Jan Dvorak
,
Department of Plant Sciences, University of California, Davis, CA
Olin Anderson
,
USDA ARS, Western Regional Research Center, Albany, CA
Jeffrey L. Bennetzen
,
Dept. of Genetics, University of Georgia, Athens, GA
Xiongtao Dai
,
Dept. of Statistics, 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
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
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
Frank M. You
,
Cereal Research Centre, Morden, MB, Canada
Tingting Zhu
,
Department of Plant Sciences, University of California, Davis, Davis, CA
The aim of this NSF-funded project (IOS-1238231) is to generate a reference sequence for the genome of Aegilops tauschii, one of the three diploid progenitors of common (hexaploid) wheat. The 1C size of the Ae. tauschii genome is between 4 and 5 Gbp, and the genome was estimated to contain nearly 90% repeated sequences. We use therefore the ordered-clone genome sequencing approach to produce a high-confidence reference sequence. We constructed a bacterial artificial chromosome (BAC)-based physical map of the Ae. tauschii genome and selected clones making up a minimum tiling path (MTP) consisting of 42,822 BAC clones across 3,578 BAC contigs. MTP clones and about 15,000 singleton are individually grown, cells are combined into eight-clone pools, and BAC DNA is isolated from the clone pools. Indexed fragment libraries containing 320 clones are constructed for sequencing with the Illumina MiSeq next-generation sequencing platform. The reads are assembled with SOAPdenovo. To validate the assembled scaffolds, we are constructing an optical nanomap of the Ae. tauschii genome using the BioNano Irys platform. Scaffolds are aligned against the nanomap, oriented, and if discrepancies are encountered they are edited. Genes, pseudogenes, and transposable elements are annotated. As of the middle of November, 2014, most of the BAC clones making up the MTP of the seven Ae. tauschii chromosomes and 2,000 singletons have been sequenced and scaffolds assembled. Those of chromosomes 1D, 2D, and 3D are being annotated. Scaffolds anchored on the physical map are publicly available on the project website (http://aegilops.wheat.ucdavis.edu/ATGSP/).
