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This Week in Genome Research: Jan 23, 2013

A team from the J. Craig Venter Institute and the Hospital for Sick Children reports on a sperm sequencing-based method for getting chromosome-length haplotype information for individuals whose diploid genome has already been sequenced. In their Genome Research study, the researchers highlighted the feasibility of this approach by using it to haplotype HuRef — better known as Craig Venter's genome — using sequence data from 96 individual haploid sperm cells. "This approach exploits the haploid nature of sperm cells, and employs a combination of genotyping and low-coverage sequencing on a short-read platform," the study's authors note. "In addition to generating chromosome-length haplotypes, the approach can directly identify recombination events (averaging 1.1 per chromosome) with a median resolution of less than 100 [kilobases]."

Our sister publication In Sequence has more on the study, here.

Researchers with the Robert Koch Institute in Germany, the University College Cork, and the Wellcome Trust Sanger Institute, and elsewhere used a combination of genome sequence data and phylogenomics to trace the emergence of a pandemic clone of methicillin-resistant Staphylococcus aureus known as EMRSA-15 that was first detected in the UK roughly two decades ago and has since spread to other parts of the world. Based on phylogenomic analyses done with genome sequence data for 193 S. aureus isolates sharing the same multi-locus sequence features as the pandemic clone, the team determined that the ancestors of the EMRSA-15 clone were community-associated, drug sensitive bugs that first acquired methicillin resistance and started causing healthcare-related infections in England in the 1980s. From there, it seems, a sub-clone took on resistance to another antibiotic, fluoroquinolone, the study authors say.

Finally, the HudsonAlpha Institute for Biotechnology's Richard Myers leads a team of American researchers following the ebb and flow of DNA methylation in various human cell lines and tissues. Using reduced representation bisulfite sequencing, the group assessed methylation at the single-base resolution in 82 cell lines or tissues. And by folding in information from RNA-sequencing and chromatin immunoprecipitation plus sequencing experiments, the investigators got a glimpse at how DNA methylation varies with respect to features in the genome such as gene expression or chromatin profiles. Together, this work "provides an atlas of DNA methylation across diverse and well-characterized samples," Myers and his colleagues say, "and enables new discoveries about DNA methylation and its role in gene regulation and disease."