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Genetic variation of the human Y chromosome plays a key part in studies of human evolution, population history, genealogy, forensics and male medical genetics. This Review outlines how next-generation sequencing has contributed to recent progress in these fields.
Whereas once it was only possible to generate reference genome sequences one at a time, it is now feasible to design genomic experiments to maximize functional comparisons and contrasts among many genomes. Investigating the diversity of a number of related parasite genomes and their transcriptomes in multiple contexts increasingly shows us ways to intervene in the ecological and evolutionary strategies of pathogens.
Binning based on differential read coverage, rather than sequence composition, allows separation of metagenomic sequence reads into species-level clusters that can be assembled into single chromosomes.
Shigella sonnei is an important cause of bacterial dysentery in the developed world and has also recently emerged in transitional countries. Phylogenetic analysis based on whole-genome sequencing of a global sample has detailed the recent evolutionary history of this pathogen and shed light on the genetic changes associated with this epidemiological shift.