Reference gene prediction in the hexaploid bread wheat genome

With its large genome size of ca.17 Gb and high repeat content, the hexaploid bread wheat genome poses a great challenge not only for genome assembly but also for gene prediction and annotation. While the gene space of wheat has been surveyed and analysed previously in wheat draft sequence assemblies (Brenchley et al 2012, IWGSC 2014), a comprehensive annotation of genic elements in the upcoming wheat reference genome assembly will facilitate new studies and provide the basis for further in-depth curation. Here we outline the gene prediction process in bread wheat using our in-house Triticeae gene prediction pipeline and discuss typical challenges, problems and solutions as well as the supporting evidence, such as transcriptome data, used for gene calling. To achieve a high-quality reference annotation that will provide a stable foundation for all downstream analyses, gene predictions will be compared and combined with results from other annotation pipelines within the IWGSC. We will outline the process of integrating these resources into a single reference annotation as well as touch issues and protocols for the functional annotation of the resulting gene calls.