MaizeCODE (zea maize), An Initial Analysis of Functional Elements in the Maize Genome

The MaizeCODE project is fundamentally a discovery-based genome annotation effort utilizing a variety of cost-effective high-throughput sequencing assays to collectively interrogate common strains/genomes and derivative sample types. These data will be used to construct a plant/maize genomics database with associated metadata, workflows and analysis pipelines for the project and community. These will be implemented on CyVerse, an NSF funded platform and therefore accessible to NSF researches to use in an unrestricted fashion, to process their data through and/or to reproduce our results and update them as desired. These data will serve as a basis for further annotation efforts in “wild type” backgrounds and ideally as a centralized genomics living repository for additional maize high-throughput assays. Further curation of this repository will allow community-wide standardization for plant genomics data, ease their integration into analysis pipelines (for example, in order to update older data to newer versions of assemblies) and/or expand upon current analyses to incorporate novel features and data types.