Whole Genome Assembly Validation with BioNano Genome Map

Luo, Ming-Cheng

Date: Tuesday, June 7, 2016
Time: 11:30 AM

Room: Waterfront 1

Ming-Cheng Luo , Department of Plant Sciences, University of California, Davis, CA

Tingting Zhu , Department of Plant Sciences, University of California, Davis, CA

Karin R. Deal , Department of Plant Sciences, University of California, Davis, CA

Juan C. Rodriguez , Department of Plant Sciences, University of California, Davis, CA

Aleksey Zimin , Johns Hopkins University, School of Medicine, Baltimore, MD

Daniela Puiu , Johns Hopkins University, School of Medicine, Baltimore, MD

Steven L. Salzberg , Johns Hopkins University, School of Medicine, Baltimore, MD

Richard Hall , Pacific Biosciences, Menlo Park, CA

Jan Dvorak , Department of Plant Sciences, University of California, Davis, CA

Aegilops tauschii is the donor of the D genome of hexaploid wheat (Triticum aestivum). A high-quality sequence of its genome is critically needed as a reference for wheat genomics. The large size and great complexity of the Ae. tauschii genome represent a big challenge for genome sequencing. We took advantage of the available bacterial artificial chromosome (BAC) clone-based physical map for the Ae. tauschii genome and sequenced the minimum tiling path in pools consisting of eight overlapping BAC clones with the Illumina MiSeq platform. We assembled scaffolds and merged them with whole-genome shotgun (WGS) scaffolds assembled by NRGene and with Pacific Biosciences (PacBio) long-reads. We also generated BioNano genome maps for Ae. tauschii and the wheat D genome. We deployed the BioNano maps in scaffold validation and the construction of Ae. tauschii superscaffolds and pseudomolecules. In addition to this integrated approach, we also generated WGS assemblies of the same Ae. tauschii accession with PacBio WGS reads corrected with Illumina reads and PacBio-only read assemblies. Whole genome BioNano maps are used to assess the fate of assemblies generated by NRGene, PacBio-only and PacBio-Illumina hybrid assembly pipelines. This work is part of the National Science Foundation Project IOS-1238231 to generate a reference sequence for the genome of Ae. tauschii (http://aegilops.wheat.ucdavis.edu/ATGSP/).