Automated update, revision and quality control of the Zea mays genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes

The large size and relative complexity of many plant genomes makes creation, quality control, and dissemination of high quality gene-structure annotations challenging. In response we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here we report the use of MAKER-P to update and revise the Zea mays B73 RefGen_v3 annotation build (5b+) in less than three hours using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build; added additional untranslated regions (UTR) to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of a large and diverse evidence datasets), identified 102,370 pseudogene fragments, and created an additional 2,522 non-coding gene annotations. We also describe a method for de novo training of MAKER-P for annotation of novel grass genomes. Collectively these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes