and interference, which increase stochastic variation in evolutionary outcomes," they continued, "and the deterministic action of selection on individual mutations, which favors parallel evolutionary solutions in replicate populations."

Stephen Kingsmore, director of the Children's Mercy Hospitals and Clinics Center for Genomic Medicine, led a team of investigators reporting in Science Translational Medicine on metabolomic and proteomic signatures associated with poor outcomes in individuals who have developed sepsis, a form of systemic inflammation that can be traced back to an underlying infection.

Drawing from more than 1,000 individuals admitted to emergency rooms at three US hospitals over several years, the team used liquid chromatography, gas chromatography, and mass spectrometry to do metabolomic and proteomic profiling on blood samples from individuals with community-acquired sepsis or with systemic inflammation in the absence of infection.

Data from samples taken at admission and again after 24 hours indicated that individuals who survived uncomplicated sepsis, severe sepsis, or septic shock had metabolomic and proteomic patterns in their blood that resembled one another.

But the investigators saw distinct differences within the group of patients with community-acquired sepsis who succumbed to their condition during the following week or month. Compared with uninfected controls and sepsis survivors, that group tended to show shifts in blood metabolite and protein profiles related to fatty acid transport pathways, beta oxidation, gluconeogenesis, and citric acid cycle activity.

"[T]he analytes and pathways that differentiate sepsis survival and death hold promise as potential prognostic biomakers," Kingsmore and colleagues noted, "and may also be useful as targets for the development of new therapies for patients at higher risk of death."

An Imperial College London-led group used genome sequencing to search for loci that have been subject to artificial selection in lab rats. As they reported in Cell, the researchers sequenced the genomes of more than two dozen rat strains. Among them were 11 strains developed through inbreeding to study conditions such as hypertension, diabetes, and insulin resistance.

By comparing sequences in the disease model strains with their respective control strains, other lab rat strains, and two previously sequenced rat strains, the team catalogued 9.6 million SNPs, 3.5 million small insertions and deletions, and nearly 720,000 structural variants present in the rat genomes.

Using high-quality SNPs unearthed in the analysis, the investigators subsequently teased apart phylogenetic relationships between the rat strains. They also focused in on groups of genes that tended to evolve together as well as sequences showing signs of artificial selection.

"We believe this to be the first evolutionary analysis of artificial selection for disease phenotypes," Imperial College London researcher Timothy Aitman, the study's corresponding author, and his colleagues noted, "and suggest that further analysis of these genes will confirm many of them as new genes for these phenotypes that will shed light on the pathogenesis of these conditions in rats and humans."

Genomics In The Journals is a weekly feature pointing readers to select, recently published articles involving genomics and related research.