Draft genome of the wheat A-genome progenitor Triticum urartu

Journal name:
Nature
Volume:
496,
Pages:
87–90
Date published:
DOI:
doi:10.1038/nature11997
Received
Accepted
Published online
Corrected online

Bread wheat (Triticum aestivum, AABBDD) is one of the most widely cultivated and consumed food crops in the world. However, the complex polyploid nature of its genome makes genetic and functional analyses extremely challenging. The Agenome, as a basic genome of bread wheat and other polyploid wheats, for example, T. turgidum (AABB), T. timopheevii (AAGG) and T. zhukovskyi (AAGGAmAm), is central to wheat evolution, domestication and genetic improvement1. The progenitor species of the Agenome is the diploid wild einkorn wheat T.urartu2, which resembles cultivated wheat more extensively than do Aegilops speltoides (the ancestor of the B genome3) and Ae. tauschii (the donor of the D genome4), especially in the morphology and development of spike and seed. Here we present the generation, assembly and analysis of a whole-genome shotgun draft sequence of the T.urartu genome. We identified protein-coding gene models, performed genome structure analyses and assessed its utility for analysing agronomically important genes and for developing molecular markers. Our T.urartu genome assembly provides a diploid reference for analysis of polyploid wheat genomes and is a valuable resource for the genetic improvement of wheat.

At a glance

Figures

  1. Comparison of gene families and coding domains of T.[thinsp]urartu with rice, maize, sorghum and B.[thinsp]distachyon.
    Figure 1: Comparison of gene families and coding domains of T.urartu with rice, maize, sorghum and B.distachyon.

    a, Venn diagram illustrating shared and unique gene families (gene numbers in parenthesis) among the five grass species. b, Comparison of protein families with different Pfam domains among the five species. Fourteen Pfam domains that had significant differences (P<0.001, Fisher’s exact test) in their percentages between T.urartu and the other four grass species are shown. The percentage was calculated by dividing the number of each domain by the total gene set in a given species.

  2. Synteny analysis between T.[thinsp]urartu and B.[thinsp]distachyon, and genome expansion in T.[thinsp]urartu.
    Figure 2: Synteny analysis between T.urartu and B.distachyon, and genome expansion in T.urartu.

    a, Syntenic relationships between the seven hypothetical chromosomes of T.urartu (1A–7A) and the five chromosomes of B.distachyon (Bd1–Bd5). The deletion bin maps of bread wheat 1A–7A chromosomes are noted at the bottom. b, Comparison of intergenic spaces in one representative syntenic block from T.urartu and B.distachyon. The 50-kb block from B.distachyon chromosome1 (Bd1) contains five genes (indicated by red arrowheads). The T.urartu orthologues (yellow arrowheads) of the five genes are distributed in five separate scaffolds (totalling 1,092kb). The total intergenic space in the displayed T.urartu region is more than 20-fold that in the corresponding Bd1 region.

  3. Association analysis of the TuGASR7 gene.
    Figure 3: Association analysis of the TuGASR7 gene.

    a, Indel differences between the TuGASR7 haplotypes H1 and H2 compared with their corresponding regions in the GASR7 homologues from barley (Hordeum vulgare; HvGASR7) and T. aestivum (TaGASR7). b, Phylogenetic relationships among the homologous genes of rice GASR7 from different grass species. TRIUR3_28594 is the predicted homologue of GASR7 in T.urartu. c, Typical grain lengths for the two detected TuGASR7 haplotypes, H1 (top panel) and H2 (bottom panel). For each haplotype, the seeds from four representative T.urartu accessions were photographed. To illustrate the difference in grain length more clearly, ten seeds were randomly selected from each of the compared accessions and aligned closely for the photograph.

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Sequence Read Archive

Change history

Corrected online 28 March 2013
When originally published online, in the html version Daowen Wang was not listed as a corresponding author and emails to Zhensheng Li were incorrectly sending to Daowen Wang. Both corresponding authors are now correct.

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Author information

  1. These authors contributed equally to this work.

    • Hong-Qing Ling,
    • Shancen Zhao,
    • Dongcheng Liu,
    • Junyi Wang,
    • Hua Sun &
    • Chi Zhang

Affiliations

  1. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

    • Hong-Qing Ling,
    • Dongcheng Liu,
    • Junyi Wang,
    • Hua Sun,
    • Huajie Fan,
    • Lingli Dong,
    • Huilan Wu,
    • Yiwen Li,
    • Yan Cui,
    • Shusong Zheng,
    • Biao Wang,
    • Kang Yu,
    • Wenlong Yang,
    • Xueyuan Lou,
    • Xiaofei Zhang,
    • Guangbin Luo,
    • Bairu Zhang,
    • Dingzhong Tang,
    • Qianhua Shen,
    • Pengya Xue,
    • Shenhao Zou,
    • Xin Liu,
    • Famin Wang,
    • Yanping Yang,
    • Xueli An,
    • Zhenying Dong,
    • Kunpu Zhang,
    • Xiangqi Zhang,
    • Yiping Tong,
    • Zhensheng Li,
    • Daowen Wang &
    • Aimin Zhang
  2. BGI-Shenzhen, Shenzhen 518038, China

    • Shancen Zhao,
    • Junyi Wang,
    • Chi Zhang,
    • Dong Li,
    • Yong Tao,
    • Chuan Gao,
    • Xiaosen Guo,
    • Qinsi Liang,
    • Jie Chen,
    • Mingji Feng,
    • Jianbo Jian,
    • Ying Jiang,
    • Junjie Liu,
    • Zhaobao Wang,
    • Yuhui Sha,
    • Jian Wang,
    • Huanming Yang &
    • Jun Wang
  3. State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong

    • Shancen Zhao
  4. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

    • Huajun Wu &
    • Xiujie Wang
  5. Department of Plant Sciences, University of California, Davis, California 95616, USA

    • Ming-Cheng Luo &
    • Jan Dvorak
  6. Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark

    • Jun Wang
  7. King Abdulaziz University, Jeddah 21589, Saudi Arabia

    • Jun Wang

Contributions

H.-Q.L., A.M.Z., Z.S.L., D.W.W., Ji.W., M.-C.L. and J.D were responsible for project initiation. Project coordination was by H.-Q.L., A.M.Z., D.W.W., Ju.W. and J.Y.W. The project was managed by H.-Q.L, B.R.Z., Ju.W., Ji.W. and H.M.Y. Data generation and analysis were performed by S.C.Z., D.C.L., H.S., Y.T., D.L., H.J.F., H.L.W., L.L.D., Y.W.L., C.G., Y.C., C.Z., X.S.G., S.S.Z., B.W., K.Y., Q.S.L., W.L.Y., X.Y.L., J.C., X.F.Z., G.B.L., H.J.W., P.Y.X., S.H.Z., X.L., F.M.W., Y.P.Y., X.L.A., Z.Y.D., K.P.Z., J.Y.W., M.J.F., J.B.J., Y.J., J.J.L., Z.B.W. and Y.H.S. The analysis was designed by H.-Q.L., A.M.Z., D.W.W., Q.H.S., D.Z.T., X.J.W., Y.P.T. and X.Q.Z. The paper was written by H.-Q.L., S.C.Z., D.C.L., H.S., A.M.Z. and D.W.W.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under accession number AOTI00000000. Sequence assemblies and all short-read data are under project accession numbers SRA030525 (genomic short reads), SRA066084 (resequencing reads), PRJNA182347 (assembly and annotation) and SRA064213 (RNA-Seq). The version described in this paper is the first version, AOTI01000000. Genomic data are also available at the Comprehensive Library for Modern Biotechnology (CLiMB) repository26.

Author details

Supplementary information

PDF files

  1. Supplementary Information (2.6 MB)

    This file contains Supplementary Text, Supplementary References, (see contents page for details), Supplementary Figures 1-18 and Supplementary Tables 1-19, 21, 23-32 (see separate files for Supplementary Tables 20 and 22).

Excel files

  1. Supplementary Data (1.4 MB)

    This file contains Supplementary Table 20 which shows assembled scaffolds mapped to wheat chromosome bins.

  2. Supplementary Data (433 KB)

    This file contains Supplementary Table 22 which shows syntenic blocks between T. urartu and B. distachyon.

Additional data