In this week's Nature, a multi-institute group of investigators uses next-generation sequencing to investigate the molecular drivers of a large-scale cholera epidemic in Yemen. The investigators sequenced the genomes of Vibrio cholerae isolates from the epidemic, as well as from neighboring regions, and analyzed their data against a global collection of more than one thousand V. cholerae isolates. They trace the epidemic to find that the Yemen sublineage originated in South Asia and caused outbreaks in East Africa before appearing in Yemen, and show that it is susceptible to several existing antibiotics. GenomeWeb has more on this, here.
Meanwhile, in Nature Genetics, researchers from 23andMe and elsewhere report an atlas of the genetic factors that contribute to osteoporosis. The investigators conducted an estimated bone mineral (eBMD) density genome-wide association study of 426,824 individuals in the UK Biobank, identifying 518 genome-wide significant loci — including 301 novel ones. By combining data from the UK Biobank and 23andMe cohorts, they were further able to find 13 bone fracture loci that are all associated with eBMD in roughly 1.2 million individuals. Additional analyses uncovered a gene that, when disrupted, increased cortical porosity and marked bone composition and strength reduction in mice and decreased mineralization in human osteoblasts. "This genetic atlas provides evidence linking associated SNPs to causal genes, offers new insight into osteoporosis pathophysiology, and highlights opportunities for drug development," the authors write.
And in Nature Plants, an international team led by scientists from the University of British Columbia presents a pan-genome analysis of the cultivated sunflower, providing insights into the flower's genetic diversity and links to wild relatives. The researchers sequenced and analyzed 287 cultivated sunflower lines, as well as 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. They find that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27 percent vary across genotypes. About 10 percent of the cultivated sunflower pan-genome was found to be derived through introgression from wild sunflower species, with genes associated with biotic resistance being over-represented among introgressed regions — an observation consistent with breeding records. These results, the authors say, demonstrate the utility of a pan-genome approach in comparative genomics studies, "facilitating a more complete view of the genetic variation represented in a gene pool, especially novel genomic components associated with traits of interest."