Comprehensive De Novo genome Assemblies and Resequencing of Diverse Individuals Provides Insights into Structural Diversity and the Relationship with Transcriptional Diversity in Maize

Maize is a species with extensive sequence diversity. The B73 reference has been foundational in advancing maize research, but does not capture the full maize pan-genome. To further understand the maize pan genome, we have generated a comprehensive de novo assembly of the inbred line PH207 to complement the existing B73 reference genome assembly. B73 is an important founder line of the Stiff Stalk pool, while PH207 is an important founder of the Iodent Non-Stiff Stalk pool, both of which have been critical components of U.S. hybrids. The PH207 assembly contains 2,869,470 contigs with an NG50 of 4,999bp that are contained within 132,022 scaffolds with an NG50 of ~504Kb, and has approximately 40K annotated gene models. We have also deeply resequenced 35 additional maize inbred lines and surveyed the transcriptomes of these individuals across tissues and time to expand our inferences from the comparison of B73 and PH207. Understanding quantitative and qualitative variation in the transcriptome as it relates to genome diversity can provide valuable insights into the biological implications of structural variation. For example, genes showing presence/absence variation between genotypes with varying stress tolerance were identified and transcriptional analysis showed that a subset of these genes are expressed in relevant root tissues. A comparative analysis between the genomes of diverse maize inbred lines and biological implications as revealed by transcriptome analysis will be discussed.