An analysis of the donkey genome is reported in this week's Nature Communications, providing insights into the domestication of this member of the horse family. A team led by scientists from the Shandong Academy of Agricultural Sciences de novo assembled a chromosome-level reference genome of one male Dezhou donkey, which they studied against the genomes of 126 domestic donkeys and seven wild asses. They find that donkeys were likely domesticated in Africa and that the modern-day animals were derived from the domestication of one common ancestral group at least 6,000 years ago. The scientists also uncover a limited level of variability in the donkey Y chromosome, similar to horses and probably due to breeding practices. The study also identifies a gene that is responsible for dun coats in both donkeys and horses and shows that the same deletion in this gene is responsible for non-dun coats in both species.
A reference-free workflow for the assembly of fully phased diploid human genomes based on single-strand sequencing and long reads is described in Nature Biotechnology this week. The strategy, developed by researchers from the University of Washington School of Medicine and collaborators, combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing with continuous long-read or high-fidelity sequencing data. The team uses their method to produce a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent in the absence of parental data. The work, the study's authors write, "should open the door for producing high-quality phased human genomes needed for personalized [structural variant] discovery in healthy and diseased individuals. Fully phased, reference-free genomes are also the first step in constructing comprehensive human pangenome references that aim to reflect the full range of human genome variation." GenomeWeb has more on this, here.
An updated version of a high-resolution spatial transcriptomics technology is described by Broad Institute researchers in this week's Nature Biotechnology. The scientists previously developed a method, called Slide-seq, that enables transcriptome-wide detection of RNAs with a spatial resolution of 10 micrometers. The investigators now report Slide-seqV2, which combines improvements in library generation, bead synthesis, and array indexing to achieve nearly an order of magnitude higher sensitivity than the original Slide-seq protocol. They show how Slide-seqV2's higher capture efficiency "expands the scope of possible analyses, including the discovery of genes with distinct patterns of subcellular localization and the tracing of developmental programs involved in fate specification through space." They also developed a publicly available Slide-seqV2 pipeline for image processing and merging of short-read sequencing and imaging data.