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This Week in Genome Biology: Sep 26, 2013

Two independent teams reporting in Genome Biology used genome and transcriptome sequencing to search for sequences that might offer clues to successfully treating the barber pole worm, Haemonchus contortus, a small livestock parasite known for its ability to acquire resistance to a range of conventional worm-targeting treatments. In one of the studies, researchers from the Wellcome Trust Sanger Institute, the University of Calgary, and elsewhere generated a draft reference genome representing a barber pole worm strain still susceptible to most treatments. That genome sequence data was complemented by transcriptome sequence data for tissues taken at different stages of the worm's life cycle. In another study, an American and Australian team did genome and transcriptome sequencing on Australian H. contortus strains. For more on the studies, check out our sister publication GenomeWeb Daily News.

An Uppsala University-led team that included representatives from the Nordic Society of Pediatric Hematology and Oncology describe four methylation signatures detected in pediatric acute lymphoblastic leukemia. The researchers performed array-based cytosine methylation profiling on tumor samples from 764 children with ALL, including 27 patients who were tested both at diagnosis and after relapse. Along with hyper-methylation sites found in all of the ALL tumors, the group saw climbs and dips in methylation corresponding with specific ALL subtypes, gene expression patterns, and relapse.

Researchers with the National Biodefense Analysis and Countermeasures Center and the US Department of Agriculture's Agricultural Research Service took a crack at sequencing and assembling complete bacterial and archaeal genomes using PacBio RS single-molecule long reads alone — work that they describe in another Genome Biology study. Based on their experience sequencing and assembling half a dozen bacterial genomes, together with an analysis of repeat patterns in almost 2,300 bacterial and archaeal genomes, the researchers determined that data from individual PacBio libraries can be sufficient to assemble gap-free, finished genomes for such microbes. "These single-library assemblies are … more accurate than typical short-read assemblies and hybrid assemblies of short and long reads," the study authors say.

The Scan

Not as High as Hoped

The Associated Press says initial results from a trial of CureVac's SARS-CoV-2 vaccine suggests low effectiveness in preventing COVID-19.

Finding Freshwater DNA

A new research project plans to use eDNA sampling to analyze freshwater rivers across the world, the Guardian reports.

Rise in Payments

Kaiser Health News investigates the rise of payments made by medical device companies to surgeons that could be in violation of anti-kickback laws.

Nature Papers Present Ginkgo Biloba Genome Assembly, Collection of Polygenic Indexes, More

In Nature this week: a nearly complete Ginkgo biloba genome assembly, polygenic indexes for dozens of phenotypes, and more.