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This Week in Genome Research: Jun 21, 2017

An international team led by investigators at the Wellcome Trust Sanger Institute in the UK takes a look at population genomics and genome dynamics in Chlamydia trachomatis, a bacterial species notorious for its role in sexually transmitted infections and infections that can lead to blindness. Using genome sequence data for 563 C. trachomatis isolates, including more than 450 not described in previous studies, the researchers delineated two key evolutionary phases in the pathogen's history and performed analyses that refined the timeline for its diversification. "Temporal analysis indicates that lineages have recently expanded in the space of thousand of years, rather than the millions of years previously thought," they write, "a finding that dramatically changes our understanding of this pathogen's history."

A population genomics study of the opportunistic fungal pathogen Cryptococcus neoformans explores selective pressures in the environment that appear to have bumped up fungal virulence in humans as well. For that study, researchers from the Broad Institute and elsewhere did genome sequencing on nearly 400 C. neoformans isolates from African-specific and global lineages, using phylogenetics, comparative genomics, phenotypic analyses, and a genome-wide association approach to get a closer look at C. neoformans relationships, virulence, responses to selection, and more. The study's authors say their data "highlight the complex evolutionary interplay between adaptation to natural environments and opportunistic infections, and that selection on specific pathways may predispose isolates to human virulence."

A team from the US, UK, Germany, and Canada describe a non-coding mutation identified in individuals with an autosomal recessive microcephaly-micromelia syndrome (MMS) that has so far been found in just one First Nations population in northern Saskatchewan. With the help of RNA sequencing — combined with genome, exome, or targeted sequencing — the researchers narrowed in on a non-coding variant that altered splicing of DONSON, a gene suspected of contributing to embryonic development based on their follow-up mouse experiments and gene expression analyses.