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This Week in Genome Research: Feb 1, 2017

A University of California, Santa Cruz-led team presents an improved genome assembly for the American alligator, Alligator mississippiensis, which was used to explore features of temperature-dependent sex determination in crocodilians. With the help of Chicago in vitro proximity ligation scaffolding, the researchers improved the contiguity and quality of an alligator genome assembly first described in 2014, which subsequently served to scaffold saltwater crocodile and gharial genomes. By folding in transcriptome sequence data from American alligator embryos incubated at temperatures linked to male or female development, they began teasing out parts of the genome suspected of responding to estrogen signaling.

Gut, skin, and mouth microbiome features seem to blend together in infants born prematurely, according to a Genome Research study published by researchers from the University of California, Berkeley, and elsewhere. The team used metagenomic sequencing to assess microbes in dozens of fecal, skin, or tongue swab samples from two premature infants at a Pittsburgh hospital in the month after birth, identifying shared bacterial populations at multiple sites in each infant. "The ability of identical strains to colonize multiple body sites underscores the habit flexibility of initial colonists," the authors write, "whereas differences in microbial replication rates between body sites suggest differences in host control and/or resource availability." 

Finally, a team from Johns Hopkins University and elsewhere describe a computational approach for curbing sequence error rates when combining Pacific Biosciences long reads with Illumina short reads in hybrid genome assemblies. The researchers applied the algorithm — which produces so-called mega-reads en route to such hybrid assemblies — to the self-pollinating bread wheat progenitor grass plant Aegilops tauschii. They report that the algorithm led to an accurate assembly, based on comparisons with available optical mapping data and with assemblies based on bacterial artificial chromosome sequences.