Journal: PLoS Biology
Article Title: De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture
Figure Lengend Snippet: Assembly and validation of Drosophila miranda genome. A . Overview of assembly pipeline. The steps include assembly of male PacBio reads followed by scaffolding using Hi-C, and extensive QC using BioNano reads and BAC clone sequencing followed by gene and repeat annotation. B. Hi-C linkage density map. Chromatin interaction maps allow recovery of entire chromosome arms. Note that the Y-linked contigs were scaffolded separately from X-linked and autosomal contigs. Unlinked regions with many contacts indicate repetitive regions. C. Comparison of current (Dmir2.0) versus old (Dmir1.0) D . miranda assembly. Note that the Y/neo-Y was not assembled in Dmir1.0, and the dot plot indicates homology between our neo-Y assembly and the neo-X. Other repeat-rich regions, such as the large pericentromeric block on AD, are also missing from D.mir1.0. D. BAC clone mapping for assembly verification. BAC clones are color coded according to how many genomic regions they map to in our assembly; green lines indicate stitch points of scaffolds based on Hi-C contacts, and the black line gives the local repeat content along the genome. Three hundred sixty-one sequenced BAC clones (97%) map contiguously and uniquely to our genome assembly. BAC, bacterial artificial chromosome; F, female; M, male; QC, quality control; Repeat %, local repeat content.
Article Snippet: HybridScaffold was then used to produce hybrid maps from the BioNano contigs and the genomic scaffolds from our scaffolded PacBio assembly, and IrysView was used to visualize alignments of the BioNano contigs and genomic scaffolds to the hybrid ones. shows coverage of hybrid scaffolds by BioNano contigs and NGS contigs (genomic scaffolds).
Techniques: Scaffolding, Hi-C, BAC Assay, Sequencing, Blocking Assay, Clone Assay