Synthetic Long Read Sequencing with Optical Mapping Produces High Quality de novo Genomes

We have been studying methods for assembling high quality genomes from non-human mammals. Current short-read methods have come to dominate genome sequencing because they are cost-effective, rapid and accurate. However, short reads are most applicable when data can be aligned to a known reference, generally assembled with more traditional methods. Because such methods are time-consuming, costly and inefficient, we have explored approaches to de novo genome assembly using several novel approaches for sequencing and assembly. In particular, we evaluated 10X Genomics Chromium Linked-Read sequencing, with ~1M molecular indices, combined with BioNanoGenomics (BNG) optical mapping and hybrid assembly. We show that the Chromium data, assembled with Supernova v1.1 alignment software, provided long sequence blocks and, when used for de novo assembly, produced scaffolds with an N50 of 22.23 Mb with the longest individual scaffold at 84.06 Mb. When combined with BNG optical maps the scaffold N50 increased to 29.65 Mb and the longest individual scaffold increased to 84.78 Mb. Because both BNG and 10X technologies interrogate single DNA molecules they can also be used to construct haplotypes and to detect larger scale structural variants between parental chromatids. Combining the two orthogonal methods of Chromium Linked-reads with BNG optical maps is likely to make the assembly of high quality genomes routine and significantly improve our understanding of comparative genome biology.