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This Week in Genome Research: Mar 28, 2018

An international team led by German investigators explores maternal microbe transmission at birth and its role in seeding the infant gut microbiome, focusing on relatively rare microbial variants found in fecal samples to tease out microbial transmission. With this rare variant approach, the researchers tracked gut metagenomes over time in hundreds of individuals from 159 families (including infants born vaginally or by Cesarean section) relative to microbiomes in unrelated individuals profiled previously. Based on their findings, the authors argue that "the infant gut is seeded by selected maternal bacteria, which expand to form a stable community, with a rare but stable continuing strain influx over time.

Researchers from the UK, Kenya, France, and the US present findings from a malaria parasite genome study focused on the avian malaria parasites Plasmodium relictum and P. gallinaceum. In newly generated draft genome assemblies, the team annotated nearly 5,300 P. gallinaceum genes and more than 5,100 genes in the P. relictum genome, including 50 genes in conserved sequence sites that were shared between the avian malaria parasites but were missing in previously sequenced Plasmodium parasites. Along with analyses of the parasite's gene content, the authors teased out Plasmodium phylogenetic relationships, searched for signs of selection in parasite genomes, and uncovered transposable elements in the avian malaria parasites.

Finally, a Whitehead Institute- and MIT-led team takes a look at sex chromosome evolution, using microRNA target site phylogeny to reconstruct gene dosage sensitivity on the ancestral autosomal chromosomes that ultimately morphed into the X and Y sex chromosomes. The miRNA targets provided insights into the genes retained on the shrunken Y chromosome or subjected to X chromosome inactivation (XCI) on the female sex chromosome, the researchers report, writing, "Pre-existing heterogeneities in dosage sensitivity, manifesting as differences in the extent of miRNA-mediated repression, predicted either the retention of a Y homolog or the acquisition of XCI following Y gene decay."