Integrated Approach Towards Sequencing a Large and Complex Genome - iPlant Portal Facilitates Management of Big Data

Aegilops tauschii is one of the three diploid progenitors of common (hexaploid) wheat. Its genome is expected to be between 4 and 5 Gb and was estimated to contain nearly 90% repeated sequences. The aim of the National Science Foundation funded project “Sequencing the Aegilops tauschii genome” (http://aegilops.wheat.ucdavis.edu/ATGSP/) is to generate a high-quality reference sequence for the genome of Ae. tauschii which ultimately serves as a reference for the wheat genome due to its close relationship with wheat. A bacterial artificial chromosome (BAC)-based physical map of accession AL8/78 was constructed. A minimum tiling path of 42,025 BAC clones was constructed and eight-clone pools across 3,578 BAC contigs and 2,000 singleton clones were sequenced with the Illumina MiSeq platform and scaffolds were assembled. We also generated whole genome shotgun sequences by Illumina HiSeq platform and the Pacific Biosciences platform. Pseudomolecules were constructed by integrating the assembled BAC pool sequence scaffolds, linkage maps, whole genome shotgun Illumina assembly, and PacBio sequences. The NSF-funded project involves several institutions nationally and internationally. The iPlant portal enables us to effectively manage the large volumes of diverse data generated within the project. The pseudomolecules are now available, we plan to use any of the tools provided at iPlant for further analysis.