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This Week in Genome Biology: Dec 18, 2013

Researchers from France, Portugal, and the US describe a transcriptome sequence-based population genomics study of the giant Galapagos tortoise, Chelonoidis genus. Using sequences from five giant Galapagos tortoises and representatives from related species, the study's authors saw signs of weak purifying selection and low genetic diversity in C. genus, including diminished diversity in immune-related genes. On the other hand, genes involved in stress response appear to be prone to enhanced selective pressure. Together, such patterns point to low effective population sizes for the endangered animal over extended periods of time.

A single-cell genomic study provides insights into the genetic diversity and phylogeny of bacteria from a freshwater clade of SAR11 — a bacterial group better known for its marine representatives. Uppsala University's Siv Andersson and colleagues from Sweden, Germany, and the US performed single-cell sequencing and genome assembly on 10 freshwater SAR11 cells collected in three different freshwater lakes. Compared to their saltwater counterparts, the freshwater bugs had diminished recombination to mutation ratios but a boost in nucleotide substitutions, the study's authors report, hinting that "the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade."

A Broad Institute-led team took a genome-wide association approach to track down nearly three dozen loci linked to heritable forms of the dog bone cancer osteosarcoma. Using genotyping data on hundreds of greyhounds, Rottweilers, and Irish wolfhounds, the researchers narrowed in on 33 osteosarcoma-associated sites in the dog genome that appear to explain between 55 percent and 85 percent of inherited risk for the disease, depending on the breed. The most pronounced association involved regulatory variants near a CDKN2A/B locus that's often rearranged in canine osteosarcoma tumors. Our sister publication GenomeWeb Daily News has more on the study.