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This Week in PLOS: Feb 8, 2016

In PLOS Genetics, a French team explores the transfer of host genetic material into viruses, focusing on baculoviruses infecting two moth species. Through deep sequencing experiments on 21 baculovirus populations, the researchers uncovered 86 DNA sequences suspected of making their way from the moth genome into the viruses during the infection process. The set included 69 transposable elements and 17 previously undescribed moth sequences, the authors note. Further, some stretches of moth DNA were subsequently found in other insect species prone to baculovirus infections suggesting the virus may contribute to horizontal gene transfer between species. Consequently, they say, "potential uncontrolled gene spread associated with the use of viruses produced in insect cells as gene delivery vectors and/or biopesticides should … be evaluated."

Canadian researchers reporting in PLOS One provide a comparison of sample preparation protocols for those doing next-generation, whole-genome sequencing on the tuberculosis-causing bacteria Mycobacterium tuberculosis. The team did a head-to-head comparison of Nextera and Illumina TruSeq library preparation kits, taking into account the quality of both the original DNA samples and the resulting genome sequence data. The results suggest that such sequencing experiments rely heavily on the purity and base composition of the M. tuberculosis DNA available for sequencing. However, the group reported that its genome sequence data was more uniform for M. tuberculosis samples prepared with the TruSeq kit.

Also in PLOS One, a team from China characterizes copy number variations in two local pig breeds, the Xiang and Kele pigs. When they used the PorcineSNP60 genotyping array to test samples from 98 Xiang pigs and 22 Kele pigs, the researchers identified 172 candidate CNVs affecting some 660 pig genes, particularly those involved in sensory perception-, cognition-, and reproduction-related processes. More than half overlapped with CNVs described in prior pig studies, though a subset of the suspected CNVs turned up only in the Kele pigs and others appeared to be specific to Xiang pigs with either large or small litter sizes. "Our results … may be useful in future assessments of the associations between CNVs and important phenotypes in Xiang and Kele pigs to ultimately help protect these rare breeds," the authors write.