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This Week in PLOS: Oct 28, 2014

In PLOS One, researchers from Japan describe the 18S ribosomal RNA gene sequencing method they used to catalog the types of parasitic helminth worms present in the intestines of nine wild rats — seven from the Rattus norvegicus species and two R. rattus — sampled at either a downtown restaurant or a suburban zoo in the Japanese city of Miyazaki. All but one of the rats carried nematode worms in their intestine, the team notes. And the investigators demonstrated that they could explore the diversity of these worms not only by sequencing DNA from isolated worms, but also through 18S sequencing on DNA in rat fecal samples.

Researchers from China and the UK performed transcriptome sequencing on two leaf types from an alpine plant with translucent leaf bracts for another PLOS One paper. Using almost 200 million transcriptome sequence reads generated from upper bract leaf and lower rosulate leaf samples from the same glasshouse plant (Rheum nobile) stem, the team identified 25,249 glasshouse plant unigenes, including nearly 2,000 genes showing enhanced expression in one of the two leaf types — findings that are expected to offer clues to the plant's unusual biological features and its adaptation to alpine environments.

An international team led by investigators at Texas A&M University used a custom tiling oligoarray to characterize copy number variation patterns in more than three dozen normal horses from 16 domestic horse breeds and two Przewalski horses. As reported in PLOS Genetics, the analysis uncovered more than 250 CNV-prone regions in the horse genome, with CNV prevalence varying by breed compared to the Thoroughbred reference genome. Together with findings from past studies, the results indicate that the genome may contain up to 1,500 different CNV compared to the horse reference genome — a collection that the study's authors used to explore a sex chromosome-related developmental condition in half a dozen more horses.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.