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This Week in Genome Biology: Jun 17, 2015

A UK team led by investigators at the University of Birmingham describes the real-time nanopore sequencing strategy it used to help track Salmonella enterica serovar Enteritidis transmission and trajectory during an outbreak in 2014. Along with rapid whole-genome sequencing protocols performed using Illumina's MiSeq instrument, the researchers looked at the feasibility of sequencing S. Enteritidis isolates collected during the outbreak with Oxford Nanopore's MinION machine. "Both approaches yielded reliable and actionable clinical information on the Salmonella outbreak in less than half a day," the study's author say, noting that the MinION sequencing method made it possible to identify species from clinical samples within just 20 minutes.

Researchers from the University of Pennsylvania and elsewhere outline results from a single-cell transcriptome sequencing study of cells from mouse and rat tissues. The team did deep single-cell RNA-seq patterns in 91 mouse cells and 18 rat cells, representing five mouse tissue types and two rat tissues, respectively. By comparing expression patterns in individual cells and in RNA sequences from bulk tissue samples, the investigators began delineating the variation that's present within and between cell types.

Using an ultra-dense genetic mapping method, a Nanjing Agricultural University group made improvements to the genome assembly for the allopolyploid cotton plant Gossypium hirsutum and began unraveling a clearer picture of the plant's structural variations. The researchers relied on genotype-by-sequencing to narrow in on nearly five million SNPs markers using sequence data for parental plants and for dozens of tetraploid cotton plants developed by crossing G. hirsutum with G. barbadense. From there, they came up with a linkage map for ordering scaffolds of cotton sequence, detecting rearrangements, and uncovering recombination hotspots in the cotton genome.