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2. BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

Author

Staňková, Helena, Hastie, Alex, Chan, Saki, Vrána, Jan, Tulpová, Zuzana, Kubaláková, Marie, Visendi, Paul, Hayashi, Satomi, Luo, Mingcheng, Batley, Jacqueline, Edwards, David, Doležel, Jaroslav, and Šimková, Hana

Subjects
chromosomes, flow sorting, optical mapping, physical map, sequencing, wheat, Biotechnology, Chromosome Mapping, Chromosomes, Artificial, Bacterial, Chromosomes, Plant, Genome, Plant, Sequence Analysis, DNA, Tandem Repeat Sequences, Triticum
Abstract

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.

Published
2016

3. Chromosomal Genomics of Barley

Author

Šimková, Hana, Kubaláková, Marie, Vrána, Jan, Cápal, Petr, Doležel, Jaroslav, Kole, Chittaranjan, Series Editor, Stein, Nils, editor, and Muehlbauer, Gary J., editor

Published
2018
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4. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

Author

Consortium, The International Wheat Genome Sequencing, Mayer, Klaus FX, Rogers, Jane, Doležel, Jaroslav, Pozniak, Curtis, Eversole, Kellye, Feuillet, Catherine, Gill, Bikram, Friebe, Bernd, Lukaszewski, Adam J, Sourdille, Pierre, Endo, Takashi R, 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, Sandve, Simen Rød, Lien, Sigbjørn, 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, 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, Mikaël, Keller, Beat, and Praud, Sebastien

Subjects
Agricultural, Veterinary and Food Sciences, Biological Sciences, Genetics, Human Genome, Bread, Chromosomes, Plant, Evolution, Molecular, Gene Order, Genetic Variation, Genome, Plant, Molecular Sequence Annotation, Phylogeny, Plant Proteins, Polyploidy, Sequence Analysis, DNA, Transcriptome, Triticum, International Wheat Genome Sequencing Consortium, General Science & Technology
Abstract

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

Published
2014

5. A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS)

Author

Šimková, Hana, Šafář, Jan, Suchánková, Pavla, Kovářová, Pavlína, Bartoš, Jan, Kubaláková, Marie, Janda, Jaroslav, Číhalíková, Jarmila, Mago, Rohit, Lelley, Tamas, and Doležel, Jaroslav

Subjects
Biological Sciences, Genetics, Biotechnology, Human Genome, Chromosomes, Artificial, Bacterial, Chromosomes, Plant, DNA, Plant, Flow Cytometry, Genome, Plant, Genomic Library, In Situ Hybridization, Fluorescence, Karyotyping, Plant Diseases, Secale, Translocation, Genetic, Triticum, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics, Biological sciences, Biomedical and clinical sciences
Abstract

BackgroundGenomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C approximately 7,900 Mbp) with prevalence of DNA repeats (> 90%). An attractive possibility is to dissect the genome to small parts after flow sorting particular chromosomes and chromosome arms. To test this approach, we have chosen 1RS chromosome arm, which represents only 5.6% of the total rye genome. The 1RS arm is an attractive target as it carries many important genes and because it became part of the wheat gene pool as the 1BL.1RS translocation.ResultsWe demonstrate that it is possible to sort 1RS arm from wheat-rye ditelosomic addition line. Using this approach, we isolated over 10 million of 1RS arms using flow sorting and used their DNA to construct a 1RS-specific BAC library, which comprises 103,680 clones with average insert size of 73 kb. The library comprises two sublibraries constructed using HindIII and EcoRI and provides a deep coverage of about 14-fold of the 1RS arm (442 Mbp). We present preliminary results obtained during positional cloning of the stem rust resistance gene SrR, which confirm a potential of the library to speed up isolation of agronomically important genes by map-based cloning.ConclusionWe present a strategy that enables sorting short arms of several chromosomes of rye. Using flow-sorted chromosomes, we have constructed a deep coverage BAC library specific for the short arm of chromosome 1R (1RS). This is the first subgenomic BAC library available for rye and we demonstrate its potential for positional gene cloning. We expect that the library will facilitate development of a physical contig map of 1RS and comparative genomics of the homoeologous chromosome group 1 of wheat, barley and rye.

Published
2008

9. Chromosome Genomics in the Triticeae

Author

Doležel, Jaroslav, Šimková, Hana, Kubaláková, Marie, Šafář, Jan, Suchánková, Pavla, Číhalíková, Jarmila, Bartoš, Jan, Valárik, Miroslav, Muehlbauer, Gary J., editor, and Feuillet, Catherine, editor

Published
2009
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10. Flow Sorting and Sequencing Meadow Fescue Chromosome 4F

Author

Kopecký, David, Martis, Mihaela, Číhalíková, Jarmila, Hřibová, Eva, Vrána, Jan, Bartoš, Jan, Kopecká, Jitka, Cattonaro, Federica, Stočes, Štěpán, Novák, Petr, Neumann, Pavel, Macas, Jiří, Šimková, Hana, Studer, Bruno, Asp, Torben, Baird, James H., Navrátil, Petr, Karafiátová, Miroslava, Kubaláková, Marie, Šafář, Jan, Mayer, Klaus, and Doležel, Jaroslav

Published
2013

11. Reticulate Evolution of the Rye Genome

Author

Martis, Mihaela M., Zhou, Ruonan, Haseneyer, Grit, Schmutzer, Thomas, Vrána, Jan, Kubaláková, Marie, König, Susanne, Kugler, Karl G., Scholz, Uwe, Hackauf, Bernd, Korzun, Viktor, Schön, Chris-Carolin, Doležel, Jaroslav, Bauer, Eva, Mayer, Klaus F.X., and Stein, Nils

Published
2013

15. Flow Sorting Plant Chromosomes

Author

Vrána, Jan, primary, Cápal, Petr, additional, Číhalíková, Jarmila, additional, Kubaláková, Marie, additional, and Doležel, Jaroslav, additional

Published
2016
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17. Unlocking the Barley Genome by Chromosomal and Comparative Genomics

Author

Mayer, Klaus F.X., Martis, Mihaela, Hedley, Pete E., Šimková, Hana, Liu, Hui, Morris, Jenny A., Steuernagel, Burkhard, Taudien, Stefan, Roessner, Stephan, Gundlach, Heidrun, Kubaláková, Marie, Suchánková, Pavla, Murat, Florent, Felder, Marius, Nussbaumer, Thomas, Graner, Andreas, Salse, Jerome, Endo, Takashi, Sakai, Hiroaki, Tanaka, Tsuyoshi, ltoh, Takeshi, Sato, Kazuhiro, Platzer, Matthias, Matsumoto, Takashi, Scholz, Uwe, Doležel, Jaroslav, Waugh, Robbie, and Stein, Nils

Published
2011
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33. Flow Cytogenetics

Author

Doležel, Jaroslav, primary, Kubaláková, Marie, additional, Vrána, Jan, additional, and Bartoš, Jan, additional

Published
2004
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35. Sorting of plant chromosomes

Author

Doležel, Jaroslav, primary, Lysák, Martin A., additional, Kubaláková, Marie, additional, Šimková, Hana, additional, Macas, Jiří, additional, and Lucretti, Sergio, additional

Published
2001
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39. A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS)

Author

Číhalíková Jarmila, Janda Jaroslav, Kubaláková Marie, Bartoš Jan, Kovářová Pavlína, Suchánková Pavla, Šafář Jan, Šimková Hana, Mago Rohit, Lelley Tamas, and Doležel Jaroslav

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Genomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C~7,900 Mbp) with prevalence of DNA repeats (> 90%). An attractive possibility is to dissect the genome to small parts after flow sorting particular chromosomes and chromosome arms. To test this approach, we have chosen 1RS chromosome arm, which represents only 5.6% of the total rye genome. The 1RS arm is an attractive target as it carries many important genes and because it became part of the wheat gene pool as the 1BL.1RS translocation. Results We demonstrate that it is possible to sort 1RS arm from wheat-rye ditelosomic addition line. Using this approach, we isolated over 10 million of 1RS arms using flow sorting and used their DNA to construct a 1RS-specific BAC library, which comprises 103,680 clones with average insert size of 73 kb. The library comprises two sublibraries constructed using HindIII and EcoRI and provides a deep coverage of about 14-fold of the 1RS arm (442 Mbp). We present preliminary results obtained during positional cloning of the stem rust resistance gene SrR, which confirm a potential of the library to speed up isolation of agronomically important genes by map-based cloning. Conclusion We present a strategy that enables sorting short arms of several chromosomes of rye. Using flow-sorted chromosomes, we have constructed a deep coverage BAC library specific for the short arm of chromosome 1R (1RS). This is the first subgenomic BAC library available for rye and we demonstrate its potential for positional gene cloning. We expect that the library will facilitate development of a physical contig map of 1RS and comparative genomics of the homoeologous chromosome group 1 of wheat, barley and rye.

Published
2008
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40. Shifting the limits in wheat research and breeding using a fully annotated reference genome

Author

Appels, Rudi, Eversole, Kellye, Stein, Nils, Feuillet, Catherine, Keller, Beat, Rogers, Jane, Pozniak, Curtis J., Choulet, Frédéric, Distelfeld, Assaf, Poland, Jesse, Ronen, Gil, Sharpe, Andrew G., Barad, Omer, Baruch, Kobi, Keeble-gagnère, Gabriel, Mascher, Martin, Ben-zvi, Gil, Josselin, Ambre-aurore, Himmelbach, Axel, Balfourier, François, Gutierrez-gonzalez, Juan, Hayden, Matthew, Koh, Chushin, Muehlbauer, Gary, Pasam, Raj K., Paux, Etienne, Rigault, Philippe, Tibbits, Josquin, Tiwari, Vijay, Spannagl, Manuel, Lang, Daniel, Gundlach, Heidrun, Haberer, Georg, Mayer, Klaus F. X., Ormanbekova, Danara, Prade, Verena, Šimková, Hana, Wicker, Thomas, Swarbreck, David, Rimbert, Hélène, Felder, Marius, Guilhot, Nicolas, Kaithakottil, Gemy, Keilwagen, Jens, Leroy, Philippe, Lux, Thomas, Twardziok, Sven, Venturini, Luca, Juhász, Angéla, Abrouk, Michael, Fischer, Iris, Uauy, Cristobal, Borrill, Philippa, Ramirez-gonzalez, Ricardo H., Arnaud, Dominique, Chalabi, Smahane, Chalhoub, Boulos, Cory, Aron, Datla, Raju, Davey, Mark W., Jacobs, John, Robinson, Stephen J., Steuernagel, Burkhard, Van Ex, Fred, Wulff, Brande B. H., Benhamed, Moussa, Bendahmane, Abdelhafid, Concia, Lorenzo, Latrasse, David, Bartoš, Jan, Bellec, Arnaud, Berges, Hélène, Doležel, Jaroslav, Frenkel, Zeev, Gill, Bikram, Korol, Abraham, Letellier, Thomas, Olsen, Odd-arne, Singh, Kuldeep, Valárik, Miroslav, Van Der Vossen, Edwin, Vautrin, Sonia, Weining, Song, Fahima, Tzion, Glikson, Vladimir, Raats, Dina, Číhalíková, Jarmila, Toegelová, Helena, Vrána, Jan, Sourdille, Pierre, Darrier, Benoit, Barabaschi, Delfina, Cattivelli, Luigi, Hernandez, Pilar, Galvez, Sergio, Budak, Hikmet, Jones, Jonathan D. G., Witek, Kamil, Yu, Guotai, Small, Ian, Melonek, Joanna, Zhou, Ruonan, Belova, Tatiana, Kanyuka, Kostya, King, Robert, Nilsen, Kirby, Walkowiak, Sean, Cuthbert, Richard, Knox, Ron, Wiebe, Krysta, Xiang, Daoquan, Rohde, Antje, Golds, Timothy, Čížková, Jana, Akpinar, Bala Ani, Biyiklioglu, Sezgi, Gao, Liangliang, N’daiye, Amidou, Kubaláková, Marie, Šafář, Jan, Alfama, Françoise, Adam-blondon, Anne-françoise, Flores, Raphael, Guerche, Claire, Loaec, Mikaël, Quesneville, Hadi, Condie, Janet, Ens, Jennifer, Maclachlan, Ron, Tan, Yifang, Alberti, Adriana, Aury, Jean-marc, Barbe, Valérie, Couloux, Arnaud, Cruaud, Corinne, Labadie, Karine, Mangenot, Sophie, Wincker, Patrick, Kaur, Gaganpreet, Luo, Mingcheng, Sehgal, Sunish, Chhuneja, Parveen, Gupta, Om Prakash, Jindal, Suruchi, Kaur, Parampreet, Malik, Palvi, Sharma, Priti, Yadav, Bharat, Singh, Nagendra K., Khurana, Jitendra P., Chaudhary, Chanderkant, Khurana, Paramjit, Kumar, Vinod, Mahato, Ajay, Mathur, Saloni, Sevanthi, Amitha, Sharma, Naveen, Tomar, Ram Sewak, Holušová, Kateřina, Plíhal, Ondřej, Clark, Matthew D., Heavens, Darren, Kettleborough, George, Wright, Jon, Balcárková, Barbora, Hu, Yuqin, Salina, Elena, Ravin, Nikolai, Skryabin, Konstantin, Beletsky, Alexey, Kadnikov, Vitaly, Mardanov, Andrey, Nesterov, Michail, Rakitin, Andrey, Sergeeva, Ekaterina, Handa, Hirokazu, Kanamori, Hiroyuki, Katagiri, Satoshi, Kobayashi, Fuminori, Nasuda, Shuhei, Tanaka, Tsuyoshi, Wu, Jianzhong, Cattonaro, Federica, Jiumeng, Min, Kugler, Karl, Pfeifer, Matthias, Sandve, Simen, Xun, Xu, Zhan, Bujie, Batley, Jacqueline, Bayer, Philipp E., Edwards, David, Hayashi, Satomi, Tulpová, Zuzana, Visendi, Paul, Cui, Licao, Du, Xianghong, Feng, Kewei, Nie, Xiaojun, Tong, Wei, Wang, Le, Appels, Rudi, Eversole, Kellye, Stein, Nils, Feuillet, Catherine, Keller, Beat, Rogers, Jane, Pozniak, Curtis J., Choulet, Frédéric, Distelfeld, Assaf, Poland, Jesse, Ronen, Gil, Sharpe, Andrew G., Barad, Omer, Baruch, Kobi, Keeble-gagnère, Gabriel, Mascher, Martin, Ben-zvi, Gil, Josselin, Ambre-aurore, Himmelbach, Axel, Balfourier, François, Gutierrez-gonzalez, Juan, Hayden, Matthew, Koh, Chushin, Muehlbauer, Gary, Pasam, Raj K., Paux, Etienne, Rigault, Philippe, Tibbits, Josquin, Tiwari, Vijay, Spannagl, Manuel, Lang, Daniel, Gundlach, Heidrun, Haberer, Georg, Mayer, Klaus F. X., Ormanbekova, Danara, Prade, Verena, Šimková, Hana, Wicker, Thomas, Swarbreck, David, Rimbert, Hélène, Felder, Marius, Guilhot, Nicolas, Kaithakottil, Gemy, Keilwagen, Jens, Leroy, Philippe, Lux, Thomas, Twardziok, Sven, Venturini, Luca, Juhász, Angéla, Abrouk, Michael, Fischer, Iris, Uauy, Cristobal, Borrill, Philippa, Ramirez-gonzalez, Ricardo H., Arnaud, Dominique, Chalabi, Smahane, Chalhoub, Boulos, Cory, Aron, Datla, Raju, Davey, Mark W., Jacobs, John, Robinson, Stephen J., Steuernagel, Burkhard, Van Ex, Fred, Wulff, Brande B. H., Benhamed, Moussa, Bendahmane, Abdelhafid, Concia, Lorenzo, Latrasse, David, Bartoš, Jan, Bellec, Arnaud, Berges, Hélène, Doležel, Jaroslav, Frenkel, Zeev, Gill, Bikram, Korol, Abraham, Letellier, Thomas, Olsen, Odd-arne, Singh, Kuldeep, Valárik, Miroslav, Van Der Vossen, Edwin, Vautrin, Sonia, Weining, Song, Fahima, Tzion, Glikson, Vladimir, Raats, Dina, Číhalíková, Jarmila, Toegelová, Helena, Vrána, Jan, Sourdille, Pierre, Darrier, Benoit, Barabaschi, Delfina, Cattivelli, Luigi, Hernandez, Pilar, Galvez, Sergio, Budak, Hikmet, Jones, Jonathan D. G., Witek, Kamil, Yu, Guotai, Small, Ian, Melonek, Joanna, Zhou, Ruonan, Belova, Tatiana, Kanyuka, Kostya, King, Robert, Nilsen, Kirby, Walkowiak, Sean, Cuthbert, Richard, Knox, Ron, Wiebe, Krysta, Xiang, Daoquan, Rohde, Antje, Golds, Timothy, Čížková, Jana, Akpinar, Bala Ani, Biyiklioglu, Sezgi, Gao, Liangliang, N’daiye, Amidou, Kubaláková, Marie, Šafář, Jan, Alfama, Françoise, Adam-blondon, Anne-françoise, Flores, Raphael, Guerche, Claire, Loaec, Mikaël, Quesneville, Hadi, Condie, Janet, Ens, Jennifer, Maclachlan, Ron, Tan, Yifang, Alberti, Adriana, Aury, Jean-marc, Barbe, Valérie, Couloux, Arnaud, Cruaud, Corinne, Labadie, Karine, Mangenot, Sophie, Wincker, Patrick, Kaur, Gaganpreet, Luo, Mingcheng, Sehgal, Sunish, Chhuneja, Parveen, Gupta, Om Prakash, Jindal, Suruchi, Kaur, Parampreet, Malik, Palvi, Sharma, Priti, Yadav, Bharat, Singh, Nagendra K., Khurana, Jitendra P., Chaudhary, Chanderkant, Khurana, Paramjit, Kumar, Vinod, Mahato, Ajay, Mathur, Saloni, Sevanthi, Amitha, Sharma, Naveen, Tomar, Ram Sewak, Holušová, Kateřina, Plíhal, Ondřej, Clark, Matthew D., Heavens, Darren, Kettleborough, George, Wright, Jon, Balcárková, Barbora, Hu, Yuqin, Salina, Elena, Ravin, Nikolai, Skryabin, Konstantin, Beletsky, Alexey, Kadnikov, Vitaly, Mardanov, Andrey, Nesterov, Michail, Rakitin, Andrey, Sergeeva, Ekaterina, Handa, Hirokazu, Kanamori, Hiroyuki, Katagiri, Satoshi, Kobayashi, Fuminori, Nasuda, Shuhei, Tanaka, Tsuyoshi, Wu, Jianzhong, Cattonaro, Federica, Jiumeng, Min, Kugler, Karl, Pfeifer, Matthias, Sandve, Simen, Xun, Xu, Zhan, Bujie, Batley, Jacqueline, Bayer, Philipp E., Edwards, David, Hayashi, Satomi, Tulpová, Zuzana, Visendi, Paul, Cui, Licao, Du, Xianghong, Feng, Kewei, Nie, Xiaojun, Tong, Wei, and Wang, Le

Abstract

Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat.

Published
2018

42. Additional file 3: Figure S1. of Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order

Author

Xiao, Jin, Keli Dai, Fu, Lian, Vrána, Jan, Kubaláková, Marie, Wentao Wan, Haojie Sun, Zhao, Jing, Chunyan Yu, Yufeng Wu, Abrouk, Michael, Haiyan Wang, Doležel, Jaroslav, and Xiue Wang

Subjects
food and beverages
Abstract

Sequence length distribution of 1977 genes of H. villosa chromosome 4VS. Figure S2. Percentage distribution of the GO entries for H. villosa 4VS genes. The most represented entries within the three ontologies (Molecular function, Biological process and Cellular component) are indicated. Figure S3. Synteny between chromosomes of H. villosa and other species. (A) Conservation of synteny between H. villosa chromosome 4VS and Brachypodium (B. distachyon), rice (Oryza sativa) and sorghum (Sorghum bicolor). (B) Conservation of synteny between H. villosa chromosome 4VS and wheat chromosome 4A, 4B and 4D. The Venn diagrams display the numbers of genes shared between 4VS and one reference genome (outer cycle), and the number of shared conserved genes among the three grass genomes (inner cycle). Figure S4. Comparison of the 4VS genome zipper based on Brachypodium chromosomes 1 and 4 with Ae. tauschii chromosome 4D. Y-axis: the virtual 4VS gene order is marked from 1 to 785; X-axis: the corresponding scaffold in bins. (PPTX 966 kb)

Published
2017
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44. Sequencing flow-sorted short arm of Haynaldia villosa chromosome 4V provides insights into its molecular structure and virtual gene order

Author

Xiao, Jin, primary, Dai, Keli, additional, Fu, Lian, additional, Vrána, Jan, additional, Kubaláková, Marie, additional, Wan, Wentao, additional, Sun, Haojie, additional, Zhao, Jing, additional, Yu, Chunyan, additional, Wu, Yufeng, additional, Abrouk, Michael, additional, Wang, Haiyan, additional, Doležel, Jaroslav, additional, and Wang, Xiue, additional

Published
2017
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45. Rapid gene isolation in barley and wheat by mutant chromosome sequencing

Author

Sánchez-Martín, Javier, Steuernagel, Burkhard, Ghosh, Sreya, Herren, Gerhard, Hurni, Severine, Adamski, Nikolai, Vrána, Jan, Kubaláková, Marie, Krattinger, Simon G, Wicker, Thomas, Doležel, Jaroslav, Keller, Beat, Wulff, Brande B H, Sánchez-Martín, Javier, Steuernagel, Burkhard, Ghosh, Sreya, Herren, Gerhard, Hurni, Severine, Adamski, Nikolai, Vrána, Jan, Kubaláková, Marie, Krattinger, Simon G, Wicker, Thomas, Doležel, Jaroslav, Keller, Beat, and Wulff, Brande B H

Abstract

Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to parental chromosomes. We apply MutChromSeq to six mutants each of the barley Eceriferum-q gene and the wheat Pm2 genes. This approach unambiguously identified single candidate genes that were verified by Sanger sequencing of additional mutants. MutChromSeq enables reference-free forward genetics in barley and wheat, thus opening up their pan-genomes to functional genomics.

Published
2016

46. 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

47. Rapid gene isolation in barley and wheat by mutant chromosome sequencing

Author

Sánchez-Martín, Javier, primary, Steuernagel, Burkhard, additional, Ghosh, Sreya, additional, Herren, Gerhard, additional, Hurni, Severine, additional, Adamski, Nikolai, additional, Vrána, Jan, additional, Kubaláková, Marie, additional, Krattinger, Simon G., additional, Wicker, Thomas, additional, Doležel, Jaroslav, additional, Keller, Beat, additional, and Wulff, Brande B. H., additional

Published
2016
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50. A haplotype specific to North European wheat (Triticum aestivum L.)

Author

Tsõmbalova, Jelena, primary, Karafiátová, Miroslava, additional, Vrána, Jan, additional, Kubaláková, Marie, additional, Peuša, Hilma, additional, Jakobson, Irena, additional, Järve, Mari, additional, Valárik, Miroslav, additional, Doležel, Jaroslav, additional, and Järve, Kadri, additional

Published
2016
Full Text
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