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This Week in PNAS: Mar 5, 2019

Using 98 metagenome-assembled archaea genomes from five Yellowstone National Park hot spring samples and more than 1,400 publicly available archaea sequences, researchers from Stanford University, the Chan Zuckerberg Biohub, and elsewhere explore methanogen ancestry, including a lineage falling outside of a euryarchaeal phylum containing the most fully characterized methanogenic archaea. With these data, the authors identified a "complete and divergent hydrogenotrophic methanogenesis pathway in a thermophilic order of the Verstraetearchaeota. Moreover, they say, their results "support the ancient origin of hydrogenotrophic methanogenesis, suggest that methylotrophic methanogenesis might be a later adaptation of specific orders, and provide insight into how the transition from hydrogenotrophic to methyloptrophic methanogenesis might have occurred."

A University College London-led team takes a look at within-host human cytomegalovirus genetic diversity. Using deep sequencing, the researchers considered dozens of samples collected over time from eight immune-compromised children with HCMV infections. They also profiled single timepoint samples for 35 immunosuppressed individuals and 15 individuals with congenital HCMV infections, tallying within- and between-host HCMV haplotypes and documenting recombination in the strains through comparisons to one another and to nine other DNA- or RNA-based viruses. The results suggest that the "high HCMV diversity present in some samples is caused by co-infection with multiple distinct strains," the authors write, "and provide reassurance that within the host diversity for single-strain HCMV infections is not greater than for other herpesviruses. 

Members of an international team led by investigators in Portugal dig into the genetics of coloring in the European common wall lizard, Podarcis muralis, focusing on the yellow-, orange-, and red-producing pterin and carotenoid pigments. After characterizing the pigments and skin cell organization patterns in five wall lizard color morphs with the help of liquid chromatography-mass spec and transmission electron microscopy, respectively, the researchers assembled and annotated a reference genome assembly for P. muralis. From there, they re-sequenced 154 wall lizards from two sites in the Pyrenees, identifying distinct regulatory regions that distinguished color morphs with differing orange and yellow pigment production. "[T]he color polymorphism in the common wall lizard is associated with changes in two small regions of the genome containing genes with crucial roles in pterin and carotenoid metabolism," the authors write.