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This Week in Genome Biology: Mar 2, 2011

In a paper published online in Genome Biology this week, a team led by investigators at the Baylor College of Medicine reports a draft genome sequence of Dictyostelium purpureum, a social amoeba. When compared with the D. discoideum sequence, the D. purpuream genome appears to have undergone little functional change, despite the species' divergence from a common ancestor approximately 400 million years ago, according to the Baylor-led team. The team adds that "genes involved in the social stage evolved more rapidly than others, consistent with either relaxed selection or accelerated evolution due to social conflict."

In a Genome Biology methods paper, researchers at the Max Planck Institute for Evolutionary Anthropology, along with their colleagues, "describe a PCA-based genome scan approach to analyze genome-wide admixture structure and introduce wavelet transform analysis as a method for estimating the time of admixture." For the first part, the team says that sequential, stepwise PCA — or StepPCO — is performed along each chromosome of an individual from an admixed population as well as those from individuals in respective parental populations. "The idea behind the method is straightforward: when two populations admix, genetic recombination starts breaking 'ancestral' genomes into blocks of different sizes, so that the genomes of the descendants of an admixture event are composed of different combinations of these ancestral blocks," the authors write. As for the wavelet transform method, the team applied it to genome-wide SNP data obtain from eight admixed populations and found that it "offers better resolution than existing methods for dating admixture."

Researchers at the Broad Institute this week report an approach for "analyzing and minimizing PCR amplification bias in Illumina sequencing libraries." First, to evaluate the sources of base-composition bias, the team used qPCR to trace sequences ranging from 6 percent to 90 percent GC content; the researcgers say that PCR during library preparation is a " principal source of bias and optimized the conditions." For this, the team introduces a protocol that "significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate" in Genome Biology this week.

Investigators at the European Bioinformatics Institute respond to Milinkovitch et al.'s 2010 paper "2x genomes — depth does matter," by saying that Ensembl project data contains low-coverage genomes, and that these must be considered when including 2x mammalian genomes in phylogenetic analyses. "Our analyses show that low coverage genome sequence per se is likely to generate a large number of artifactual duplications," the authors write, though they add that they mean in no way to undermine the validity of the Ensembl project, as they say it "incorporates among the best analytical tools for phylogeny inference and identification of valid versus ambiguous duplication nodes in gene trees." Still, as they "tend to think that most end-users in the genomic community wish to see the correct gene trees and corresponding valid gene duplication and gene loss events," the authors suggest that their findings provide "strong support for additional sequencing programs as well as for extensive analytical efforts."