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This Week in Genome Biology: Apr 10, 2013

In the early, online edition of Genome Biology, an international team led by investigators at Washington University's Genome Institute presents findings from an effort to sequence and scrutinize the western painted turtle genome. Using DNA from a female of the Chrysemys picta bellii species from southern Washington, the group cobbled together a genome assembly that was subsequently compared with sequences from reptiles and other vertebrates. The comparisons, coupled with transcript sequence data, revealed information about the turtle species' relationships and served as a means of learning more about the turtle's atypical traits — from cold tolerance to the ability to live in low oxygen conditions.

For more on this study, check out a related story appearing in our sister publication GenomeWeb Daily News.

The mountain pine beetle appears to have snagged at least one enzyme-coding gene from bacteria through horizontal gene transfer, according to another genome sequencing study. Researchers from the University of British Columbia and elsewhere put together a draft genome assembly for the mountain pine beetle, Dendroctonus ponderosae Hopkins, which has destroyed large swaths of pine forest in that Canadian province and other parts of western North America. In addition to finding some genetic variants and sex chromosome clues in the genome sequence, the team identified several intriguing enzyme-coding genes, including bits of bacterial sequence coding for a sucrose-6-phosphate hydrolase enzyme.

Finally, BGI-Shenzhen's Jun Wang and colleagues from China, Denmark, and Saudi Arabia describe apparent genetic adaptations to a high altitude environment that were unearthed in the genome of ground tit, Pseudopodoces humilis, a bird species native to the high-altitude Qinghai-Tibet Plateau. From the billion base ground tit assembly — believed to cover more than 95 percent of the bird's overall genome — the researchers found almost 17,000 predicted protein coding genes, as well as 1.7 million SNPs and various repeat sequences. When they examined gene family expansions and searched for signs of selection, the team found several genes involved in cardiac function, hinting that such processes may contribute to high altitude adaptation in the bird.