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Genomics In The Journals: Nov 8, 2012

NEW YORK (GenomeWeb News) – In the early, online edition of Proceedings of the National Academy of Sciences, Swedish researchers report on their study of population structure in Atlantic herring, Clupea harengus.

The team put together an exome reference sequence for the fish using muscle transcriptome sequence data from a lone herring representative caught near Sweden. This sequence data was subsequently compared with pooled genomic DNA sequence generated for 50 herrings apiece from eight populations in the Baltic Sea, North Sea, and Atlantic Ocean. With this reference genome-free approach, they explained, the investigators identified almost 441,000 SNPs. Among them was a subset of variants that proved useful for starting to assess population structure, differentiation, and selection patterns in the fish.

"This study provides insights concerning the population structure of an important marine fish," senior author Leif Andersson, a researcher affiliated with Uppsala University and the Swedish University of Agricultural Sciences, and his colleagues wrote, "and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection."

A team from the National Institute of Allergy and Infectious Diseases has taken a look at the metabolic and transcriptional patterns that coincide with different stages of development in the human pathogen Chlamydia trachomatis for another paper slated to appear online in PNAS.

The researchers relied on a cell-free culture strategy to study the bacterial species, which has an obligate intracellular life stage — known as the reticulate body stage — that makes it tricky to study. Through analyses that included carbon usage patterns, metabolic activity, and expression profiling at more than 900 sites in the C. trachomatis genome, the investigators determined that both the bug's infectious elementary body and its intracellular reticulate body form have high levels of metabolic and biosynthetic activity.

"The findings presented herein will facilitate the study of chlamydial metabolism and physiology under controlled nutritional and physiochemical conditions," senior author Ted Hackstadt, a researcher with NIAID's host-parasite interactions section, and his colleagues wrote. "Moreover, robust axenic metabolic activity will complement current research tools used to study chlamydiae, including the recent development of genetic tools."

A team from Colombia, the US, and Sweden used data at three-dozen fluorescently-labeled microsatellite and simple sequence repeat marker data to look at population structure in cultivated common beans and in wild bean plants belonging to the same Phaseolus vulgaris species.

As they report in PLoS ONE, the researchers compared patterns in hundreds of wild and cultivated bean genotypes. Results of their analyses point to slightly higher genetic diversity in the wild bean plant genotypes as a group, though the cultivated plants also tended to have fairly high diversity at the markers considered. When it looked at how wild bean plants clustered with one another, meanwhile, the team found five populations showing genetic differentiation from one another. These populations, dubbed the Mesoamerican, Guatemalan, Colombian, Ecuadorian-Peruvian, and Andean gene pools, provided new insights into cultivated bean plant domestication.

"Results suggest geographic isolation, founder effects, or natural selection could have created the different semi-discrete populations of wild beans," Uppsala University evolutionary biology researcher Andrés Cortés, the study's senior author, and colleagues wrote, "and that multiple domestications and introgression were involved in creating the diversity of cultivated beans."

In both insects and nematode worms, genetic variants contributing to phosphine gas resistance are found in and around an oxidation and reduction-related site in the gene coding for the dihydrolipoamide dehydroxenase, or DLD, enzyme, according to a study by investigators from the University of Queensland and elsewhere.

As they report in Science, the researchers began by looking at mutant forms of the nematode Caenorhabditis elegans that are resistant to the redox-active phosphine gas, which is used as a fumigant for helping grain fend off pest insects. Through complementation analyses of these mutants, along with gene mapping experiments based on mutant strain crosses, the team determined that the gene coding for DLD was among those influencing phosphine susceptibility. Likewise, their follow-up experiments suggest that the enzyme has a role in phosphine resistance in Rhyzopertha dominica and Tribolium castaneum insects as well.

Even so, the study authors noted that some of the same DLD mutations that render C. elegans more resistant to phosphine actually enhance its sensitivity to another gas called arsine, suggesting that that fumigant might serve as a food-guarding substitute in some instances where phosphine-resistant pests occur.

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

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