Genome Assembly and Analysis of the Maize (Zea mays L.) Iodent Inbred PH207

Crosses between Stiff Stalk and Iodent heterotic families predominate among contemporary U.S. maize hybrids. The genome of the Stiff Stalk inbred ‘B73’ represents the current maize reference. To gain further context of heterosis and diversity, we assemble the genome of the Iodent inbred ‘PH207’. Obtaining a reliable de novo assembly of large and complex genomes from next-generation sequencing data poses a significant computational challenge. We utilized multiple sequencing platforms and a creative assembly strategy to obtain the PH207 genome. Our first step was to use the novel algorithm GenoMagic^TM DeNovo Assembler to assemble the Illumina short read data. These data were obtained from multiple insert size libraries, both paired-end and mate-pair, at a cumulative depth of ~220x. Overall, we obtained 156K scaffolds (>500bp) with an N50 of 50Kb. Supporting the accuracy and comprehensiveness of this assembly, 93% of annotated mRNA from B73 and 97% of the PH207 transcriptome data (RNA-Seq reads) aligned to the PH207 scaffolds. In addition, kmer analysis suggests that PH207 genome size is ~2.5GB, or 5 - 10% larger than the B73 reference genome. We present the metrics and detailed methodology employed in obtaining the final assembly, including the incorporation of and improvement from long read data.  We also compare and contrast structural variations between PH207 and B73, including single nucleotide polymorphism, and genic copy number and presence absence variation.