Improving Whole Genome Shotgun Assemblies with Physical Maps Based on Imaging Ultra-Long Single DNA

<p>We use the red flour beetle, a pest of stored grain, as a genetic model organism for developmental studies. As members of the i5k, we join scientists around the globe who are gearing up to sequencing 5000 insect genomes to improve human welfare and understand key ecosystem services that insects provide. By investigating insect genomes, we can take a fresh look at how insects transmit some of the most devastating diseases of humans, livestock, and plants on one hand, yet also serve as medical models for cancer, obesity, alcoholism, and neurological disease on the other.<br>Genome sequencing is becoming very affordable, but genome assembly is still challenging. Most are basically drafts of the genome, but even heavily curated reference assemblies contain misassemblies and truncations or gaps in repetitive regions. We are using a form of optical mapping to validate and extend the contigs and scaffolds that constitute a genome assembly. The 7x draft assembly of the red flour beetle, Tribolium castaneum 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 linkage group 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 sequence. 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.Bspq1 and labeled with fluorescent nucleotides. Individual molecules were imaged on a massively parallel scale in nanochannels printed on silicon chips. Consensus maps of 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.</p> <p>