Jan Dvorak
,
Department of Plant Sciences, University of California, Davis, Davis, CA
Olin D. Anderson
,
Western Regional Research Center, Albany, CA
Jeffrey L. Bennetzen
,
Dept. of Genetics, University of Georgia, Athens, GA
Xiongtao Dai
,
Dept. of Statistics, Davis, CA
Matthew W. Dawson
,
University of California, Davis, CA
Karin R. Deal
,
Department of Plant Sciences, University of California, Davis, Davis, CA
Katrien M. Devos
,
Institute of Plant Breeding, Genetics and Genomics (Dept. of Crop and Soil Sciences), and Dept. of Plant Biology, University of Georgia, Athens, GA
Jaroslav Dolezel
,
Institute of Experimental Botany, Olomouc, Czech Republic
Yong Q. Gu
,
USDA ARS, Western Regional Research Center, Albany, CA
Naxin Huo
,
Dept. of Plant Sciences, Davis, CA
Karl G. Kugler
,
Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
Philippe Leroy
,
INRA UMR 1095 GDEC, Clermont-Ferrand, France
Yong Liang
,
China Agricultural University, Beijing, China
Zhiyong Liu
,
China Agricultural University, Beijing, China
Ming-Cheng Luo
,
Department of Plant Sciences, UC Davis, Davis, CA
Eric Lyons
,
School of Plant Sciences, iPlant Collaborative, Tucson, AZ
Zhengqiang Ma
,
Nanjing Agricultural University, Nanjing, China
Long Mao
,
Chinese Academy of Agricultural Sciences, Beijing, China
Klaus F.X. Mayer
,
Helmholtz Center Munich - Plant Genome and Systems Biology, Neuherberg, Germany
W. Richard McCombie
,
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Pat McGuire
,
Department of Plant Sciences, University of California, Davis, Davis, CA
Hans-Georg Mueller
,
Dept. of Statistics, Davis, CA
Shuhong Ouyang
,
China Agricultural University, Beijing, China
Geo Pertea
,
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
Carol Soderlund
,
University of Arizona/Bio5 Institute, Tucson, AZ
Qixin Sun
,
Northwest A&F University, Yangling, China
Sven O. Twardziok
,
Helmholtz Center Munich - Plant Genome and Systems Biology, Neuherberg, Germany
Hao Wang
,
Institute of Plant Breeding, Genetics and Genomics, and Dept. of Plant Biology, University of Georgia, Athens, GA
Yi Wang
,
Department of Plant Sciences, University of California, Davis, CA
Zhenzhong Wang
,
China Agricultural University, Beijing, China
Thomas Wicker
,
University of Zurich, Zurich, Switzerland
Lichan Xiao
,
China Agricultural University, Beijing, China
Mengyuan Xiao
,
University of California, Davis, CA
Frank M. You
,
Cereal Research Centre, Morden, MB, Canada
Tingting Zhu
,
Department of Plant Sciences, University of California, Davis, Davis, CA
Aleksey Zimin
,
University of Maryland, College Park, MD
The aim of this project (NSF IOS-1238231) is to generate a reference sequence for the genome of Aegilops tauschii, one of the diploid progenitors of hexaploid wheat. Because of the large size of the genome, we used the ordered-clone approach as the primary strategy to sequence the Ae. tauschii genome. We constructed a bacterial artificial chromosome (BAC)-based physical map of accession AL8/78, sequenced 42,025 BAC clones of a minimum tiling path across 3,578 BAC contigs and 2,000 singletons in eight-clone pools with the Illumina MiSeq platform, and assembled scaffolds with SOAPdenovo2. We also produced HiSeq 2500 whole-genome shotgun reads for accession AL8/78, which NRGene assembled with their DeNovoMAGICTM software. We merged the two assemblies and generated assembly v2.0, for which the N50 of contigs and scaffolds were 93,210 and 2,884,388 bp, respectively. To validate the assembled scaffolds and assist with the construction of pseudomolecules, we constructed optical BioNano genome (BNG) maps of Ae. tauschii accessions AL8/78 and CIae23, merged them, aligned scaffolds against the BNG contigs, oriented and edited them, and produced seven pseudomolecules of a total length of 4,025,304,143 bp. Transposable element annotation revealed that 80% of the genome consists of transposable elements, which we classified into 3,326 families, of which 1,658 were newly described. Preliminary annotation suggested 37,000 high-confidence genes in the genome.
