Perennial Ryegrass: Unravelling the Structure and Content of a Many-Faced Genome

Assembly and annotation of the perennial ryegrass genome suffers from its large genome size, complex organization and a highly repetitive and polymorphic content. The current draft assembly of the perennial ryegrass genome represents 54% of the estimated nuclear genome size. A comparison of gene space completeness measures showed that the gene space partition has been well assembled, but that gene prediction is yet incomplete (Veeckman et al., 2016). In order to study the ryegrass genome content, we have complemented the current annotation set with transcript evidence and aligned proteomes of closely related species and have used the Evidence Modeler (Haas et al., 2008) to create a consensus gene set. This novel set contains 1785 newly predicted gene models and is thereby better suited for comparative genomics analyses. Additionally, we present novel strategies to identify genetic diversity for 500 candidate genes by population scale resequencing and show how highly polymorphic regions influence read mapping and variant calling. The novel gene models proved to be 10% more accurate, resulting in a more robust interpretation of functional consequences of SNPs and indels. Moreover, these models can be used as evidence for gene prediction on future genome assemblies.