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This Week in Genome Biology: Jun 5, 2013

In the early, online version of Genome Biology, an international team describes findings from an effort to sequence the genome of a commonly grown, green-podded cacao cultivar called Theobroma cacao Matina 1-6. The US Department of Agriculture-Agriculture Research Service's David Kuhn and colleagues from Mars, Indiana University, Hudson Alpha Institute for Biotechnology, IBM, and elsewhere put together a genome assembly representing around 346 million of the estimated 445 million bases in the Matina 1-6 cultivar's genome. Through comparisons with an already sequenced cultivar, gene expression profiling, and other analyses, the team tracked down genes with apparent ties to cacao traits of interest, including pod color.

A Broad Institute-led team reports on computational schemes for detecting and understanding bias in DNA sequence reads. The researchers assessed human and microbial sequence data generated with Illumina, Ion Torrent, Pacific Biosciences, and Complete Genomics platforms, using their methods to look at the nature and source of sequence biases across technologies, sequence sources, and library types. "The assays presented in this paper provide a comprehensive view of sequencing bias, which can be used to drive laboratory improvements and to monitor production processes," the Broad's David Jaffe and colleagues wrote. "Development guided by these assays should result in improve genome assemblies and better coverage of biologically important loci."

Selection pressure protects long non-coding RNAs, or lncRNAs, from mutation in the fruit fly genome, but the same level of selection against mutations doesn't carry over to human lncRNAs, according to a study by two University of Oxford researchers. The pair scrutinized SNP patterns in intergenic lncRNA sequences from 163 Drosophila melanogaster strains and 174 humans. Whereas intergenic lncRNAs in fruit flies tend to harbor a higher-than-usual proportion of rare variants, they found, selection against such changes was less stringent in the human genome, where selection on lncRNAs between genes appeared neutral. Based on such patterns, study authors postulated that "while the sequences of lncRNAs will be well conserved across insect species, such loci in mammals will accumulate greater proportions of deleterious changes through genetic drift."