Improving the Tribolium draft Assembly with Physical Maps Based on Imaging Ultra-Long Single DNA Molecules

Genome assemblies come in all qualities. Most are basically drafts of the genome, but even the most heavily curated assemblies contain misassemblies and truncations or gaps in repetitive regions. The 7x draft assembly of the Tribolium genome is based on paired-end Sanger sequencing of 4-6 Kb insert plasmid libraries, scaffolded with paired-end reads from 40Kb fosmid and ~130Mb BAC clones.  The total assembled length of ~156 Mb represents 75% of the estimated genome (200Mb) and presumably lacks a significant portion of repetitive DNA.  Superscaffolds or chromosome builds (ChLG 2-10 and X) were constructed by mapping molecular markers from the genetic recombination map to the assembly scaffolds, anchoring greater than 90% of the assembled sequence¹. 

To improve this draft assembly, we constructed physical maps of the T. castaneum genome. Using the irys system designed by BioNano Genomics (http://www.bionanogenomics.com/).  Ultra long molecules (Mb) were nicked on one strand with Nt.BspQI and labeled with fluorescent nucleotides. Individual molecules were imaged on a massively parallel scale in nanochannels etched on silicon chips. Consensus maps de novo assembled from the imaged molecules were compared with in silico maps generated from the assembly sequence.  Here we report our progress on using these comparisons to validate the assembly in regions were they agree and reanalyze the assembly in regions were they do not. Additional scaffolds have been anchored to the chromosomes, order and orientation of scaffolds have been corrected, and scaffolds have been extended by spanning repetitive regions.  

Nature 2008 452:949-55.