A large-scale genome-wide association study appearing in this week's Nature Neuroscience identifies genetic variants associated with the re-experiencing of trauma that characterizes post-traumatic stress disorder. The study's investigators examined 146,660 European Americans and 19,983 African Americans in the US Million Veteran Program and found eight genetic regions associated with PTSD in the European-American cohort, as well as a potential link with a gene that encodes a stress-hormone receptor. No significant associations were observed in the African-American cohort of the sample, a finding that may be due to the smaller size of this population. GenomeWeb has more on this, here.
A new hybrid metagenomic assembler that combines short- and long-read technologies is described in this week's Nature Biotechnology. Called OPERA-MS, the assembler integrates assembly-based metagenome clustering with repeat-aware, exact scaffolding to accurately assemble complex communities, according to its developers. Experimentation shows OPERA-MS assembles metagenomes with greater base pair accuracy than long-read, higher contiguity than short-read, and fewer assembly errors than non-metagenomic hybrid assemblers. The researchers used the technology to assemble 28 gut metagenomes of antibiotic-treated patients and show that the inclusion of long nanopore reads produces more contiguous assemblies, including more than 80 closed plasmid or phage sequences and a new 263 kbp jumbo phage.
The genome of the Komodo dragon — the largest living monitor lizard — is presented in this week's Nature Ecology & Evolution. An international research team sequenced the Komodo dragon's genome and generated a high-resolution de novo chromosome-assigned genome assembly using a hybrid approach of long-range sequencing and single-molecule optical mapping. By comparing this genome to those of related species, the scientists find evidence of positive selection in pathways related to energy metabolism, cardiovascular homeostasis, and hemostasis. They discover species-specific expansions of a chemoreceptor gene family related to pheromone and kairomone sensing in the Komodo dragon and other lizard lineages. The findings reveal the underpinnings of the Komodo dragon's unique sensory and cardiovascular systems, and suggest that selective pressure changed hemostasis genes to help the lizard evade the anticoagulant effects of its own saliva. The Scan also covers the Komodo dragon genome, here.