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2. Additional file of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement

Author

Muñoz-Amatriaín, María, Yanwen Xiong, Schmitt, Mark R, Bilgic, Hatice, Budde, Allen D, Shiaoman Chao, Smith, Kevin P, and Muehlbauer, Gary J

Subjects
hemic and lymphatic diseases, food and beverages, human activities
Abstract

Additional file of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement

Published
2021
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3. Additional file 2 of Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement

Author

Muñoz-Amatriaín, María, Yanwen Xiong, Schmitt, Mark R, Bilgic, Hatice, Budde, Allen D, Shiaoman Chao, Smith, Kevin P, and Muehlbauer, Gary J

Abstract

Additional file 2:Venn diagrams of the differentially expressed genes between the most recent and older genotypes at both time points. The figure shows the intersection among three data sets corresponding to: all probe sets on the Barley1 GeneChip, the differentially expressed genes between the "most recent" lines, and the genes differentially expressed between the "older" lines. (PPT 175 KB)

Published
2021
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5. Multiple wheat genomes reveal global variation in modern breeding

Author

Walkowiak, Sean, Gao, Liangliang, Monat, Cecile, Haberer, Georg, Kassa, Mulualem T, Brinton, Jemima, Ramirez-Gonzalez, Ricardo H, Kolodziej, Markus C, Delorean, Emily, Thambugala, Dinushika, Klymiuk, Valentyna, Byrns, Brook, Gundlach, Heidrun, Bandi, Venkat, Siri, Jorge Nunez, Nilsen, Kirby, Aquino, Catharine, Himmelbach, Axel, Copetti, Dario, Ban, Tomohiro, Venturini, Luca, Bevan, Michael, Clavijo, Bernardo, Koo, Dal-Hoe, Ens, Jennifer, Wiebe, Krystalee, N'Diaye, Amidou, Fritz, Allen K, Gutwin, Carl, Fiebig, Anne, Fosker, Christine, Fu, Bin Xiao, Accinelli, Gonzalo Garcia, Gardner, Keith A, Fradgley, Nick, Gutierrez-Gonzalez, Juan, Halstead-Nussloch, Gwyneth, Hatakeyama, Masaomi, Koh, Chu Shin, Deek, Jasline, Costamagna, Alejandro C, Fobert, Pierre, Heavens, Darren, Kanamori, Hiroyuki, Kawaura, Kanako, Kobayashi, Fuminori, Krasileva, Ksenia, Kuo, Tony, McKenzie, Neil, Murata, Kazuki, Nabeka, Yusuke, Paape, Timothy, Padmarasu, Sudharsan, Percival-Alwyn, Lawrence, Kagale, Sateesh, Scholz, Uwe, Sese, Jun, Juliana, Philomin, Singh, Ravi, Shimizu-Inatsugi, Rie, Swarbreck, David, Cockram, James, Budak, Hikmet, Tameshige, Toshiaki, Tanaka, Tsuyoshi, Tsuji, Hiroyuki, Wright, Jonathan, Wu, Jianzhong, Steuernagel, Burkhard, Small, Ian, Cloutier, Sylvie, Keeble-Gagnère, Gabriel, Muehlbauer, Gary, Tibbets, Josquin, Nasuda, Shuhei, Melonek, Joanna, Hucl, Pierre J, Sharpe, Andrew G, Clark, Matthew, Legg, Erik, Bharti, Arvind, Langridge, Peter, Hall, Anthony, Uauy, Cristobal, Mascher, Martin, Krattinger, Simon G, Handa, Hirokazu, Shimizu, Kentaro K, Distelfeld, Assaf, Chalmers, Ken, Keller, Beat, Mayer, Klaus FX, Poland, Jesse, Stein, Nils, McCartney, Curt A, Spannagl, Manuel, Wicker, Thomas, and Pozniak, Curtis J

Subjects
Internationality, Insecta, DNA Copy Number Variations, General Science & Technology, Acclimatization, Centromere, NLR Proteins, Genetic Introgression, Polyploidy, Genetics, Animals, Polymorphism, Triticum, Plant Proteins, Plant Diseases, Genome, Human Genome, Chromosome Mapping, Molecular, Genetic Variation, Genomics, Single Nucleotide, Plant, Plant Breeding, Haplotypes, Genes, DNA Transposable Elements, Edible Grain, Cloning, Biotechnology
Abstract

Advances in genomics have expeditedthe improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Published
2020

6. Additional file 4 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

Author

Cuesta-Marcos, Alfonso, Szűcs, Péter, Close, Timothy J, Filichkin, Tanya, Muehlbauer, Gary J, Smith, Kevin P, and Hayes, Patrick M

Abstract

Additional file 4:Figure S1. Neighbor-Joining phylogenetic cluster analyses of several re-sequenced genes of the barley CAP Core set. Confidence values on the branches are based on 1000 bootstraps. For each gene, sequence length and number of lines used is indicated in the heading of each cluster. Number of genotypes per haplotype is indicated in brackets. (PPT 150 KB)

Published
2020
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7. Additional file 7 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

Author

Cuesta-Marcos, Alfonso, Szűcs, Péter, Close, Timothy J, Filichkin, Tanya, Muehlbauer, Gary J, Smith, Kevin P, and Hayes, Patrick M

Abstract

Additional file 7:Figure S3. Sequence alignment of HvHOX1 from seven accessions with different VRS1 haplotypes. Similarity is shown to four levels. (DOC 38 KB)

Published
2020
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8. Additional file 6 of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

Author

Cuesta-Marcos, Alfonso, Szűcs, Péter, Close, Timothy J, Filichkin, Tanya, Muehlbauer, Gary J, Smith, Kevin P, and Hayes, Patrick M

Subjects
food and beverages
Abstract

Additional file 6:Figure S2. Schematic representation of VRN-H1 intron 1 found in the barley CAP Core set (102 genotypes). Deletion types are named based on the first cultivar whose sequence was deposited in GenBank. Edges of exons 1 and 2 are indicated by flanking black boxes. Gaps represent deletions (>50 bp) relative to the full-length Strider allele. The 2.8 kb barley-wheat conserved region (dashed line) and the 436 bp vernalization critical region (dotted box) are indicated. Number of genotypes per deletion type is denoted. (PPT 110 KB)

Published
2020
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12. Additional file of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

Author

Cuesta-Marcos, Alfonso, Szűcs, Péter, Close, Timothy J, Filichkin, Tanya, Muehlbauer, Gary J, Smith, Kevin P, and Hayes, Patrick M

Subjects
food and beverages
Abstract

Additional file of Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

Published
2020
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15. MOESM1 of TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools

Author

CéCile Monat, Sudharsan Padmarasu, Lux, Thomas, Wicker, Thomas, Gundlach, Heidrun, Himmelbach, Axel, Ens, Jennifer, Chengdao Li, Muehlbauer, Gary, Schulman, Alan, Waugh, Robbie, Braumann, Ilka, Pozniak, Curtis, Scholz, Uwe, Mayer, Klaus, Spannagl, Manuel, Stein, Nils, and Mascher, Martin

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, ComputingMilieux_COMPUTERSANDEDUCATION, Data_FILES, ComputerApplications_COMPUTERSINOTHERSYSTEMS
Abstract

Additional file 1. Supplementary Tables and Figures.

Published
2019
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16. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L

Author

Beier, Sebastian, Himmelbach, Axel, Colmsee, Christian, Zhang, Xiao-Qi, Barrero, Roberto A., Zhang, Qisen, Li, Lin, Bayer, Micha, Bolser, Daniel, Taudien, Stefan, Groth, Marco, Felder, Marius, Hastie, Alex, Šimková, Hana, Staňková, Helena, Vrána, Jan, Chan, Saki, Muñoz-Amatriaín, María, Ounit, Rachid, Wanamaker, Steve, Schmutzer, Thomas, Aliyeva-Schnorr, Lala, Grasso, Stefano, Tanskanen, Jaakko, Sampath, Dharanya, Heavens, Darren, Cao, Sujie, Chapman, Brett, Dai, Fei, Han, Yong, Li, Hua, Li, Xuan, Lin, Chongyun, McCooke, John K., Tan, Cong, Wang, Songbo, Yin, Shuya, Zhou, Gaofeng, Poland, Jesse A., Bellgard, Matthew I., Houben, Andreas, Doležel, Jaroslav, Ayling, Sarah, Lonardi, Stefano, Langridge, Peter, Muehlbauer, Gary J., Kersey, Paul, Clark, Matthew D., Caccamo, Mario, Schulman, Alan H., Platzer, Matthias, Close, Timothy J., Hansson, Mats, Zhang, Guoping, Braumann, Ilka, Li, Chengdao, Waugh, Robbie, Scholz, Uwe, Stein, Nils, Mascher, Martin, Institute of Biotechnology, Alan Schulman / Principal Investigator, and Viikki Plant Science Centre (ViPS)

Subjects
Statistics and Probability, Data Descriptor, Plant genetics, ASSEMBLIES, Library and Information Sciences, Education, Genome assembly algorithms, Genetics, DNA sequencing, Genome, Human Genome, 1184 Genetics, developmental biology, physiology, food and beverages, Chromosome Mapping, Hordeum, Plant, FRAMEWORK, LIBRARIES, Computer Science Applications, ALIGNMENT, BIAS, BACTERIAL ARTIFICIAL CHROMOSOMES, Statistics, Probability and Uncertainty, PHYSICAL MAP, Sequence Analysis, Genome, Plant, Information Systems, GENERATION
Abstract

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. `Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).

Published
2017

23. Additional file 5: Figure S2. of Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias

Author

Li, Lin, Briskine, Roman, Schaefer, Robert, Schnable, Patrick, Myers, Chad, Flagel, Lex, Springer, Nathan, and Muehlbauer, Gary

Abstract

Co-expression divergence in terms of shortest network path, edge connectivity of a duplicate pair, and local clustering coefficient. (A) WGD duplicates had significantly shorter path edges than inserted and tandem duplicate genes. (B) WGD duplicates had significantly higher edge connectivity than inserted and tandem duplicate genes. (C) Maize1 and maize2 genes had significantly lower local clustering coefficient than non-syntenic genes (usually generated by inserted and tandem duplications). (D) and (E) Shortest network path and edge connectivity of a duplicate pair were associated with synonymous mutation rate (dS). (PDF 740 kb)

Published
2016
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25. Additional file 5: Figure S2. of Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias

Author

Li, Lin, Briskine, Roman, Schaefer, Robert, Schnable, Patrick, Myers, Chad, Flagel, Lex, Springer, Nathan, and Muehlbauer, Gary

Abstract

Co-expression divergence in terms of shortest network path, edge connectivity of a duplicate pair, and local clustering coefficient. (A) WGD duplicates had significantly shorter path edges than inserted and tandem duplicate genes. (B) WGD duplicates had significantly higher edge connectivity than inserted and tandem duplicate genes. (C) Maize1 and maize2 genes had significantly lower local clustering coefficient than non-syntenic genes (usually generated by inserted and tandem duplications). (D) and (E) Shortest network path and edge connectivity of a duplicate pair were associated with synonymous mutation rate (dS). (PDF 740 kb)

Published
2016
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27. Additional file 1: Figure S1. of Differential transcriptomic responses to Fusarium graminearum infection in two barley quantitative trait loci associated with Fusarium head blight resistance

Author

Yadong Huang, Li, Lin, Smith, Kevin, and Muehlbauer, Gary

Abstract

Graphical genotypes of the 2Hb8 R and 6Hb7 R NILs. Figure S2. The R NILs accumulated less DON and ergosterol than the respective susceptible genotypes M69 and Lacey. Figure S3. Flowchart of the experimental setup and RNA-Seq analysis. Figure S4. Number of RNA-Seq reads generated for each sample that were filtered and uniquely mapped. Figure S5. Correlation coefficients of biological replicates used in RNA-Seq experiments. Figure S6. Correlation of RNA-Seq and qRT-PCR results of 13 genes and one lncRNA. Figure S7. MapMan visualization of FHB-responsive DEGs involved in general metabolic pathways in M69 at 48 hai and 96 hai. Figure S8. Categorization of induced (red) or repressed (blue) genes in Lacey at 48 and 96 h after F. graminearum inoculation. Figure S9. Categorization of induced (red) or repressed (blue) genes in the 6Hb7 R NIL compared to Lacey at 48 and 96 h after F. graminearum inoculation. Figure S10. Identification and characterization of lncRNAs from barley spike samples. Figure S11. Amino acid sequence alignment of three cysteine-rich receptor-like kinases using Jalview. (DOCX 6130 kb)

Published
2016
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28. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

Author

Muñoz-Amatriaín, María, Lonardi, Stefano, Luo, MingCheng, Madishetty, Kavitha, Svensson, Jan T, Moscou, Matthew J, Wanamaker, Steve, Jiang, Tao, Kleinhofs, Andris, Muehlbauer, Gary J, Wise, Roger P, Stein, Nils, Ma, Yaqin, Rodriguez, Edmundo, Kudrna, Dave, Bhat, Prasanna R, Chao, Shiaoman, Condamine, Pascal, Heinen, Shane, Resnik, Josh, Wing, Rod, Witt, Heather N, Alpert, Matthew, Beccuti, Marco, Bozdag, Serdar, Cordero, Francesca, Mirebrahim, Hamid, Ounit, Rachid, Wu, Yonghui, You, Frank, Zheng, Jie, Simková, Hana, Dolezel, Jaroslav, Grimwood, Jane, Schmutz, Jeremy, Duma, Denisa, Altschmied, Lothar, Blake, Tom, Bregitzer, Phil, Cooper, Laurel, Dilbirligi, Muharrem, Falk, Anders, Feiz, Leila, Graner, Andreas, Gustafson, Perry, Hayes, Patrick M, Lemaux, Peggy, Mammadov, Jafar, and Close, Timothy J

Subjects
Hordeum vulgare L, Genome, gene distribution, Human Genome, Molecular Sequence Data, synteny, Plant Biology & Botany, Bacterial, food and beverages, Plant Biology, Hordeum, Aegilops tauschii, BAC sequencing, Plant, Barley [HarvEST], Chromosomes, Vaccine Related, recombination frequency, Barley, Artificial, Genetics, centromere BACs, Biochemistry and Cell Biology, Biotechnology
Abstract

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15622 BACs representing the minimal tiling path of 72052 physical-mapped gene-bearing BACs. This generated ~1.7Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae.tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.

Published
2015

29. Genome interplay in the grain transcriptome of hexaploid bread wheat

Author

Pfeifer, Matthias, Kugler, Karl, Sandve, Simen, Zhan, Bujie, Rudi, Heidi, Hvidsten, Torgeir, Mayer, Klaus, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam, Sourdille, Pierre, Endo, Takashi, Kubaláková, Marie, Číhalíková, Jarmila, Dubská, Zdeňka, Vrána, Jan, Šperková, Romana, Šimková, Hana, Febrer, Melanie, Clissold, Leah, Mclay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K, Khurana, Jitendra, Akhunov, Eduard, Choulet, Frédéric, Alberti, Adriana, Barbe, Valérie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Lien, Sigbjørn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H, Clavijo, Bernardo J, Wright, Jonathan, Spannagl, Manuel, Martis, Mihaela M, Mascher, Martin, Chapman, Jarrod, Poland, Jesse A, Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S, Muehlbauer, Gary J, Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Véronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Hélène, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Françoise, Couderc, Loïc, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikael, Keller, Beat, Praud, Sébastien, Plant Genome and Systems Biology, Helmholtz Diabetes Center at Helmholtz Zentrum, Norwegian University of Life Sciences (NMBU), University of Norway, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Norwegian Research Council 199387, Deutsche Forschungsgemeinschaft (DFG) SFB924, German Federal Ministry of Education and Research (BMBF), European Commission's 7th Framework Program, Plant Genome and Systems Biology (PGSB), Helmholtz Zentrum München = German Research Center for Environmental Health, Centre for Integrative Genetics, Department of Chemistry, Biotechnology and Food Science, Eversole Associates, Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), University of Saskatchewan [Saskatoon] (U of S), Bayer Crop Science, Kansas State Univ, Dept Plant Pathol, Manhattan, KS 66506 USA, Partenaires INRAE, Department of Botany and Plant Sciences [Riverside], University of California [Riverside] (UC Riverside), University of California (UC)-University of California (UC), Graduate School of Agriculture, Kyoto University, Kyoto, Japan, Centre of the Region Haná for Biotechnological and Agricultural Research [Univ Palacký] (CRH), Faculty of Science [Univ Palacký], Palacky University Olomouc-Palacky University Olomouc-Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS), Centre of the Region Haná for Biotechnological and Agricultural Research, Fraunhofer Institute for Intelligent Analysis and Information Systems (Fraunhofer IAIS), Fraunhofer (Fraunhofer-Gesellschaft), National Research Centre Plant Biotechnology, Dept Plant Pathol, Kansas State University, Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bayer Cropscience, Institute of Crop Sciences of CAAS [Beijing] (ICS CAAS), Chinese Academy of Agricultural Sciences (CAAS), National Institute of Agrobiological Sciences (NIAS), National Institute of Agrobiological Sciences, Natl Inst Agrobiol Sci, JST-CREST, Japan Science and Technology Agency, Global Institute of Food Security, School of Agriculture and Food Sciences, Australian Centre for Plant Functional Genomics, University of Queensland [Brisbane], Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, The Sainsbury Laboratory [Norwich] (TSL), Genome Analysis Centre, John Innes Centre [Norwich], Biotechnology and Biological Sciences Research Council (BBSRC), European Synchrotron Radiation Facility (ESRF), German Research Center for Environmental Health - Helmholtz Center München (GmbH), MIPS/IBIS, Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben), DOE Joint Genome Institute [Walnut Creek], United States Department of Energy, The James Hutton Institute, Inst Bioinformat & Syst Biol, Munich Informat Ctr Prot Sequences, Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institute of Plant Biology, Universität Zürich [Zürich] = University of Zurich (UZH), Fac Engn & Nat Sci, Sabanci University [Istanbul], Genomics Research Centre, Consiglio per la Ricerca e Sperimentazione in Agricoltura, York University, Agriculture Victoria Research, Department of Economic Development, Jobs, Transport and Resources, AgriBio, Centre for Comparative Genomics, Murdoch University, CUBE Division of Computational Systems Biology, University of Vienna [Vienna], Department of Plant Pathology, Shizuoka University, Diversity Arrays Technology Pty Ltd (DArT P/L), Centre de Recherche de Chappes, BIOGEMMA, Research Council of Norway [199387], German Research Foundation (DFG) [SFB924], German Federal Ministry of Education and Research (BMBF), European Project: 283496,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2011-2,TRANSPLANT(2011), Helmholtz-Zentrum München (HZM), Univ Saskatchewan, Dept Plant Sci, Saskatoon, SK, Canada, University of California [Riverside] (UCR), University of California-University of California, Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, University of Saskatchewan, John Innes Centre, and University of Zurich

Subjects
MESH: Genome, Plant, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, [SDV]Life Sciences [q-bio], Gene Dosage, 01 natural sciences, Genome, MESH: Gene Dosage, Endosperm, Transcriptome, Gene Expression Regulation, Plant, Triticum, Cancer, Plant Proteins, International Wheat Genome Sequencing Consortium, 2. Zero hunger, Genetics, 0303 health sciences, Multidisciplinary, MESH: Plant Proteins, food and beverages, alignment, Bread, MESH: Edible Grain, starchy endosperm, reveals, Genome, Plant, Biotechnology, profiles, General Science & Technology, Cereals, MESH: Triticum, Biology, Gene dosage, MESH: Endosperm, Polyploidy, MESH: Bread, 03 medical and health sciences, Polyploid, MESH: Polyploidy, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], MD Multidisciplinary, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene family, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, MESH: Gene Expression Regulation, Plant, Gene, Metabolic and endocrine, 030304 developmental biology, Whole genome sequencing, triticum, MESH: Transcriptome, Human Genome, Plant, Gene Expression Regulation, germination, gene expression, RNA, identification, Edible Grain, protein, 010606 plant biology & botany
Abstract

Allohexaploid bread wheat ( Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type–specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type– and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.

Published
2014
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30. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Author

Mayer, Klaus F. X., Rogers, Jane, Jaroslav Dolezel, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam J., Sourdille, Pierre, Endo, Takashi R., Kubalakova, Marie, Cihalikova, Jarmila, Dubska, Zdenka, Vrana, Jan, Sperkova, Romana, Simkova, Hana, Febrer, Melanie, Clissold, Leah, Mclay, Kirsten, Singh, Kuldeep, Chhuneja, Parveen, Singh, Nagendra K., Khurana, Jitendra, Akhunov, Eduard, Choulet, Frederic, Alberti, Adriana, Barbe, Valerie, Wincker, Patrick, Kanamori, Hiroyuki, Kobayashi, Fuminori, Itoh, Takeshi, Matsumoto, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, Wu, Jianzhong, Ogihara, Yasunari, Handa, Hirokazu, Maclachlan, P. Ron, Sharpe, Andrew, Klassen, Darrin, Edwards, David, Batley, Jacqueline, Olsen, Odd-Arne, Sandve, Simen Rod, Lien, Sigbjorn, Steuernagel, Burkhard, Wulff, Brande, Caccamo, Mario, Ayling, Sarah, Ramirez-Gonzalez, Ricardo H., Clavijo, Bernardo J., Wright, Jonathan, Pfeifer, Matthias, Spannagl, Manuel, Martis, Mihaela M., Mascher, Martin, Chapman, Jarrod, Poland, Jesse A., Scholz, Uwe, Barry, Kerrie, Waugh, Robbie, Rokhsar, Daniel S., Muehlbauer, Gary J., Stein, Nils, Gundlach, Heidrun, Zytnicki, Matthias, Jamilloux, Veronique, Quesneville, Hadi, Wicker, Thomas, Faccioli, Primetta, Colaiacovo, Moreno, Stanca, Antonio Michele, Budak, Hikmet, Cattivelli, Luigi, Glover, Natasha, Pingault, Lise, Paux, Etienne, Sharma, Sapna, Appels, Rudi, Bellgard, Matthew, Chapman, Brett, Nussbaumer, Thomas, Bader, Kai Christian, Rimbert, Helene, Wang, Shichen, Knox, Ron, Kilian, Andrzej, Alaux, Michael, Alfama, Francoise, Couderc, Loic, Guilhot, Nicolas, Viseux, Claire, Loaec, Mikael, Keller, Beat, Praud, Sebastien, and IWGSC

31. The Repetitive Landscape of the Barley Genome

Author

Heidrun Gundlach, Alan H. Schulman, Thomas Wicker, Stein, Nils, Muehlbauer, Gary J., Institute of Biotechnology, and Doctoral Programme in Plant Sciences

Subjects
0106 biological sciences, 0301 basic medicine, 2. Zero hunger, Transposable element, food and beverages, Chromosome, Promoter, Biology, 01 natural sciences, Genome, 03 medical and health sciences, chemistry.chemical_compound, genomic DNA, 030104 developmental biology, chemistry, Evolutionary biology, Sequence motif, Gene, 1183 Plant biology, microbiology, virology, DNA, 010606 plant biology & botany
Abstract

While transposable elements (TEs) comprise the bulk of plant genomic DNA, how they contribute to genome structure and organization is still poorly understood. Especially, in large genomes where TEs make the majority of genomic DNA, it is still unclear whether TEs target specific chromosomal regions or whether they simply accumulate where they are best tolerated. The barley genome with its vast repetitive fraction is an ideal system to study chromosomal organization and evolution of TEs. Genes make only about 2% of the genome, while over 80% is derived from TEs. The TE fraction is composed of at least 350 different families. However, 50% of the genome is comprised of only 15 high-copy TE families, while all other TE families are present in moderate or low-copy numbers. The barley genome is highly compartmentalized with different types of TEs occupying different chromosomal “niches”, such as distal, interstitial or proximal regions of chromosome arms. Furthermore, gene space represents its own distinct genomic compartment that is enriched in small non-autonomous DNA transposons, suggesting that these TEs specifically target promoters and downstream regions. Some TE families also show a strong preference to insert in specific sequence motifs which may, in part, explain their distribution. The family-specific distribution patterns result in distinct TE compositions of different chromosomal compartments.

Published
2018
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