Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome-based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein-coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small-scale evolutionary rearrangements, in addition to providing evidence for the 4AL-5AL-7BS translocation in wild emmer wheat. Chromosome-based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.

Centre of the Region Haná for Biotechnological and Agricultural Research Institute of Experimental Botany Olomouc Czech Republic

Department of Molecular Biology and Ecology of Plants Faculty of Life Sciences Tel Aviv University Tel Aviv Israel

Department of Plant Sciences and Plant Pathology Cereal Genomics Lab Montana State University Bozeman MT USA

Instituto de Agricultura Sostenible Cordoba Spain

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Akpinar, B.A. and Budak, H. (2016) Dissecting miRNAs in wheat D genome progenitor, Aegilops tauschii. Front. Plant Sci. 7, 1–17. PubMed PMC

Akpinar, B.A. , Lucas, S.J. , Vr, J. , Dole, J. and Budak, H. (2014) Sequencing chromosome 5D of Aegilops tauschii and comparison with its allopolyploid descendant bread wheat (Triticum aestivum). Plant Biotechnol. J. 13, 740–752. PubMed

Akpinar, B.A. , Kantar, M. and Budak, H. (2015a) Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress. Funct. Integr. Genomics, 15, 587–598. PubMed

Akpinar, B.A. , Yuce, M. , Lucas, S. , Vrána, J. , Burešová, V. , Doležel, J. and Budak, H. (2015b) Molecular organization and comparative analysis of chromosome 5B of the wild wheat ancestor Triticum dicoccoides. Sci. Rep. 5, 10763. PubMed PMC

Akpinar, B.A. , Lucas, S. and Budak, H. (2016) A large‐scale chromosome‐specific SNP discovery guideline. Funct. Integr. Genomics, 17, 97–105. PubMed

Alptekin, B. , Akpinar, B.A. and Budak, H. (2017) A comprehensive prescription for plant miRNA identification. Front. Plant Sci. 7, 2058. PubMed PMC

Avni, R. , Nave, M. , Barad, O. , Baruch, K. , Twardziok, S.O. , Gundlach, H. , Hale, I. PubMed

Berkman, P.J. , Skarshewski, A. , Lorenc, M.T. , Lai, K. , Duran, C. , Ling, E.Y. , Stiller, J. PubMed

Berkman, P.J. , Lai, K. , Lorenc, M.T. and Edwards, D. (2012a) Next‐generation sequencing applications for wheat crop improvement. Am. J. Bot. 99, 365–371. PubMed

Berkman, P.J. , Skarshewski, A. , Manoli, S. , Lorenc, M.T. , Stiller, J. , Smits, L. , Lai, K. PubMed

Budak, H. , Akpinar, B.A. , Unver, T. and Turktas, M. (2013a) Proteome changes in wild and modern wheat leaves upon drought stress by two‐dimensional electrophoresis and nanoLC‐ESI‐MS/MS. Plant Mol. Biol. 83, 89–103. PubMed

Budak, H. , Kantar, M. and Kurtoglu, K.Y. (2013b) Drought tolerance in modern and wild wheat. Scientific World J. 2013, 548246. PubMed PMC

Cagirici, H.B. , Alptekin, B. and Budak, H. (2017) RNA sequencing and co‐expressed long non‐coding RNA in modern and wild wheats. Sci. Rep. 7, 10670. PubMed PMC

Camacho, C. , Coulouris, G. , Avagyan, V. , Ma, N. , Papadopoulos, J. , Bealer, K. and Madden, T.L. (2009) BLAST+: architecture and applications. BMC Bioinform. 10, 421. PubMed PMC

Chikhi, R. and Medvedev, P. (2014) Informed and automated k‐mer size selection for genome assembly. Bioinformatics, 30, 31–37. PubMed

Choulet, F. , Wicker, T. , Rustenholz, C. , Paux, E. , Salse, J. , Leroy, P. , Schlub, S. PubMed PMC

Choulet, F. , Alberti, A. , Theil, S. , Glover, N. , Barbe, V. , Daron, J. , Pingault, L. PubMed

Conesa, A. and Götz, S. (2008) Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics, 2008, 619832. PubMed PMC

Distelfeld, A. (2016) Assembly and Validation of the Wild Emmer Wheat Genome. In Plant and Animal Genome XXIV Conference. Plant and Animal Genome. Available at: https://pag.confex.com/pag/xxiv/webprogram/Paper18477.html [Accessed May 11, 2016].

Distelfeld, A. , Tranquilli, G. , Li, C. , Yan, L. and Dubcovsky, J. (2009) Genetic and molecular characterization of the VRN2 loci in tetraploid wheat. Plant Physiol. 149, 245–257. PubMed PMC

Ergen, N.Z. and Budak, H. (2009) Sequencing over 13 000 expressed sequence tags from six subtractive cDNA libraries of wild and modern wheats following slow drought stress. Plant, Cell Environ. 32, 220–236. PubMed

Ergen, N.Z. , Thimmapuram, J. , Bohnert, H.J. and Budak, H. (2009) Transcriptome pathways unique to dehydration tolerant relatives of modern wheat. Funct. Integr. Genomics, 9, 377–396. PubMed

Feuillet, C. , Leach, J.E. , Rogers, J. , Schnable, P.S. and Eversole, K. (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci. 16, 77–88. PubMed

Hao, M. , Luo, J. , Zhang, L. , Yuan, Z. , Zheng, Y. , Zhang, H. and Liu, D. (2013) In situ hybridization analysis indicates that 4AL‐5AL‐7BS translocation preceded subspecies differentiation of Triticum turgidum. Genome, 56, 303–305. PubMed

Henry, R.J. , Rangan, P. and Furtado, A. (2016) Functional cereals for production in new and variable climates. Curr. Opin. Plant Biol. 30, 11–18. PubMed

Hernandez, P. , Martis, M. , Dorado, G. , Pfeifer, M. , Gálvez, S. , Schaaf, S. , Jouve, N. PubMed

Iizumi, T. , Yokozawa, M. , Sakurai, G. , Travasso, M.I. , Romanenkov, V. , Oettli, P. , Newby, T.

Jia, J. , Zhao, S. , Kong, X. , Li, Y. , Zhao, G. , He, W. , Appels, R. PubMed

Kantar, M. , Akpınar, B.A. , Valárik, M. , Lucas, S.J. , Doležel, J. , Hernández, P. and Budak, H. (2012) Subgenomic analysis of microRNAs in polyploid wheat. Funct. Integr. Genomics, 12, 465–479. PubMed

Klionsky, D. , Agholme, L. , Agnello, M. , Agostinis, P. , Aguirre‐Ghiso, J.A. , Ahn, H.J. , Ait‐Mohamed, O. PubMed PMC

Krzywinski, M. , Schein, J. , Birol, I. , Connors, J. , Gascoyne, R. , Horsman, D. , Jones, S.J. PubMed PMC

Kurtoglu, K.Y. , Kantar, M. , Lucas, S.J. and Budak, H. (2013) Unique and conserved microRNAs in wheat chromosome 5D revealed by next‐generation sequencing. PLoS ONE, 8, e69801. PubMed PMC

Kurtoglu, K.Y. , Kantar, M. and Budak, H. (2014) New wheat microRNA using whole‐genome sequence. Funct. Integr. Genomics, 14, 363–379. PubMed

Kuzuoglu‐Ozturk, D. , Cebeci Yalcinkaya, O. , Akpinar, B.A. , Mitou, G. , Korkmaz, G. , Gozuacik, D. and Budak, H. (2012) Autophagy‐related gene, TdAtg8, in wild emmer wheat plays a role in drought and osmotic stress response. Planta, 236, 1081–1092. PubMed

Li, L. , Stoeckert, C.J. and Roos, D.S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178–2189. PubMed PMC

Li, F. , Pignatta, D. , Bendix, C. , Brunkard, J.O. , Cohn, M.M. , Tung, J. and Sun, H. (2011a) MicroRNA regulation of plant innate immune receptors. Proc. Natl. Acad. Sci. USA, 109, 1790–1795. PubMed PMC

Li, Y. , Li, C. , Xia, J. and Jin, Y. (2011b) Domestication of transposable elements into MicroRNA genes in plants. PLoS ONE, 6, e19212. PubMed PMC

Ling, H.‐Q. , Zhao, S. , Liu, D. , Wang, J. , Sun, H. , Zhang, C. , Fan, H. PubMed

Liu, H. , Searle, I.R. , Watson‐Haigh, N.S. , Baumann, U. , Mather, D.E. , Able, A.J. PubMed PMC

Lowe, T.M. and Eddy, S.R. (1997) tRNAscan‐SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 0955–0964. PubMed PMC

Lucas, S.J. and Budak, H. (2012) Sorting the wheat from the chaff: identifying miRNAs in genomic survey sequences of Triticum aestivum chromosome 1AL. A. A. Aboobaker, ed. PLoS ONE, 7, e40859. PubMed PMC

Lucas, S.J. , Akpinar, B.A. , Šimková, H. , Kubaláková, M. , Doležel, J. and Budak, H. (2014) Next‐generation sequencing of flow‐sorted wheat chromosome 5D reveals lineage‐specific translocations and widespread gene duplications. BMC Genom. 15, 1–18. PubMed PMC

Luo, M. , Gu, Y.Q. , You, F.M. , Deal, K.R. , Ma, Y. , Hu, Y. PubMed PMC

Marcussen, T. , Sandve, S.R. , Heier, L. , Spannagl, M. , Pfeifer, M. , International Wheat Genome Sequencing Consortium , Jakobsen, K.S. PubMed

Mayer, K.F. , Waugh, R. , Brown, J.W. , Schulman, A. , Langridge, P. , Platzer, M. , Fincher, G.B. PubMed

Mayer, K.F. , Rogers, J. , Doležel, J. , Pozniak, C. , Eversole, K. , Feuillet, C. , Gill, B. PubMed

Nagy, P. , Hegedus, K. , Pircs, K. , Varga, Á. and Juhász, G. (2014) Different effects of Atg2 and Atg18 mutations on Atg8a and Atg9 trafficking during starvation in Drosophila. FEBS Lett. 588, 408–413. PubMed PMC

Nevo, E. and Chen, G. (2010) Drought and salt tolerances in wild relatives for wheat and barley improvement. Plant, Cell Environ. 33, 670–685. PubMed

Nussbaumer, T. , Martis, M.M. , Roessner, S.K. , Pfeifer, M. , Bader, K.C. , Sharma, S. , Gundlach, H. PubMed PMC

Paterson, A.H. , Bowers, J.E. , Bruggmann, R. , Dubchak, I. , Grimwood, J. , Gundlach, H. , Haberer, G. PubMed

Paux, E. , Faure, S. , Choulet, F. , Roger, D. , Gauthier, V. , Martinant, J.P. , Sourdille, P. PubMed

Pei, D. , Zhang, W. , Sun, H. , Wei, X. , Yue, J. and Wang, H. (2014) Identification of autophagy‐related genes ATG4 and ATG8 from wheat (Triticum aestivum L.) and profiling of their expression patterns responding to biotic and abiotic stresses. Plant Cell Rep. 33, 1697–1710. PubMed

Pourkheirandish, M. , Hensel, G. , Kilian, B. , Senthil, N. , Chen, G. , Sameri, M. , Azhaguvel, P. PubMed

Sahoo, R.K. , Gill, S.S. and Tuteja, N. (2012) Pea DNA helicase 45 promotes salinity stress tolerance in IR64 rice with improved yield. Plant Signal. Behav. 7, 1042–1046. PubMed PMC

Sela, H. , Spiridon, L.N. , Petrescu, A.J. , Akerman, M. , Mandel‐Gutfreund, Y. , Nevo, E. , Loutre, C. PubMed PMC

Simpson, J.T. , Wong, K. , Jackman, S.D. , Schein, J.E. , Jones, S.J.M. and Birol, I. (2009) ABySS: a parallel assembler for short read sequence data. Genome Res. 19, 1117–1123. PubMed PMC

Sun, L. , Luo, H. , Bu, D. , Zhao, G. , Yu, K. , Zhang, C. , Liu, Y. PubMed PMC

Tanaka, T. , Antonio, B.A. , Kikuchi, S. , Matsumoto, T. , Nagamura, Y. , Numa, H. , Sakai, H. PubMed PMC

Tanaka, T.S. , Kobayashi, F.U. , Joshi, G.I.R.I.P.R. , Onuki, R. , Sakai, H. , Kanamori, H. , Wu, J. PubMed PMC

The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463, 763–768. PubMed

Tuteja, N. (2010) A Method to Confer Salinity Stress Tolerance to Plants by Helicase Overexpression. In Helicases. pp. 377–387. Available at: http://link.springer.com/10.1007/978-1-60327-355-8. PubMed DOI

Vatansever, R. , Filiz, E. and Eroglu, S. (2017) Genome‐wide exploration of metal tolerance protein (MTP) genes in common wheat (Triticum aestivum): insights into metal homeostasis and biofortification. Biometals, 30, 217–235. PubMed

Venora, G. , Blangiforti, S. , Castiglione, M.R. , Pignone, D. , Losavio, F. and Cremonini, R. (2002) Chromatin organisation and computer aided karyotyping of Triticum durum Desf. cv. Timilia. Caryologia, 55, 91–98.

Vitulo, N. , Albiero, A. , Forcato, C. , Campagna, D. , Dal Pero, F. , Bagnaresi, P. , Colaiacovo, M. PubMed PMC

Wu, T.D. and Watanabe, C.K. (2005) GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21, 1859–1875. PubMed

Xie, W. and Nevo, E. (2008) Wild emmer: genetic resources, gene mapping and potential for wheat improvement. Euphytica, 164, 603–614.

Yan, L. (2004) The wheat VRN2 gene is a flowering repressor down‐regulated by vernalization. Science, 303, 1640–1644. PubMed PMC

Yue, J. , Sun, H. , Zhang, W. , Pei, D. , He, Y. and Wang, H. (2015) Wheat homologs of yeast ATG6 function in autophagy and are implicated in powdery mildew immunity. BMC Plant Biol. 15, 1–15. PubMed PMC

Zhai, J. , Jeong, D.‐H. , De Paoli, E. , Park, S. , Rosen, B.D. , Li, Y. , González, A.J. PubMed PMC

Zhu, Q.H. , Fan, L. , Liu, Y. , Xu, H. , Llewellyn, D. and Wilson, I. (2013) miR482 regulation of NBS‐LRR defense genes during fungal pathogen infection in cotton. PLoS ONE, 8, e84390. PubMed PMC

Zimin, A.V. , Puiu, D. , Hall, R. , Kingan, S. , Clavijo, B.J. and Salzberg, S.L. (2017) The first near‐complete assembly of the hexaploid bread wheat genome, Triticum aestivum. Gigascience, 6, 1–7. PubMed PMC

The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat