Systemic Comparison Of The Zea mays RefGen V2, V3 and Maker-P De Novo Gene Models

We have used MAKER-P’s quality control and annotation management functionalities in order to compare and contrast the Zea mays RefGen V2 and V3 gene models. We have also re-annotated Zea mays using MAKER-P in order to provide a third point of reference for our comparisons.   We will present an overview of these three datasets in terms of their physical characteristics, e.g. gene numbers, lengths, exon numbers, UTRs and alterative splicing, and how these traits vary among shared genes and those unique to each dataset. We will also present the results of a systematic investigation of the three annotation datasets in the context of their supporting evidence. For these analyses we have broken the gene-models into three categories based upon synteny, orthology, and homology to other plants, and used MAKER’s AED metric to quantify their goodness of fit to their supporting evidence. Support is highly consistent with degree of conservation, with syntenic orthologs the best supported; there are however some interesting exceptions to this trend.  Highlights from an analysis of RNA-seq data and their relationship to the gene-models, and a characterization of nearly 500 new and well-supported maize genes present in the V3 RefGen build will also be presented.