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This Week in PNAS: Mar 25, 2014

In a study slated to appear online this week in the Proceedings of the National Academy of Sciences, researchers from Italy, the UK, and Australia described genomic efforts to characterize Haemophilus influenzae isolates that lack the outer capsule that's used for typing other strains of the pathogen. The team did whole-genome sequencing on 89 of these so-called "non-typeable" H. influenza isolates that were either involved in disease cases or carried without obvious symptoms. Along with data from eight non-typeable H. influenza isolates sequenced previously, the data made it possible to pick up polymorphisms, define gene families, and retrace relationships amongst isolates in the collection. The data supported the notion that many of the capsule-free H. influenza isolates stem from clonal evolution, the study authors note, though they also tracked down distinct clades of the bugs.

A team from China and the US takes a look at genome dominance in polyploid organisms from the flowering plant lineage for another PNAS study. By comparing transposon and small RNA patterns in polyploid Brassica rapa and Arabidopsis thaliana genomes, the researchers found that the process by which one sub-genome becomes more dominant, gene-rich, and prone to gene expression is largely heritable. Moreover, their findings suggest that the same sub-genomes typically remain dominant even after additional genome duplication events — in part due to differences in transposon silencing of genes in the sub-genomes within each polyploid plant.

Finally, researchers from China and the US present a model for interpreting gene co-expression patterns found in the vertebrate brain using gene expression information generated for different adult mouse brain cell types and brain regions as part of the Allen Brain Atlas effort. "Importantly, our model enables single-cell transcriptome analysis to be extended to the spatial distribution of cell types," the study's authors say, noting that the approach is expected to remain relevant to understanding gene co-expression patterns in the brain even as cell type descriptions and taxonomy advance.