In Genome Research this week, Michael Brudno and his colleagues at the University of Toronto describe a method to detect copy-number variation via mated short reads, wherein "matepairs mapping discordantly to the reference serve to indicate the presence of variation." CNVer — the team's algorithm — combines this information and allows researchers to "mitigate the sequencing biases that cause uneven local coverage and accurately predict CNVs." Brudno et al. used CNVer on a recently described genome of a Yoruban individual and detected 4,879 CNVs. "CNVer can reconstruct the absolute copy counts of segments of the donor genome and evaluate the feasibility of using CNVer with low coverage datasets," the authors add.
A trio of researchers at the University of Washington in Seattle has detected signatures of positive selection in 10 human exomes. In a paper appearing online in Genome Research, the team describe their methodology: first, they examined "putatively selected loci from four previous genome-wide scans of SNP genotypes and demonstrate that these regions indeed show unusual population genetic patterns in the exome data." Then, using a "series of conservative criteria based on
exome polymorphism," they fine-scale mapped signatures of selection, and in many instances were able to decipher a candidate SNP. The team sequenced "a portion of one novel candidate locus, IVL, in 74 individuals" of diverse ethnicities, and suggest that exome data sets will become "powerful tools for identifying adaptive genetic variation."
Yann Surget-Groba and Juan Montoya-Burgos at the University of Geneva in Switzerland report two techniques for the "optimization of de novo transcriptome assembly from next-generation sequencing data." The first technique, the multiple-k method, "relies on the observation that the use of a single k-mer length by current de novo assemblers is suboptimal to assemble transcriptomes where the sequence coverage of transcripts is highly heterogeneous." The second method depends on the use of a reference proteome, and uses "mapping against the closest available reference proteome for scaffolding contigs that map onto the same protein." The scaffolding using translation mapping method, as Surget-Groba and Montoya-Burgos call it, "considerably improves the assembly with few errors," they write.
Also in Genome Research this week, investigators at the University of Chicago describe the "age-dependent chromosomal distribution of male-biased genes in Drosophila." The team found an "excess of young X-linked male-biased genes" in their genome-wide analysis and that "the switch between X-linked and autosomal enrichment of male-biased genes was also present in the distribution of both protein-coding genes on the D. pseudoobscura neo-X chromosome and microRNA genes of D. melanogaster." The authors suggest that the evolution of male-biased genes may be more complicated than was previously thought.