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This Week in Genome Biology: Jan 28, 2015

Researchers from Switzerland, Norway, and Germany describe efforts to sequence, assembly, and begin analyzing the draft genome of a perennial flowering plant called Primula veris that can produce two types of flowers, a trait known as heterostyly. Using a combination of Illumina, Ion Proton, and Pacific Biosciences sequencing technologies, the team put together an almost 302 million base de novo assembly spanning roughly 63 percent of the plant's complete genome. With the help of data produced by transcriptome sequencing, restriction-associated DNA sequencing, and so on, they uncovered more than 19,500 predicted protein genes in the genome, including 113 genes believed to contribute to distinct flower features in heterostylous P. veris plants.

DNA methylation patterns appear to shift in human adipose tissue following weight loss with the help of gastric bypass surgery, according to another Genome Biology study. Researchers from the Institute of Environmental Science in New Zealand did array-based genome-wide methylation profiling on adipose tissues from 15 obese women before and after gastric bypass surgery. Their results methylation changes in both omental and sub-cutaneous fat samples. For instance, the study's authors saw a dip in hypermethylation at several sites after surgery, along with differential promoter methylation — and corresponding gene expression changes — involving genes implicated in obesity.

A German-led team outlines a new computational approach called the "Tumor-specimen suited RNA-seq Unified Pipeline" (TRUP), which it designed to track down fusion genes contributing to lung cancer development based on transcriptome sequence data. After validating the TRUP approach using lung cancer cell lines and published RNA sequence data on small cell lung cancer samples, the researchers used it to assess 17 primary lung adenocarcinoma samples. The method compared favorably with other approaches for finding transcript chimeras, they report, revealing new and known rearrangements based on breakpoint assembly information.