Comparative Structural Genomics of Zea mays Inbred Lines B73 and Mo17

Complex genomes primarily consist of non-genic, highly repetitive and copy number variable genomic dark matter including heterochromatin, mobile genetic elements, and other non-coding components surrounding islands of more static protein coding sequences. Other types of variable structural elements also populate the genome, ranging in size from a handful of base-pairs to many millions and affecting both genic and non-genic regions. Structure variable (SV) sequences can be either unbalanced (Copy Number Variable) or balanced (equal net copy at distinct loci) and are comprised of inversions, duplications, translocations, presence absence variants (PAV) and complex combinations thereof. The extreme levels of variation observed in Zea mays, the pervasive mobile genetic element content, and the inherent instability of its genome all make it an ideal model system for studying genomic structural variation and its phenotypic consequences. Previously, technical challenges have limited our ability to accurately resolve and characterize SV regions of the genome. Repetitive elements longer than the length of a sequencing read typically cannot be assembled and result in fragmentation of the genome assembly. Consequently, SV longer than the length of an assembled contig typically cannot be reliably detected. In order to to detect and quantify large SV, we generated highly contiguous optical maps for maize inbred lines B73 and Mo17 using BioNano Genome mapping. We concurrently analyzed fixed-length substrings of size k (k-mers) derived from near-raw sequencing data for both lines in order to generate a base-pair resolution snapshot of highly repetitive and variable elements.