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This Week in Nature: Jun 15, 2017

In Nature this week, a Cold Spring Harbor Laboratory-led team publishes an improved maize reference genome, which was assembled and annotated using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, the new assembly features a 52-fold increase in contig length, as well as significant improvements in the assembly of intergenic spaces and centromeres. The work demonstrates that high-quality assemblies of other repeat-rich and large-genome plants is feasible and can "extend our understanding of the genetic diversity that forms the basis of the phenotypic diversity in … economically important plants," the authors write.

And in Nature Biotechnology, a multi-institute group of researchers reports on 1,003 reference genomes sequenced as part of the Genome Encyclopedia of Bacteria and Archaea initiative. The genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25 percent, while comparative analyses with previously available finished and draft genomes reveal a 10.5 percent increase in novel protein families as a function of phylogenetic diversity. The new resource, the authors note, marks the largest single release of reference genomes to date, although they note that the "bacterial and archaeal isolate sequence space is still far from saturated." GenomeWeb has more on this study, here.

The Scan

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.

Study Examines Relationship Between Cellular Metabolism, DNA Damage Repair

A new study in Molecular Systems Biology finds that an antioxidant enzyme shifts from mitochondria to the nucleus as part of the DNA damage response.

Stem Cell Systems Target Metastatic Melanoma in Mouse Model

Researchers in Science Translational Medicine describe a pair of stem cell systems aimed at boosting immune responses against metastatic melanoma in the brain.

Open Pediatric Brain Tumor Atlas Team Introduces Genomic Data Collection, Analytical Tools

A study in Cell Genomics outlines open-source methods being used to analyze and translate whole-genome, exome, and RNA sequence data from the Pediatric Brain Tumor Atlas.