Scientists from the University of Nottingham report a new computational tool for targeted nanopore sequencing of gigabase-sized genomes. Called Readfish, the approach uses graphical processing unit base-calling and does not require the complex signal mapping algorithms and specialized sample preparation of other approaches, the scientists write in this week's Nature Biotechnology. They use Readfish to show enrichment of specific chromosomes from the human genome and of low-abundance organisms in mixed populations without a priori knowledge of sample composition, as well as to enrich targeted panels comprising thousands of exons from 10,000 human genes and 717 genes implicated in cancer.
A pair of studies in last week's Nature explore the genomic diversity of barley and wheat, two of the world's most agriculturally important and genetically complex crop plants. In the first study, a group led by Leibniz Institute of Plant Genetics and Crop Plant Research scientists construct chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley — including landraces, cultivars, and a wild barley — that represent the plant's global diversity. Through their analyses, the investigators uncover pervasive variation in genes and non-coding regions among the assemblies, including abundant large inversion polymorphisms in current elite barley germplasms, one of which is likely the product of mutation breeding. In the second study, a University of Saskatchewan team and collaborators generated 10 chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat. Comparative analyses uncovered "extensive structural rearrangements, introgressions from wild relatives, and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses," the researchers state. The assemblies are expected to aid in future wheat gene discovery and breeding efforts.
Using a range of sequencing technologies, a team led by Northwestern University investigators has generated a comprehensive map of transcriptome, cis-regulatory element, heterochromatin, methylome, and 3D genome organization in the zebrafish. As reported in Nature last week, the researchers performed RNA-sequencing, ATAC-seq, chromatin immunoprecipitation-sequencing, whole-genome bisulfite sequencing, and Hi-C experiments in up to 11 adult and two embryonic tissues from the zebrafish to build their map. They also compared zebrafish, human, and mouse regulatory elements to identify evolutionarily conserved and species-specific regulatory sequences and networks. "The breadth and depth of the data establish a genomic foundation for conducting further human disease modelling and biological studies in zebrafish," they write.