Accessing the Genetic Dark Matter: Using BioNano Technology to Identify Large-Scale Repeat Structures in Maize

Complex genome assembly has improved dramatically with advent of long-range sequencing/assembly techniques commercially available. An example of those are BioNano Genomics generating Optical maps using next-generation mapping (NGM) Irys System, and other long range sequencing approaches such as PacBio.

The recently released maize B73 reference genome was assembled using a hybrid scaffold approach that combined PacBio sequence and BioNano maps. While this is an excellent assembly with long contig N50, there are areas where BioNano map is continuous but the matching sequence data could not be identified. We analyzed the BioNano maps corresponding to the largest of these sequence gaps (>100 kbp) and found that many are associated with either large duplications (CNV) with low copy number or short tandem repeats with high copy number. These include the locations of the 45S and 5S rDNA arrays and several centromeric repeat arrays. In addition, we show that the P1 locus, which has 11 nearly-perfect copies in the B73 reference genome, has nine copies in another maize inbred W22, demonstrating the utility of using NGM to assess structural variation.

Finally, the data reveals multiple previously unknown large-scale repeat structures (CNV), many of which likely include genes. These results point to limitation of current sequencing methodologies and highlight the value of using NGM generated ultra-long 150 kbp -2 Mbp molecules for the accurate assembly of the maize genome, a process that is both cost effective and fast.