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This Week in PLOS: Jun 11, 2018

In PLOS Genetics, Australian researchers explore potential contributions that trans-chromosomal interactions may make to immune system development in mammalian cells. Using HiC chromosome conformation capture, the team tallied up chromosome interactions in mouse and human immune cells — namely, CD4+ T cells, CD8+ T cells, and B cells. Though they did detect trans-chromosomal interactions using this approach, most were removed after quality control steps and/or follow-up expression profiling. "[O]ur findings question the existence of stable, gene-regulatory trans-chromosomal interactions underlying immune cell identity," the investigators conclude from these and other experiments.

Researchers from the UK, Thailand, and elsewhere present findings from a comparative genomic analysis of the scrub typhus-causing pathogen Orientia tsutsugamushi, a mite-transmitted obligate intracellular bacterial species, in a paper appearing in PLOS Neglected Tropical Diseases. Using a combination of single-molecule, long read sequencing and short read polishing, the team generated high-quality genome assemblies for half a dozen O. tsutsugamushi strains and draft assemblies for two more, comparing the strains to one another and to strains sequenced in the past. The analyses highlighted 657 genes shared across the core O. tsutsugamushi genome, while providing a look at genome expansions and phylogenetic relationships within the Orientia genus.

A team from Brazil and the US takes a look at genetic diversity in a wild plant believed to be ancestral to a tropical crop plant called annatto (Bixa orellana). As they report in PLOS One, the researchers profiled 16 microsatellite loci in 170 plant samples from B. orellana (urucurana variety) populations from 10 sites in the Amazonia region. From the allelic patterns identified in the wild annatto plants, coupled with ecological niche modeling, they uncovered between-population differentiation in B. orellana var. urucurana, often coinciding with geographic distance and isolation. "Our map of the potential distribution of the species allowed the identification of other potential areas of occurrence in Amazonia and in northern South America," the authors write, adding that the work "demonstrates how ecological and anthropic factors may have an impact on the genetics of a native Amazonian species."