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This Week in PNAS: Jun 18, 2013

In a study appearing online this week in the Proceedings of the National Academy of Sciences, a Japanese team describes findings from a genome sequencing study focused on the Pacific bluefin tuna, Thunnus orientalis. An analysis of the genome revealed more than 26,400 predicted protein-coding genes, including genes coding for rhodopsin and opsin pigments poised to pick up blue, green, red, and UV light. Within genes coding for the color-sensing proteins, researchers found substitutions and duplications suspected of helping bluefish tuna differentiate between blue and green. If so, that could confer an evolutionary advantage in the fish's ocean environment, they say, perhaps explaining some aspects of the tuna's predatory proficiency. GenomeWeb Daily News has more on the study, here.

The molecular diversity detected in a nematode worm Caenorhabditis brenneri is the highest detected among eukaryotic species so far, according to another PNAS study. University of Toronto researchers used SNP profiles in nearly three dozen C. brenneri strains from South America, South Asia, and other parts of the world to get a glimpse at diversity in C. elegans' out-breeding cousin. Polymorphisms were pronounced in the tiny worm, study authors found, with nucleotide diversity on par with that present in diverse bacterial species. "This is not an artifact of cryptic species divergence," they conclude, "but reflects an enormous pan-tropical population, confirmed by fully viable genetic crosses between continents, extensive intra-locus recombination, selection on codon use, and only weak geographic genetic structure."

Finally, an international team led by investigators in Portugal considers the consequences of ambiguous codon use in fungi, using the pathogen Candida albicans as a model organism. That organism was selected as it seems to withstand the type of proteome variability the researchers focused on — the occasional substitution of the amino acid serine at a codon that normally dictates the presence of a leucine residue. Using C. albicans strains designed to have less flexibility at the codon in question, investigators began unraveling ties between amino acid ambiguity at this codon, fungal genome diversity, and phenotypic features in the organism.