Shifting the limits in wheat research and breeding using a fully annotated reference genome
Publication Date: |
2018-08-17
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Publisher: |
American Association for the Advancement of Science (AAAS)
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Print ISSN: |
0036-8075
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Electronic ISSN: |
1095-9203
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Topics: |
Biology
Chemistry and Pharmacology
Geosciences
Computer Science
Medicine
Natural Sciences in General
Physics
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Keywords: |
Botany, Ecology, Online Only
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Published by: |
_version_ | 1836399030294282240 |
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autor | The International Wheat Genome Sequencing Consortium (IWGSC), IWGSC Ref; Seq principal investigators:, Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., IWGSC whole-genome assembly principal investigators:, Pozniak, C. J., Stein, N., Choulet, F., Distelfeld, A., Eversole, K., Poland, J., Rogers, J., Ronen, G., Sharpe, A. G., Whole-genome sequencing and assembly:, Pozniak, C., Ronen, G., Stein, N., Barad, O., Baruch, K., Choulet, F., Keeble-Gagnere, G., Mascher, M., Sharpe, A. G., Ben-Zvi, G., Josselin, A.-A., Hi-C data-based scaffolding:, Stein, N., Mascher, M., Himmelbach, A., Whole-genome assembly quality control and analyses:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Rogers, J., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Josselin, A.-A., Koh, C., Muehlbauer, G., Pasam, R. K., Paux, E., Pozniak, C. J., Rigault, P., Sharpe, A. G., Tibbits, J., Tiwari, V., Pseudomolecule assembly:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Josselin, A.-A., Rogers, J., Ref; Seq genome structure and gene analyses:, Spannagl, M., Choulet, F., Lang, D., Gundlach, H., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Ormanbekova, D., Paux, E., Prade, V., Simkova, H., Wicker, T., Automated annotation:, Choulet, F., Spannagl, M., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Gundlach, H., Haberer, G., Kaithakottil, G., Keilwagen, J., Lang, D., Leroy, P., Lux, T., Mayer, K. F. X., Twardziok, S., Venturini, L., Manual gene curation:, Appels, R., Rimbert, H., Choulet, F., Juhasz, A., Keeble-Gagnere, G., Subgenome comparative analyses:, Choulet, F., Spannagl, M., Lang, D., Abrouk, M., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Wicker, T., Transposable elements:, Choulet, F., Wicker, T., Gundlach, H., Lang, D., Spannagl, M., Phylogenomic analyses:, Lang, D., Spannagl, M., Appels, R., Fischer, I., Transcriptome analyses and RNA-seq data:, Uauy, C., Borrill, P., Ramirez-Gonzalez, R. H., Appels, R., Arnaud, D., Chalabi, S., Chalhoub, B., Choulet, F., Cory, A., Datla, R., Davey, M. W., Hayden, M., Jacobs, J., Lang, D., Robinson, S. J., Spannagl, M., Steuernagel, B., Tibbits, J., Tiwari, V., van Ex, F., Wulff, B. B. H., Whole-genome methylome:, Pozniak, C. J., Robinson, S. J., Sharpe, A. G., Cory, A., Histone mark analyses:, Benhamed, M., Paux, E., Bendahmane, A., Concia, L., Latrasse, D., BAC chromosome MTP IWGSC-Bayer Whole-Genome Profiling (WGP) tags:, Rogers, J., Jacobs, J., Alaux, M., Appels, R., Bartos, J., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O.-A., Simkova, H., Singh, K., Valarik, M., van der Vossen, E., Vautrin, S., Weining, S., Chromosome LTC mapping and physical mapping quality control:, Korol, A., Frenkel, Z., Fahima, T., Glikson, V., Raats, D., Rogers, J., RH mapping:, Tiwari, V., Gill, B., Paux, E., Poland, J., Optical mapping:, Dolezel, J., Cihalikova, J., Simkova, H., Toegelova, H., Vrana, J., Recombination analyses:, Sourdille, P., Darrier, B., Gene family analyses:, Appels, R., Spannagl, M., Lang, D., Fischer, I., Ormanbekova, D., Prade, V., CBF gene family:, Barabaschi, D., Cattivelli, L., Dehydrin gene family:, Hernandez, P., Galvez, S., Budak, H., NLR gene family:, Steuernagel, B., Jones, J. D. G., Witek, K., Wulff, B. B. H., Yu, G., PPR gene family:, Small, I., Melonek, J., Zhou, R., Prolamin gene family:, Juhasz, A., Belova, T., Appels, R., Olsen, O.-A., WAK gene family:, Kanyuka, K., King, R., Stem solidness (SSt1) QTL team:, Nilsen, K., Walkowiak, S., Pozniak, C. J., Cuthbert, R., Datla, R., Knox, R., Wiebe, K., Xiang, D., Flowering locus C (FLC) gene team:, Rohde, A., Golds, T., Genome size analysis:, Dolezel, J., Cizkova, J., Tibbits, J., Micro; RNA and t; RNA annotation:, Budak, H., Akpinar, B. A., Biyiklioglu, S., Genetic maps and mapping:, Muehlbauer, G., Poland, J., Gao, L., Gutierrez-Gonzalez, J., NDaiye, A., BAC libraries and chromosome sorting:, Dolezel, J., Simkova, H., Cihalikova, J., Kubalakova, M., Safar, J., Vrana, J., BAC pooling, BAC library repository, and access:, Berges, H., Bellec, A., Vautrin, S., IWGSC sequence and data repository and access:, Alaux, M., Alfama, F., Adam-Blondon, A.-F., Flores, R., Guerche, C., Letellier, T., Loaec, M., Quesneville, H., Physical maps and BAC-based sequences:, 1; A BAC sequencing and assembly:, Pozniak, C. J., Sharpe, A. G., Walkowiak, S., Budak, H., Condie, J., Ens, J., Koh, C., Maclachlan, R., Tan, Y., Wicker, T., 1; B BAC sequencing and assembly:, Choulet, F., Paux, E., Alberti, A., Aury, J.-M., Balfourier, F., Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., 1; D, 4; D, and 6; D physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 2; AL physical mapping:, Singh, K., Chhuneja, P., Gupta, O. P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., 2; AS physical mapping:, Singh, N. K., Khurana, J., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R. S., 2; B, 2; D, 4; B, 5; BL, and 5; DL IWGSC-Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers, J., Jacobs, J., Alaux, M., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., van der Vossen, E., Vautrin, S., 3; AL physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 3; DS physical mapping and BAC sequencing and assembly:, Bartos, J., Holusova, K., Plihal, O., 3; DL BAC sequencing and assembly:, Clark, M. D., Heavens, D., Kettleborough, G., Wright, J., 4; A physical mapping, BAC sequencing, assembly, and annotation:, Valarik, M., Abrouk, M., Balcarkova, B., Holusova, K., Hu, Y., Luo, M., 5; BS BAC sequencing and assembly:, Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., 6; B BAC sequencing and assembly:, Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., 7; A physical mapping and BAC sequencing:, Appels, R., Hayden, M., Keeble-Gagnere, G., Rigault, P., Tibbits, J., 7; B physical mapping, BAC sequencing, and assembly:, Olsen, O.-A., Belova, T., Cattonaro, F., Jiumeng, M., Kugler, K., Mayer, K. F. X., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., 7; DS BAC sequencing and assembly:, Simkova, H., Abrouk, M., Batley, J., Bayer, P. E., Edwards, D., Hayashi, S., Toegelova, H., Tulpova, Z., Visendi, P., 7; DL physical mapping and BAC sequencing:, Weining, S., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Figures:, Borrill, P., Gundlach, H., Galvez, S., Kaithakottil, G., Lang, D., Lux, T., Mascher, M., Ormanbekova, D., Prade, V., Ramirez-Gonzalez, R. H., Spannagl, M., Stein, N., Uauy, C., Venturini, L., Manuscript writing team:, Stein, N., Appels, R., Eversole, K., Rogers, J., Borrill, P., Cattivelli, L., Choulet, F., Hernandez, P., Kanyuka, K., Lang, D., Mascher, M., Nilsen, K., Paux, E., Pozniak, C. J., Ramirez-Gonzalez, R. H., Simkova, H., Small, I., Spannagl, M., Swarbreck, D., Uauy, C. |
beschreibung | An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. |
citation_standardnr | 6320909 |
datenlieferant | ipn_articles |
feed_id | 25 |
feed_publisher | American Association for the Advancement of Science (AAAS) |
feed_publisher_url | http://www.aaas.org/ |
insertion_date | 2018-08-17 |
journaleissn | 1095-9203 |
journalissn | 0036-8075 |
publikationsjahr_anzeige | 2018 |
publikationsjahr_facette | 2018 |
publikationsjahr_intervall | 7984:2015-2019 |
publikationsjahr_sort | 2018 |
publisher | American Association for the Advancement of Science (AAAS) |
quelle | Science |
relation | http://science.sciencemag.org/cgi/content/short/361/6403/eaar7191?rss=1 |
schlagwort | Botany, Ecology, Online Only |
search_space | articles |
shingle_author_1 | The International Wheat Genome Sequencing Consortium (IWGSC), IWGSC Ref; Seq principal investigators:, Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., IWGSC whole-genome assembly principal investigators:, Pozniak, C. J., Stein, N., Choulet, F., Distelfeld, A., Eversole, K., Poland, J., Rogers, J., Ronen, G., Sharpe, A. G., Whole-genome sequencing and assembly:, Pozniak, C., Ronen, G., Stein, N., Barad, O., Baruch, K., Choulet, F., Keeble-Gagnere, G., Mascher, M., Sharpe, A. G., Ben-Zvi, G., Josselin, A.-A., Hi-C data-based scaffolding:, Stein, N., Mascher, M., Himmelbach, A., Whole-genome assembly quality control and analyses:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Rogers, J., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Josselin, A.-A., Koh, C., Muehlbauer, G., Pasam, R. K., Paux, E., Pozniak, C. J., Rigault, P., Sharpe, A. G., Tibbits, J., Tiwari, V., Pseudomolecule assembly:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Josselin, A.-A., Rogers, J., Ref; Seq genome structure and gene analyses:, Spannagl, M., Choulet, F., Lang, D., Gundlach, H., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Ormanbekova, D., Paux, E., Prade, V., Simkova, H., Wicker, T., Automated annotation:, Choulet, F., Spannagl, M., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Gundlach, H., Haberer, G., Kaithakottil, G., Keilwagen, J., Lang, D., Leroy, P., Lux, T., Mayer, K. F. X., Twardziok, S., Venturini, L., Manual gene curation:, Appels, R., Rimbert, H., Choulet, F., Juhasz, A., Keeble-Gagnere, G., Subgenome comparative analyses:, Choulet, F., Spannagl, M., Lang, D., Abrouk, M., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Wicker, T., Transposable elements:, Choulet, F., Wicker, T., Gundlach, H., Lang, D., Spannagl, M., Phylogenomic analyses:, Lang, D., Spannagl, M., Appels, R., Fischer, I., Transcriptome analyses and RNA-seq data:, Uauy, C., Borrill, P., Ramirez-Gonzalez, R. H., Appels, R., Arnaud, D., Chalabi, S., Chalhoub, B., Choulet, F., Cory, A., Datla, R., Davey, M. W., Hayden, M., Jacobs, J., Lang, D., Robinson, S. J., Spannagl, M., Steuernagel, B., Tibbits, J., Tiwari, V., van Ex, F., Wulff, B. B. H., Whole-genome methylome:, Pozniak, C. J., Robinson, S. J., Sharpe, A. G., Cory, A., Histone mark analyses:, Benhamed, M., Paux, E., Bendahmane, A., Concia, L., Latrasse, D., BAC chromosome MTP IWGSC-Bayer Whole-Genome Profiling (WGP) tags:, Rogers, J., Jacobs, J., Alaux, M., Appels, R., Bartos, J., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O.-A., Simkova, H., Singh, K., Valarik, M., van der Vossen, E., Vautrin, S., Weining, S., Chromosome LTC mapping and physical mapping quality control:, Korol, A., Frenkel, Z., Fahima, T., Glikson, V., Raats, D., Rogers, J., RH mapping:, Tiwari, V., Gill, B., Paux, E., Poland, J., Optical mapping:, Dolezel, J., Cihalikova, J., Simkova, H., Toegelova, H., Vrana, J., Recombination analyses:, Sourdille, P., Darrier, B., Gene family analyses:, Appels, R., Spannagl, M., Lang, D., Fischer, I., Ormanbekova, D., Prade, V., CBF gene family:, Barabaschi, D., Cattivelli, L., Dehydrin gene family:, Hernandez, P., Galvez, S., Budak, H., NLR gene family:, Steuernagel, B., Jones, J. D. G., Witek, K., Wulff, B. B. H., Yu, G., PPR gene family:, Small, I., Melonek, J., Zhou, R., Prolamin gene family:, Juhasz, A., Belova, T., Appels, R., Olsen, O.-A., WAK gene family:, Kanyuka, K., King, R., Stem solidness (SSt1) QTL team:, Nilsen, K., Walkowiak, S., Pozniak, C. J., Cuthbert, R., Datla, R., Knox, R., Wiebe, K., Xiang, D., Flowering locus C (FLC) gene team:, Rohde, A., Golds, T., Genome size analysis:, Dolezel, J., Cizkova, J., Tibbits, J., Micro; RNA and t; RNA annotation:, Budak, H., Akpinar, B. A., Biyiklioglu, S., Genetic maps and mapping:, Muehlbauer, G., Poland, J., Gao, L., Gutierrez-Gonzalez, J., NDaiye, A., BAC libraries and chromosome sorting:, Dolezel, J., Simkova, H., Cihalikova, J., Kubalakova, M., Safar, J., Vrana, J., BAC pooling, BAC library repository, and access:, Berges, H., Bellec, A., Vautrin, S., IWGSC sequence and data repository and access:, Alaux, M., Alfama, F., Adam-Blondon, A.-F., Flores, R., Guerche, C., Letellier, T., Loaec, M., Quesneville, H., Physical maps and BAC-based sequences:, 1; A BAC sequencing and assembly:, Pozniak, C. J., Sharpe, A. G., Walkowiak, S., Budak, H., Condie, J., Ens, J., Koh, C., Maclachlan, R., Tan, Y., Wicker, T., 1; B BAC sequencing and assembly:, Choulet, F., Paux, E., Alberti, A., Aury, J.-M., Balfourier, F., Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., 1; D, 4; D, and 6; D physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 2; AL physical mapping:, Singh, K., Chhuneja, P., Gupta, O. P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., 2; AS physical mapping:, Singh, N. K., Khurana, J., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R. S., 2; B, 2; D, 4; B, 5; BL, and 5; DL IWGSC-Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers, J., Jacobs, J., Alaux, M., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., van der Vossen, E., Vautrin, S., 3; AL physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 3; DS physical mapping and BAC sequencing and assembly:, Bartos, J., Holusova, K., Plihal, O., 3; DL BAC sequencing and assembly:, Clark, M. D., Heavens, D., Kettleborough, G., Wright, J., 4; A physical mapping, BAC sequencing, assembly, and annotation:, Valarik, M., Abrouk, M., Balcarkova, B., Holusova, K., Hu, Y., Luo, M., 5; BS BAC sequencing and assembly:, Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., 6; B BAC sequencing and assembly:, Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., 7; A physical mapping and BAC sequencing:, Appels, R., Hayden, M., Keeble-Gagnere, G., Rigault, P., Tibbits, J., 7; B physical mapping, BAC sequencing, and assembly:, Olsen, O.-A., Belova, T., Cattonaro, F., Jiumeng, M., Kugler, K., Mayer, K. F. X., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., 7; DS BAC sequencing and assembly:, Simkova, H., Abrouk, M., Batley, J., Bayer, P. E., Edwards, D., Hayashi, S., Toegelova, H., Tulpova, Z., Visendi, P., 7; DL physical mapping and BAC sequencing:, Weining, S., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Figures:, Borrill, P., Gundlach, H., Galvez, S., Kaithakottil, G., Lang, D., Lux, T., Mascher, M., Ormanbekova, D., Prade, V., Ramirez-Gonzalez, R. H., Spannagl, M., Stein, N., Uauy, C., Venturini, L., Manuscript writing team:, Stein, N., Appels, R., Eversole, K., Rogers, J., Borrill, P., Cattivelli, L., Choulet, F., Hernandez, P., Kanyuka, K., Lang, D., Mascher, M., Nilsen, K., Paux, E., Pozniak, C. J., Ramirez-Gonzalez, R. H., Simkova, H., Small, I., Spannagl, M., Swarbreck, D., Uauy, C. |
shingle_author_2 | The International Wheat Genome Sequencing Consortium (IWGSC), IWGSC Ref; Seq principal investigators:, Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., IWGSC whole-genome assembly principal investigators:, Pozniak, C. J., Stein, N., Choulet, F., Distelfeld, A., Eversole, K., Poland, J., Rogers, J., Ronen, G., Sharpe, A. G., Whole-genome sequencing and assembly:, Pozniak, C., Ronen, G., Stein, N., Barad, O., Baruch, K., Choulet, F., Keeble-Gagnere, G., Mascher, M., Sharpe, A. G., Ben-Zvi, G., Josselin, A.-A., Hi-C data-based scaffolding:, Stein, N., Mascher, M., Himmelbach, A., Whole-genome assembly quality control and analyses:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Rogers, J., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Josselin, A.-A., Koh, C., Muehlbauer, G., Pasam, R. K., Paux, E., Pozniak, C. J., Rigault, P., Sharpe, A. G., Tibbits, J., Tiwari, V., Pseudomolecule assembly:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Josselin, A.-A., Rogers, J., Ref; Seq genome structure and gene analyses:, Spannagl, M., Choulet, F., Lang, D., Gundlach, H., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Ormanbekova, D., Paux, E., Prade, V., Simkova, H., Wicker, T., Automated annotation:, Choulet, F., Spannagl, M., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Gundlach, H., Haberer, G., Kaithakottil, G., Keilwagen, J., Lang, D., Leroy, P., Lux, T., Mayer, K. F. X., Twardziok, S., Venturini, L., Manual gene curation:, Appels, R., Rimbert, H., Choulet, F., Juhasz, A., Keeble-Gagnere, G., Subgenome comparative analyses:, Choulet, F., Spannagl, M., Lang, D., Abrouk, M., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Wicker, T., Transposable elements:, Choulet, F., Wicker, T., Gundlach, H., Lang, D., Spannagl, M., Phylogenomic analyses:, Lang, D., Spannagl, M., Appels, R., Fischer, I., Transcriptome analyses and RNA-seq data:, Uauy, C., Borrill, P., Ramirez-Gonzalez, R. H., Appels, R., Arnaud, D., Chalabi, S., Chalhoub, B., Choulet, F., Cory, A., Datla, R., Davey, M. W., Hayden, M., Jacobs, J., Lang, D., Robinson, S. J., Spannagl, M., Steuernagel, B., Tibbits, J., Tiwari, V., van Ex, F., Wulff, B. B. H., Whole-genome methylome:, Pozniak, C. J., Robinson, S. J., Sharpe, A. G., Cory, A., Histone mark analyses:, Benhamed, M., Paux, E., Bendahmane, A., Concia, L., Latrasse, D., BAC chromosome MTP IWGSC-Bayer Whole-Genome Profiling (WGP) tags:, Rogers, J., Jacobs, J., Alaux, M., Appels, R., Bartos, J., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O.-A., Simkova, H., Singh, K., Valarik, M., van der Vossen, E., Vautrin, S., Weining, S., Chromosome LTC mapping and physical mapping quality control:, Korol, A., Frenkel, Z., Fahima, T., Glikson, V., Raats, D., Rogers, J., RH mapping:, Tiwari, V., Gill, B., Paux, E., Poland, J., Optical mapping:, Dolezel, J., Cihalikova, J., Simkova, H., Toegelova, H., Vrana, J., Recombination analyses:, Sourdille, P., Darrier, B., Gene family analyses:, Appels, R., Spannagl, M., Lang, D., Fischer, I., Ormanbekova, D., Prade, V., CBF gene family:, Barabaschi, D., Cattivelli, L., Dehydrin gene family:, Hernandez, P., Galvez, S., Budak, H., NLR gene family:, Steuernagel, B., Jones, J. D. G., Witek, K., Wulff, B. B. H., Yu, G., PPR gene family:, Small, I., Melonek, J., Zhou, R., Prolamin gene family:, Juhasz, A., Belova, T., Appels, R., Olsen, O.-A., WAK gene family:, Kanyuka, K., King, R., Stem solidness (SSt1) QTL team:, Nilsen, K., Walkowiak, S., Pozniak, C. J., Cuthbert, R., Datla, R., Knox, R., Wiebe, K., Xiang, D., Flowering locus C (FLC) gene team:, Rohde, A., Golds, T., Genome size analysis:, Dolezel, J., Cizkova, J., Tibbits, J., Micro; RNA and t; RNA annotation:, Budak, H., Akpinar, B. A., Biyiklioglu, S., Genetic maps and mapping:, Muehlbauer, G., Poland, J., Gao, L., Gutierrez-Gonzalez, J., NDaiye, A., BAC libraries and chromosome sorting:, Dolezel, J., Simkova, H., Cihalikova, J., Kubalakova, M., Safar, J., Vrana, J., BAC pooling, BAC library repository, and access:, Berges, H., Bellec, A., Vautrin, S., IWGSC sequence and data repository and access:, Alaux, M., Alfama, F., Adam-Blondon, A.-F., Flores, R., Guerche, C., Letellier, T., Loaec, M., Quesneville, H., Physical maps and BAC-based sequences:, 1; A BAC sequencing and assembly:, Pozniak, C. J., Sharpe, A. G., Walkowiak, S., Budak, H., Condie, J., Ens, J., Koh, C., Maclachlan, R., Tan, Y., Wicker, T., 1; B BAC sequencing and assembly:, Choulet, F., Paux, E., Alberti, A., Aury, J.-M., Balfourier, F., Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., 1; D, 4; D, and 6; D physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 2; AL physical mapping:, Singh, K., Chhuneja, P., Gupta, O. P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., 2; AS physical mapping:, Singh, N. K., Khurana, J., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R. S., 2; B, 2; D, 4; B, 5; BL, and 5; DL IWGSC-Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers, J., Jacobs, J., Alaux, M., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., van der Vossen, E., Vautrin, S., 3; AL physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 3; DS physical mapping and BAC sequencing and assembly:, Bartos, J., Holusova, K., Plihal, O., 3; DL BAC sequencing and assembly:, Clark, M. D., Heavens, D., Kettleborough, G., Wright, J., 4; A physical mapping, BAC sequencing, assembly, and annotation:, Valarik, M., Abrouk, M., Balcarkova, B., Holusova, K., Hu, Y., Luo, M., 5; BS BAC sequencing and assembly:, Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., 6; B BAC sequencing and assembly:, Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., 7; A physical mapping and BAC sequencing:, Appels, R., Hayden, M., Keeble-Gagnere, G., Rigault, P., Tibbits, J., 7; B physical mapping, BAC sequencing, and assembly:, Olsen, O.-A., Belova, T., Cattonaro, F., Jiumeng, M., Kugler, K., Mayer, K. F. X., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., 7; DS BAC sequencing and assembly:, Simkova, H., Abrouk, M., Batley, J., Bayer, P. E., Edwards, D., Hayashi, S., Toegelova, H., Tulpova, Z., Visendi, P., 7; DL physical mapping and BAC sequencing:, Weining, S., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Figures:, Borrill, P., Gundlach, H., Galvez, S., Kaithakottil, G., Lang, D., Lux, T., Mascher, M., Ormanbekova, D., Prade, V., Ramirez-Gonzalez, R. H., Spannagl, M., Stein, N., Uauy, C., Venturini, L., Manuscript writing team:, Stein, N., Appels, R., Eversole, K., Rogers, J., Borrill, P., Cattivelli, L., Choulet, F., Hernandez, P., Kanyuka, K., Lang, D., Mascher, M., Nilsen, K., Paux, E., Pozniak, C. J., Ramirez-Gonzalez, R. H., Simkova, H., Small, I., Spannagl, M., Swarbreck, D., Uauy, C. |
shingle_author_3 | The International Wheat Genome Sequencing Consortium (IWGSC), IWGSC Ref; Seq principal investigators:, Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., IWGSC whole-genome assembly principal investigators:, Pozniak, C. J., Stein, N., Choulet, F., Distelfeld, A., Eversole, K., Poland, J., Rogers, J., Ronen, G., Sharpe, A. G., Whole-genome sequencing and assembly:, Pozniak, C., Ronen, G., Stein, N., Barad, O., Baruch, K., Choulet, F., Keeble-Gagnere, G., Mascher, M., Sharpe, A. G., Ben-Zvi, G., Josselin, A.-A., Hi-C data-based scaffolding:, Stein, N., Mascher, M., Himmelbach, A., Whole-genome assembly quality control and analyses:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Rogers, J., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Josselin, A.-A., Koh, C., Muehlbauer, G., Pasam, R. K., Paux, E., Pozniak, C. J., Rigault, P., Sharpe, A. G., Tibbits, J., Tiwari, V., Pseudomolecule assembly:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Josselin, A.-A., Rogers, J., Ref; Seq genome structure and gene analyses:, Spannagl, M., Choulet, F., Lang, D., Gundlach, H., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Ormanbekova, D., Paux, E., Prade, V., Simkova, H., Wicker, T., Automated annotation:, Choulet, F., Spannagl, M., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Gundlach, H., Haberer, G., Kaithakottil, G., Keilwagen, J., Lang, D., Leroy, P., Lux, T., Mayer, K. F. X., Twardziok, S., Venturini, L., Manual gene curation:, Appels, R., Rimbert, H., Choulet, F., Juhasz, A., Keeble-Gagnere, G., Subgenome comparative analyses:, Choulet, F., Spannagl, M., Lang, D., Abrouk, M., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Wicker, T., Transposable elements:, Choulet, F., Wicker, T., Gundlach, H., Lang, D., Spannagl, M., Phylogenomic analyses:, Lang, D., Spannagl, M., Appels, R., Fischer, I., Transcriptome analyses and RNA-seq data:, Uauy, C., Borrill, P., Ramirez-Gonzalez, R. H., Appels, R., Arnaud, D., Chalabi, S., Chalhoub, B., Choulet, F., Cory, A., Datla, R., Davey, M. W., Hayden, M., Jacobs, J., Lang, D., Robinson, S. J., Spannagl, M., Steuernagel, B., Tibbits, J., Tiwari, V., van Ex, F., Wulff, B. B. H., Whole-genome methylome:, Pozniak, C. J., Robinson, S. J., Sharpe, A. G., Cory, A., Histone mark analyses:, Benhamed, M., Paux, E., Bendahmane, A., Concia, L., Latrasse, D., BAC chromosome MTP IWGSC-Bayer Whole-Genome Profiling (WGP) tags:, Rogers, J., Jacobs, J., Alaux, M., Appels, R., Bartos, J., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O.-A., Simkova, H., Singh, K., Valarik, M., van der Vossen, E., Vautrin, S., Weining, S., Chromosome LTC mapping and physical mapping quality control:, Korol, A., Frenkel, Z., Fahima, T., Glikson, V., Raats, D., Rogers, J., RH mapping:, Tiwari, V., Gill, B., Paux, E., Poland, J., Optical mapping:, Dolezel, J., Cihalikova, J., Simkova, H., Toegelova, H., Vrana, J., Recombination analyses:, Sourdille, P., Darrier, B., Gene family analyses:, Appels, R., Spannagl, M., Lang, D., Fischer, I., Ormanbekova, D., Prade, V., CBF gene family:, Barabaschi, D., Cattivelli, L., Dehydrin gene family:, Hernandez, P., Galvez, S., Budak, H., NLR gene family:, Steuernagel, B., Jones, J. D. G., Witek, K., Wulff, B. B. H., Yu, G., PPR gene family:, Small, I., Melonek, J., Zhou, R., Prolamin gene family:, Juhasz, A., Belova, T., Appels, R., Olsen, O.-A., WAK gene family:, Kanyuka, K., King, R., Stem solidness (SSt1) QTL team:, Nilsen, K., Walkowiak, S., Pozniak, C. J., Cuthbert, R., Datla, R., Knox, R., Wiebe, K., Xiang, D., Flowering locus C (FLC) gene team:, Rohde, A., Golds, T., Genome size analysis:, Dolezel, J., Cizkova, J., Tibbits, J., Micro; RNA and t; RNA annotation:, Budak, H., Akpinar, B. A., Biyiklioglu, S., Genetic maps and mapping:, Muehlbauer, G., Poland, J., Gao, L., Gutierrez-Gonzalez, J., NDaiye, A., BAC libraries and chromosome sorting:, Dolezel, J., Simkova, H., Cihalikova, J., Kubalakova, M., Safar, J., Vrana, J., BAC pooling, BAC library repository, and access:, Berges, H., Bellec, A., Vautrin, S., IWGSC sequence and data repository and access:, Alaux, M., Alfama, F., Adam-Blondon, A.-F., Flores, R., Guerche, C., Letellier, T., Loaec, M., Quesneville, H., Physical maps and BAC-based sequences:, 1; A BAC sequencing and assembly:, Pozniak, C. J., Sharpe, A. G., Walkowiak, S., Budak, H., Condie, J., Ens, J., Koh, C., Maclachlan, R., Tan, Y., Wicker, T., 1; B BAC sequencing and assembly:, Choulet, F., Paux, E., Alberti, A., Aury, J.-M., Balfourier, F., Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., 1; D, 4; D, and 6; D physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 2; AL physical mapping:, Singh, K., Chhuneja, P., Gupta, O. P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., 2; AS physical mapping:, Singh, N. K., Khurana, J., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R. S., 2; B, 2; D, 4; B, 5; BL, and 5; DL IWGSC-Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers, J., Jacobs, J., Alaux, M., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., van der Vossen, E., Vautrin, S., 3; AL physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 3; DS physical mapping and BAC sequencing and assembly:, Bartos, J., Holusova, K., Plihal, O., 3; DL BAC sequencing and assembly:, Clark, M. D., Heavens, D., Kettleborough, G., Wright, J., 4; A physical mapping, BAC sequencing, assembly, and annotation:, Valarik, M., Abrouk, M., Balcarkova, B., Holusova, K., Hu, Y., Luo, M., 5; BS BAC sequencing and assembly:, Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., 6; B BAC sequencing and assembly:, Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., 7; A physical mapping and BAC sequencing:, Appels, R., Hayden, M., Keeble-Gagnere, G., Rigault, P., Tibbits, J., 7; B physical mapping, BAC sequencing, and assembly:, Olsen, O.-A., Belova, T., Cattonaro, F., Jiumeng, M., Kugler, K., Mayer, K. F. X., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., 7; DS BAC sequencing and assembly:, Simkova, H., Abrouk, M., Batley, J., Bayer, P. E., Edwards, D., Hayashi, S., Toegelova, H., Tulpova, Z., Visendi, P., 7; DL physical mapping and BAC sequencing:, Weining, S., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Figures:, Borrill, P., Gundlach, H., Galvez, S., Kaithakottil, G., Lang, D., Lux, T., Mascher, M., Ormanbekova, D., Prade, V., Ramirez-Gonzalez, R. H., Spannagl, M., Stein, N., Uauy, C., Venturini, L., Manuscript writing team:, Stein, N., Appels, R., Eversole, K., Rogers, J., Borrill, P., Cattivelli, L., Choulet, F., Hernandez, P., Kanyuka, K., Lang, D., Mascher, M., Nilsen, K., Paux, E., Pozniak, C. J., Ramirez-Gonzalez, R. H., Simkova, H., Small, I., Spannagl, M., Swarbreck, D., Uauy, C. |
shingle_author_4 | The International Wheat Genome Sequencing Consortium (IWGSC), IWGSC Ref; Seq principal investigators:, Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., IWGSC whole-genome assembly principal investigators:, Pozniak, C. J., Stein, N., Choulet, F., Distelfeld, A., Eversole, K., Poland, J., Rogers, J., Ronen, G., Sharpe, A. G., Whole-genome sequencing and assembly:, Pozniak, C., Ronen, G., Stein, N., Barad, O., Baruch, K., Choulet, F., Keeble-Gagnere, G., Mascher, M., Sharpe, A. G., Ben-Zvi, G., Josselin, A.-A., Hi-C data-based scaffolding:, Stein, N., Mascher, M., Himmelbach, A., Whole-genome assembly quality control and analyses:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Rogers, J., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Josselin, A.-A., Koh, C., Muehlbauer, G., Pasam, R. K., Paux, E., Pozniak, C. J., Rigault, P., Sharpe, A. G., Tibbits, J., Tiwari, V., Pseudomolecule assembly:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Josselin, A.-A., Rogers, J., Ref; Seq genome structure and gene analyses:, Spannagl, M., Choulet, F., Lang, D., Gundlach, H., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Ormanbekova, D., Paux, E., Prade, V., Simkova, H., Wicker, T., Automated annotation:, Choulet, F., Spannagl, M., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Gundlach, H., Haberer, G., Kaithakottil, G., Keilwagen, J., Lang, D., Leroy, P., Lux, T., Mayer, K. F. X., Twardziok, S., Venturini, L., Manual gene curation:, Appels, R., Rimbert, H., Choulet, F., Juhasz, A., Keeble-Gagnere, G., Subgenome comparative analyses:, Choulet, F., Spannagl, M., Lang, D., Abrouk, M., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Wicker, T., Transposable elements:, Choulet, F., Wicker, T., Gundlach, H., Lang, D., Spannagl, M., Phylogenomic analyses:, Lang, D., Spannagl, M., Appels, R., Fischer, I., Transcriptome analyses and RNA-seq data:, Uauy, C., Borrill, P., Ramirez-Gonzalez, R. H., Appels, R., Arnaud, D., Chalabi, S., Chalhoub, B., Choulet, F., Cory, A., Datla, R., Davey, M. W., Hayden, M., Jacobs, J., Lang, D., Robinson, S. J., Spannagl, M., Steuernagel, B., Tibbits, J., Tiwari, V., van Ex, F., Wulff, B. B. H., Whole-genome methylome:, Pozniak, C. J., Robinson, S. J., Sharpe, A. G., Cory, A., Histone mark analyses:, Benhamed, M., Paux, E., Bendahmane, A., Concia, L., Latrasse, D., BAC chromosome MTP IWGSC-Bayer Whole-Genome Profiling (WGP) tags:, Rogers, J., Jacobs, J., Alaux, M., Appels, R., Bartos, J., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O.-A., Simkova, H., Singh, K., Valarik, M., van der Vossen, E., Vautrin, S., Weining, S., Chromosome LTC mapping and physical mapping quality control:, Korol, A., Frenkel, Z., Fahima, T., Glikson, V., Raats, D., Rogers, J., RH mapping:, Tiwari, V., Gill, B., Paux, E., Poland, J., Optical mapping:, Dolezel, J., Cihalikova, J., Simkova, H., Toegelova, H., Vrana, J., Recombination analyses:, Sourdille, P., Darrier, B., Gene family analyses:, Appels, R., Spannagl, M., Lang, D., Fischer, I., Ormanbekova, D., Prade, V., CBF gene family:, Barabaschi, D., Cattivelli, L., Dehydrin gene family:, Hernandez, P., Galvez, S., Budak, H., NLR gene family:, Steuernagel, B., Jones, J. D. G., Witek, K., Wulff, B. B. H., Yu, G., PPR gene family:, Small, I., Melonek, J., Zhou, R., Prolamin gene family:, Juhasz, A., Belova, T., Appels, R., Olsen, O.-A., WAK gene family:, Kanyuka, K., King, R., Stem solidness (SSt1) QTL team:, Nilsen, K., Walkowiak, S., Pozniak, C. J., Cuthbert, R., Datla, R., Knox, R., Wiebe, K., Xiang, D., Flowering locus C (FLC) gene team:, Rohde, A., Golds, T., Genome size analysis:, Dolezel, J., Cizkova, J., Tibbits, J., Micro; RNA and t; RNA annotation:, Budak, H., Akpinar, B. A., Biyiklioglu, S., Genetic maps and mapping:, Muehlbauer, G., Poland, J., Gao, L., Gutierrez-Gonzalez, J., NDaiye, A., BAC libraries and chromosome sorting:, Dolezel, J., Simkova, H., Cihalikova, J., Kubalakova, M., Safar, J., Vrana, J., BAC pooling, BAC library repository, and access:, Berges, H., Bellec, A., Vautrin, S., IWGSC sequence and data repository and access:, Alaux, M., Alfama, F., Adam-Blondon, A.-F., Flores, R., Guerche, C., Letellier, T., Loaec, M., Quesneville, H., Physical maps and BAC-based sequences:, 1; A BAC sequencing and assembly:, Pozniak, C. J., Sharpe, A. G., Walkowiak, S., Budak, H., Condie, J., Ens, J., Koh, C., Maclachlan, R., Tan, Y., Wicker, T., 1; B BAC sequencing and assembly:, Choulet, F., Paux, E., Alberti, A., Aury, J.-M., Balfourier, F., Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., 1; D, 4; D, and 6; D physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 2; AL physical mapping:, Singh, K., Chhuneja, P., Gupta, O. P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., 2; AS physical mapping:, Singh, N. K., Khurana, J., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R. S., 2; B, 2; D, 4; B, 5; BL, and 5; DL IWGSC-Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers, J., Jacobs, J., Alaux, M., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., van der Vossen, E., Vautrin, S., 3; AL physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 3; DS physical mapping and BAC sequencing and assembly:, Bartos, J., Holusova, K., Plihal, O., 3; DL BAC sequencing and assembly:, Clark, M. D., Heavens, D., Kettleborough, G., Wright, J., 4; A physical mapping, BAC sequencing, assembly, and annotation:, Valarik, M., Abrouk, M., Balcarkova, B., Holusova, K., Hu, Y., Luo, M., 5; BS BAC sequencing and assembly:, Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., 6; B BAC sequencing and assembly:, Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., 7; A physical mapping and BAC sequencing:, Appels, R., Hayden, M., Keeble-Gagnere, G., Rigault, P., Tibbits, J., 7; B physical mapping, BAC sequencing, and assembly:, Olsen, O.-A., Belova, T., Cattonaro, F., Jiumeng, M., Kugler, K., Mayer, K. F. X., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., 7; DS BAC sequencing and assembly:, Simkova, H., Abrouk, M., Batley, J., Bayer, P. E., Edwards, D., Hayashi, S., Toegelova, H., Tulpova, Z., Visendi, P., 7; DL physical mapping and BAC sequencing:, Weining, S., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Figures:, Borrill, P., Gundlach, H., Galvez, S., Kaithakottil, G., Lang, D., Lux, T., Mascher, M., Ormanbekova, D., Prade, V., Ramirez-Gonzalez, R. H., Spannagl, M., Stein, N., Uauy, C., Venturini, L., Manuscript writing team:, Stein, N., Appels, R., Eversole, K., Rogers, J., Borrill, P., Cattivelli, L., Choulet, F., Hernandez, P., Kanyuka, K., Lang, D., Mascher, M., Nilsen, K., Paux, E., Pozniak, C. J., Ramirez-Gonzalez, R. H., Simkova, H., Small, I., Spannagl, M., Swarbreck, D., Uauy, C. |
shingle_catch_all_1 | Shifting the limits in wheat research and breeding using a fully annotated reference genome Botany, Ecology, Online Only An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. The International Wheat Genome Sequencing Consortium (IWGSC), IWGSC Ref; Seq principal investigators:, Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., IWGSC whole-genome assembly principal investigators:, Pozniak, C. J., Stein, N., Choulet, F., Distelfeld, A., Eversole, K., Poland, J., Rogers, J., Ronen, G., Sharpe, A. G., Whole-genome sequencing and assembly:, Pozniak, C., Ronen, G., Stein, N., Barad, O., Baruch, K., Choulet, F., Keeble-Gagnere, G., Mascher, M., Sharpe, A. G., Ben-Zvi, G., Josselin, A.-A., Hi-C data-based scaffolding:, Stein, N., Mascher, M., Himmelbach, A., Whole-genome assembly quality control and analyses:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Rogers, J., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Josselin, A.-A., Koh, C., Muehlbauer, G., Pasam, R. K., Paux, E., Pozniak, C. J., Rigault, P., Sharpe, A. G., Tibbits, J., Tiwari, V., Pseudomolecule assembly:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Josselin, A.-A., Rogers, J., Ref; Seq genome structure and gene analyses:, Spannagl, M., Choulet, F., Lang, D., Gundlach, H., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Ormanbekova, D., Paux, E., Prade, V., Simkova, H., Wicker, T., Automated annotation:, Choulet, F., Spannagl, M., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Gundlach, H., Haberer, G., Kaithakottil, G., Keilwagen, J., Lang, D., Leroy, P., Lux, T., Mayer, K. F. X., Twardziok, S., Venturini, L., Manual gene curation:, Appels, R., Rimbert, H., Choulet, F., Juhasz, A., Keeble-Gagnere, G., Subgenome comparative analyses:, Choulet, F., Spannagl, M., Lang, D., Abrouk, M., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Wicker, T., Transposable elements:, Choulet, F., Wicker, T., Gundlach, H., Lang, D., Spannagl, M., Phylogenomic analyses:, Lang, D., Spannagl, M., Appels, R., Fischer, I., Transcriptome analyses and RNA-seq data:, Uauy, C., Borrill, P., Ramirez-Gonzalez, R. H., Appels, R., Arnaud, D., Chalabi, S., Chalhoub, B., Choulet, F., Cory, A., Datla, R., Davey, M. W., Hayden, M., Jacobs, J., Lang, D., Robinson, S. J., Spannagl, M., Steuernagel, B., Tibbits, J., Tiwari, V., van Ex, F., Wulff, B. B. H., Whole-genome methylome:, Pozniak, C. J., Robinson, S. J., Sharpe, A. G., Cory, A., Histone mark analyses:, Benhamed, M., Paux, E., Bendahmane, A., Concia, L., Latrasse, D., BAC chromosome MTP IWGSC-Bayer Whole-Genome Profiling (WGP) tags:, Rogers, J., Jacobs, J., Alaux, M., Appels, R., Bartos, J., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O.-A., Simkova, H., Singh, K., Valarik, M., van der Vossen, E., Vautrin, S., Weining, S., Chromosome LTC mapping and physical mapping quality control:, Korol, A., Frenkel, Z., Fahima, T., Glikson, V., Raats, D., Rogers, J., RH mapping:, Tiwari, V., Gill, B., Paux, E., Poland, J., Optical mapping:, Dolezel, J., Cihalikova, J., Simkova, H., Toegelova, H., Vrana, J., Recombination analyses:, Sourdille, P., Darrier, B., Gene family analyses:, Appels, R., Spannagl, M., Lang, D., Fischer, I., Ormanbekova, D., Prade, V., CBF gene family:, Barabaschi, D., Cattivelli, L., Dehydrin gene family:, Hernandez, P., Galvez, S., Budak, H., NLR gene family:, Steuernagel, B., Jones, J. D. G., Witek, K., Wulff, B. B. H., Yu, G., PPR gene family:, Small, I., Melonek, J., Zhou, R., Prolamin gene family:, Juhasz, A., Belova, T., Appels, R., Olsen, O.-A., WAK gene family:, Kanyuka, K., King, R., Stem solidness (SSt1) QTL team:, Nilsen, K., Walkowiak, S., Pozniak, C. J., Cuthbert, R., Datla, R., Knox, R., Wiebe, K., Xiang, D., Flowering locus C (FLC) gene team:, Rohde, A., Golds, T., Genome size analysis:, Dolezel, J., Cizkova, J., Tibbits, J., Micro; RNA and t; RNA annotation:, Budak, H., Akpinar, B. A., Biyiklioglu, S., Genetic maps and mapping:, Muehlbauer, G., Poland, J., Gao, L., Gutierrez-Gonzalez, J., NDaiye, A., BAC libraries and chromosome sorting:, Dolezel, J., Simkova, H., Cihalikova, J., Kubalakova, M., Safar, J., Vrana, J., BAC pooling, BAC library repository, and access:, Berges, H., Bellec, A., Vautrin, S., IWGSC sequence and data repository and access:, Alaux, M., Alfama, F., Adam-Blondon, A.-F., Flores, R., Guerche, C., Letellier, T., Loaec, M., Quesneville, H., Physical maps and BAC-based sequences:, 1; A BAC sequencing and assembly:, Pozniak, C. J., Sharpe, A. G., Walkowiak, S., Budak, H., Condie, J., Ens, J., Koh, C., Maclachlan, R., Tan, Y., Wicker, T., 1; B BAC sequencing and assembly:, Choulet, F., Paux, E., Alberti, A., Aury, J.-M., Balfourier, F., Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., 1; D, 4; D, and 6; D physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 2; AL physical mapping:, Singh, K., Chhuneja, P., Gupta, O. P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., 2; AS physical mapping:, Singh, N. K., Khurana, J., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R. S., 2; B, 2; D, 4; B, 5; BL, and 5; DL IWGSC-Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers, J., Jacobs, J., Alaux, M., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., van der Vossen, E., Vautrin, S., 3; AL physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 3; DS physical mapping and BAC sequencing and assembly:, Bartos, J., Holusova, K., Plihal, O., 3; DL BAC sequencing and assembly:, Clark, M. D., Heavens, D., Kettleborough, G., Wright, J., 4; A physical mapping, BAC sequencing, assembly, and annotation:, Valarik, M., Abrouk, M., Balcarkova, B., Holusova, K., Hu, Y., Luo, M., 5; BS BAC sequencing and assembly:, Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., 6; B BAC sequencing and assembly:, Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., 7; A physical mapping and BAC sequencing:, Appels, R., Hayden, M., Keeble-Gagnere, G., Rigault, P., Tibbits, J., 7; B physical mapping, BAC sequencing, and assembly:, Olsen, O.-A., Belova, T., Cattonaro, F., Jiumeng, M., Kugler, K., Mayer, K. F. X., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., 7; DS BAC sequencing and assembly:, Simkova, H., Abrouk, M., Batley, J., Bayer, P. E., Edwards, D., Hayashi, S., Toegelova, H., Tulpova, Z., Visendi, P., 7; DL physical mapping and BAC sequencing:, Weining, S., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Figures:, Borrill, P., Gundlach, H., Galvez, S., Kaithakottil, G., Lang, D., Lux, T., Mascher, M., Ormanbekova, D., Prade, V., Ramirez-Gonzalez, R. H., Spannagl, M., Stein, N., Uauy, C., Venturini, L., Manuscript writing team:, Stein, N., Appels, R., Eversole, K., Rogers, J., Borrill, P., Cattivelli, L., Choulet, F., Hernandez, P., Kanyuka, K., Lang, D., Mascher, M., Nilsen, K., Paux, E., Pozniak, C. J., Ramirez-Gonzalez, R. H., Simkova, H., Small, I., Spannagl, M., Swarbreck, D., Uauy, C. American Association for the Advancement of Science (AAAS) 0036-8075 00368075 1095-9203 10959203 |
shingle_catch_all_2 | Shifting the limits in wheat research and breeding using a fully annotated reference genome Botany, Ecology, Online Only An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. The International Wheat Genome Sequencing Consortium (IWGSC), IWGSC Ref; Seq principal investigators:, Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., IWGSC whole-genome assembly principal investigators:, Pozniak, C. J., Stein, N., Choulet, F., Distelfeld, A., Eversole, K., Poland, J., Rogers, J., Ronen, G., Sharpe, A. G., Whole-genome sequencing and assembly:, Pozniak, C., Ronen, G., Stein, N., Barad, O., Baruch, K., Choulet, F., Keeble-Gagnere, G., Mascher, M., Sharpe, A. G., Ben-Zvi, G., Josselin, A.-A., Hi-C data-based scaffolding:, Stein, N., Mascher, M., Himmelbach, A., Whole-genome assembly quality control and analyses:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Rogers, J., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Josselin, A.-A., Koh, C., Muehlbauer, G., Pasam, R. K., Paux, E., Pozniak, C. J., Rigault, P., Sharpe, A. G., Tibbits, J., Tiwari, V., Pseudomolecule assembly:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Josselin, A.-A., Rogers, J., Ref; Seq genome structure and gene analyses:, Spannagl, M., Choulet, F., Lang, D., Gundlach, H., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Ormanbekova, D., Paux, E., Prade, V., Simkova, H., Wicker, T., Automated annotation:, Choulet, F., Spannagl, M., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Gundlach, H., Haberer, G., Kaithakottil, G., Keilwagen, J., Lang, D., Leroy, P., Lux, T., Mayer, K. F. X., Twardziok, S., Venturini, L., Manual gene curation:, Appels, R., Rimbert, H., Choulet, F., Juhasz, A., Keeble-Gagnere, G., Subgenome comparative analyses:, Choulet, F., Spannagl, M., Lang, D., Abrouk, M., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Wicker, T., Transposable elements:, Choulet, F., Wicker, T., Gundlach, H., Lang, D., Spannagl, M., Phylogenomic analyses:, Lang, D., Spannagl, M., Appels, R., Fischer, I., Transcriptome analyses and RNA-seq data:, Uauy, C., Borrill, P., Ramirez-Gonzalez, R. H., Appels, R., Arnaud, D., Chalabi, S., Chalhoub, B., Choulet, F., Cory, A., Datla, R., Davey, M. W., Hayden, M., Jacobs, J., Lang, D., Robinson, S. J., Spannagl, M., Steuernagel, B., Tibbits, J., Tiwari, V., van Ex, F., Wulff, B. B. H., Whole-genome methylome:, Pozniak, C. J., Robinson, S. J., Sharpe, A. G., Cory, A., Histone mark analyses:, Benhamed, M., Paux, E., Bendahmane, A., Concia, L., Latrasse, D., BAC chromosome MTP IWGSC-Bayer Whole-Genome Profiling (WGP) tags:, Rogers, J., Jacobs, J., Alaux, M., Appels, R., Bartos, J., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O.-A., Simkova, H., Singh, K., Valarik, M., van der Vossen, E., Vautrin, S., Weining, S., Chromosome LTC mapping and physical mapping quality control:, Korol, A., Frenkel, Z., Fahima, T., Glikson, V., Raats, D., Rogers, J., RH mapping:, Tiwari, V., Gill, B., Paux, E., Poland, J., Optical mapping:, Dolezel, J., Cihalikova, J., Simkova, H., Toegelova, H., Vrana, J., Recombination analyses:, Sourdille, P., Darrier, B., Gene family analyses:, Appels, R., Spannagl, M., Lang, D., Fischer, I., Ormanbekova, D., Prade, V., CBF gene family:, Barabaschi, D., Cattivelli, L., Dehydrin gene family:, Hernandez, P., Galvez, S., Budak, H., NLR gene family:, Steuernagel, B., Jones, J. D. G., Witek, K., Wulff, B. B. H., Yu, G., PPR gene family:, Small, I., Melonek, J., Zhou, R., Prolamin gene family:, Juhasz, A., Belova, T., Appels, R., Olsen, O.-A., WAK gene family:, Kanyuka, K., King, R., Stem solidness (SSt1) QTL team:, Nilsen, K., Walkowiak, S., Pozniak, C. J., Cuthbert, R., Datla, R., Knox, R., Wiebe, K., Xiang, D., Flowering locus C (FLC) gene team:, Rohde, A., Golds, T., Genome size analysis:, Dolezel, J., Cizkova, J., Tibbits, J., Micro; RNA and t; RNA annotation:, Budak, H., Akpinar, B. A., Biyiklioglu, S., Genetic maps and mapping:, Muehlbauer, G., Poland, J., Gao, L., Gutierrez-Gonzalez, J., NDaiye, A., BAC libraries and chromosome sorting:, Dolezel, J., Simkova, H., Cihalikova, J., Kubalakova, M., Safar, J., Vrana, J., BAC pooling, BAC library repository, and access:, Berges, H., Bellec, A., Vautrin, S., IWGSC sequence and data repository and access:, Alaux, M., Alfama, F., Adam-Blondon, A.-F., Flores, R., Guerche, C., Letellier, T., Loaec, M., Quesneville, H., Physical maps and BAC-based sequences:, 1; A BAC sequencing and assembly:, Pozniak, C. J., Sharpe, A. G., Walkowiak, S., Budak, H., Condie, J., Ens, J., Koh, C., Maclachlan, R., Tan, Y., Wicker, T., 1; B BAC sequencing and assembly:, Choulet, F., Paux, E., Alberti, A., Aury, J.-M., Balfourier, F., Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., 1; D, 4; D, and 6; D physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 2; AL physical mapping:, Singh, K., Chhuneja, P., Gupta, O. P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., 2; AS physical mapping:, Singh, N. K., Khurana, J., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R. S., 2; B, 2; D, 4; B, 5; BL, and 5; DL IWGSC-Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers, J., Jacobs, J., Alaux, M., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., van der Vossen, E., Vautrin, S., 3; AL physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 3; DS physical mapping and BAC sequencing and assembly:, Bartos, J., Holusova, K., Plihal, O., 3; DL BAC sequencing and assembly:, Clark, M. D., Heavens, D., Kettleborough, G., Wright, J., 4; A physical mapping, BAC sequencing, assembly, and annotation:, Valarik, M., Abrouk, M., Balcarkova, B., Holusova, K., Hu, Y., Luo, M., 5; BS BAC sequencing and assembly:, Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., 6; B BAC sequencing and assembly:, Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., 7; A physical mapping and BAC sequencing:, Appels, R., Hayden, M., Keeble-Gagnere, G., Rigault, P., Tibbits, J., 7; B physical mapping, BAC sequencing, and assembly:, Olsen, O.-A., Belova, T., Cattonaro, F., Jiumeng, M., Kugler, K., Mayer, K. F. X., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., 7; DS BAC sequencing and assembly:, Simkova, H., Abrouk, M., Batley, J., Bayer, P. E., Edwards, D., Hayashi, S., Toegelova, H., Tulpova, Z., Visendi, P., 7; DL physical mapping and BAC sequencing:, Weining, S., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Figures:, Borrill, P., Gundlach, H., Galvez, S., Kaithakottil, G., Lang, D., Lux, T., Mascher, M., Ormanbekova, D., Prade, V., Ramirez-Gonzalez, R. H., Spannagl, M., Stein, N., Uauy, C., Venturini, L., Manuscript writing team:, Stein, N., Appels, R., Eversole, K., Rogers, J., Borrill, P., Cattivelli, L., Choulet, F., Hernandez, P., Kanyuka, K., Lang, D., Mascher, M., Nilsen, K., Paux, E., Pozniak, C. J., Ramirez-Gonzalez, R. H., Simkova, H., Small, I., Spannagl, M., Swarbreck, D., Uauy, C. American Association for the Advancement of Science (AAAS) 0036-8075 00368075 1095-9203 10959203 |
shingle_catch_all_3 | Shifting the limits in wheat research and breeding using a fully annotated reference genome Botany, Ecology, Online Only An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. The International Wheat Genome Sequencing Consortium (IWGSC), IWGSC Ref; Seq principal investigators:, Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., IWGSC whole-genome assembly principal investigators:, Pozniak, C. J., Stein, N., Choulet, F., Distelfeld, A., Eversole, K., Poland, J., Rogers, J., Ronen, G., Sharpe, A. G., Whole-genome sequencing and assembly:, Pozniak, C., Ronen, G., Stein, N., Barad, O., Baruch, K., Choulet, F., Keeble-Gagnere, G., Mascher, M., Sharpe, A. G., Ben-Zvi, G., Josselin, A.-A., Hi-C data-based scaffolding:, Stein, N., Mascher, M., Himmelbach, A., Whole-genome assembly quality control and analyses:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Rogers, J., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Josselin, A.-A., Koh, C., Muehlbauer, G., Pasam, R. K., Paux, E., Pozniak, C. J., Rigault, P., Sharpe, A. G., Tibbits, J., Tiwari, V., Pseudomolecule assembly:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Josselin, A.-A., Rogers, J., Ref; Seq genome structure and gene analyses:, Spannagl, M., Choulet, F., Lang, D., Gundlach, H., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Ormanbekova, D., Paux, E., Prade, V., Simkova, H., Wicker, T., Automated annotation:, Choulet, F., Spannagl, M., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Gundlach, H., Haberer, G., Kaithakottil, G., Keilwagen, J., Lang, D., Leroy, P., Lux, T., Mayer, K. F. X., Twardziok, S., Venturini, L., Manual gene curation:, Appels, R., Rimbert, H., Choulet, F., Juhasz, A., Keeble-Gagnere, G., Subgenome comparative analyses:, Choulet, F., Spannagl, M., Lang, D., Abrouk, M., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Wicker, T., Transposable elements:, Choulet, F., Wicker, T., Gundlach, H., Lang, D., Spannagl, M., Phylogenomic analyses:, Lang, D., Spannagl, M., Appels, R., Fischer, I., Transcriptome analyses and RNA-seq data:, Uauy, C., Borrill, P., Ramirez-Gonzalez, R. H., Appels, R., Arnaud, D., Chalabi, S., Chalhoub, B., Choulet, F., Cory, A., Datla, R., Davey, M. W., Hayden, M., Jacobs, J., Lang, D., Robinson, S. J., Spannagl, M., Steuernagel, B., Tibbits, J., Tiwari, V., van Ex, F., Wulff, B. B. H., Whole-genome methylome:, Pozniak, C. J., Robinson, S. J., Sharpe, A. G., Cory, A., Histone mark analyses:, Benhamed, M., Paux, E., Bendahmane, A., Concia, L., Latrasse, D., BAC chromosome MTP IWGSC-Bayer Whole-Genome Profiling (WGP) tags:, Rogers, J., Jacobs, J., Alaux, M., Appels, R., Bartos, J., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O.-A., Simkova, H., Singh, K., Valarik, M., van der Vossen, E., Vautrin, S., Weining, S., Chromosome LTC mapping and physical mapping quality control:, Korol, A., Frenkel, Z., Fahima, T., Glikson, V., Raats, D., Rogers, J., RH mapping:, Tiwari, V., Gill, B., Paux, E., Poland, J., Optical mapping:, Dolezel, J., Cihalikova, J., Simkova, H., Toegelova, H., Vrana, J., Recombination analyses:, Sourdille, P., Darrier, B., Gene family analyses:, Appels, R., Spannagl, M., Lang, D., Fischer, I., Ormanbekova, D., Prade, V., CBF gene family:, Barabaschi, D., Cattivelli, L., Dehydrin gene family:, Hernandez, P., Galvez, S., Budak, H., NLR gene family:, Steuernagel, B., Jones, J. D. G., Witek, K., Wulff, B. B. H., Yu, G., PPR gene family:, Small, I., Melonek, J., Zhou, R., Prolamin gene family:, Juhasz, A., Belova, T., Appels, R., Olsen, O.-A., WAK gene family:, Kanyuka, K., King, R., Stem solidness (SSt1) QTL team:, Nilsen, K., Walkowiak, S., Pozniak, C. J., Cuthbert, R., Datla, R., Knox, R., Wiebe, K., Xiang, D., Flowering locus C (FLC) gene team:, Rohde, A., Golds, T., Genome size analysis:, Dolezel, J., Cizkova, J., Tibbits, J., Micro; RNA and t; RNA annotation:, Budak, H., Akpinar, B. A., Biyiklioglu, S., Genetic maps and mapping:, Muehlbauer, G., Poland, J., Gao, L., Gutierrez-Gonzalez, J., NDaiye, A., BAC libraries and chromosome sorting:, Dolezel, J., Simkova, H., Cihalikova, J., Kubalakova, M., Safar, J., Vrana, J., BAC pooling, BAC library repository, and access:, Berges, H., Bellec, A., Vautrin, S., IWGSC sequence and data repository and access:, Alaux, M., Alfama, F., Adam-Blondon, A.-F., Flores, R., Guerche, C., Letellier, T., Loaec, M., Quesneville, H., Physical maps and BAC-based sequences:, 1; A BAC sequencing and assembly:, Pozniak, C. J., Sharpe, A. G., Walkowiak, S., Budak, H., Condie, J., Ens, J., Koh, C., Maclachlan, R., Tan, Y., Wicker, T., 1; B BAC sequencing and assembly:, Choulet, F., Paux, E., Alberti, A., Aury, J.-M., Balfourier, F., Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., 1; D, 4; D, and 6; D physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 2; AL physical mapping:, Singh, K., Chhuneja, P., Gupta, O. P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., 2; AS physical mapping:, Singh, N. K., Khurana, J., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R. S., 2; B, 2; D, 4; B, 5; BL, and 5; DL IWGSC-Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers, J., Jacobs, J., Alaux, M., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., van der Vossen, E., Vautrin, S., 3; AL physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 3; DS physical mapping and BAC sequencing and assembly:, Bartos, J., Holusova, K., Plihal, O., 3; DL BAC sequencing and assembly:, Clark, M. D., Heavens, D., Kettleborough, G., Wright, J., 4; A physical mapping, BAC sequencing, assembly, and annotation:, Valarik, M., Abrouk, M., Balcarkova, B., Holusova, K., Hu, Y., Luo, M., 5; BS BAC sequencing and assembly:, Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., 6; B BAC sequencing and assembly:, Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., 7; A physical mapping and BAC sequencing:, Appels, R., Hayden, M., Keeble-Gagnere, G., Rigault, P., Tibbits, J., 7; B physical mapping, BAC sequencing, and assembly:, Olsen, O.-A., Belova, T., Cattonaro, F., Jiumeng, M., Kugler, K., Mayer, K. F. X., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., 7; DS BAC sequencing and assembly:, Simkova, H., Abrouk, M., Batley, J., Bayer, P. E., Edwards, D., Hayashi, S., Toegelova, H., Tulpova, Z., Visendi, P., 7; DL physical mapping and BAC sequencing:, Weining, S., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Figures:, Borrill, P., Gundlach, H., Galvez, S., Kaithakottil, G., Lang, D., Lux, T., Mascher, M., Ormanbekova, D., Prade, V., Ramirez-Gonzalez, R. H., Spannagl, M., Stein, N., Uauy, C., Venturini, L., Manuscript writing team:, Stein, N., Appels, R., Eversole, K., Rogers, J., Borrill, P., Cattivelli, L., Choulet, F., Hernandez, P., Kanyuka, K., Lang, D., Mascher, M., Nilsen, K., Paux, E., Pozniak, C. J., Ramirez-Gonzalez, R. H., Simkova, H., Small, I., Spannagl, M., Swarbreck, D., Uauy, C. American Association for the Advancement of Science (AAAS) 0036-8075 00368075 1095-9203 10959203 |
shingle_catch_all_4 | Shifting the limits in wheat research and breeding using a fully annotated reference genome Botany, Ecology, Online Only An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage–related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. The International Wheat Genome Sequencing Consortium (IWGSC), IWGSC Ref; Seq principal investigators:, Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., IWGSC whole-genome assembly principal investigators:, Pozniak, C. J., Stein, N., Choulet, F., Distelfeld, A., Eversole, K., Poland, J., Rogers, J., Ronen, G., Sharpe, A. G., Whole-genome sequencing and assembly:, Pozniak, C., Ronen, G., Stein, N., Barad, O., Baruch, K., Choulet, F., Keeble-Gagnere, G., Mascher, M., Sharpe, A. G., Ben-Zvi, G., Josselin, A.-A., Hi-C data-based scaffolding:, Stein, N., Mascher, M., Himmelbach, A., Whole-genome assembly quality control and analyses:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Rogers, J., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Josselin, A.-A., Koh, C., Muehlbauer, G., Pasam, R. K., Paux, E., Pozniak, C. J., Rigault, P., Sharpe, A. G., Tibbits, J., Tiwari, V., Pseudomolecule assembly:, Choulet, F., Keeble-Gagnere, G., Mascher, M., Josselin, A.-A., Rogers, J., Ref; Seq genome structure and gene analyses:, Spannagl, M., Choulet, F., Lang, D., Gundlach, H., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Ormanbekova, D., Paux, E., Prade, V., Simkova, H., Wicker, T., Automated annotation:, Choulet, F., Spannagl, M., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Gundlach, H., Haberer, G., Kaithakottil, G., Keilwagen, J., Lang, D., Leroy, P., Lux, T., Mayer, K. F. X., Twardziok, S., Venturini, L., Manual gene curation:, Appels, R., Rimbert, H., Choulet, F., Juhasz, A., Keeble-Gagnere, G., Subgenome comparative analyses:, Choulet, F., Spannagl, M., Lang, D., Abrouk, M., Haberer, G., Keeble-Gagnere, G., Mayer, K. F. X., Wicker, T., Transposable elements:, Choulet, F., Wicker, T., Gundlach, H., Lang, D., Spannagl, M., Phylogenomic analyses:, Lang, D., Spannagl, M., Appels, R., Fischer, I., Transcriptome analyses and RNA-seq data:, Uauy, C., Borrill, P., Ramirez-Gonzalez, R. H., Appels, R., Arnaud, D., Chalabi, S., Chalhoub, B., Choulet, F., Cory, A., Datla, R., Davey, M. W., Hayden, M., Jacobs, J., Lang, D., Robinson, S. J., Spannagl, M., Steuernagel, B., Tibbits, J., Tiwari, V., van Ex, F., Wulff, B. B. H., Whole-genome methylome:, Pozniak, C. J., Robinson, S. J., Sharpe, A. G., Cory, A., Histone mark analyses:, Benhamed, M., Paux, E., Bendahmane, A., Concia, L., Latrasse, D., BAC chromosome MTP IWGSC-Bayer Whole-Genome Profiling (WGP) tags:, Rogers, J., Jacobs, J., Alaux, M., Appels, R., Bartos, J., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O.-A., Simkova, H., Singh, K., Valarik, M., van der Vossen, E., Vautrin, S., Weining, S., Chromosome LTC mapping and physical mapping quality control:, Korol, A., Frenkel, Z., Fahima, T., Glikson, V., Raats, D., Rogers, J., RH mapping:, Tiwari, V., Gill, B., Paux, E., Poland, J., Optical mapping:, Dolezel, J., Cihalikova, J., Simkova, H., Toegelova, H., Vrana, J., Recombination analyses:, Sourdille, P., Darrier, B., Gene family analyses:, Appels, R., Spannagl, M., Lang, D., Fischer, I., Ormanbekova, D., Prade, V., CBF gene family:, Barabaschi, D., Cattivelli, L., Dehydrin gene family:, Hernandez, P., Galvez, S., Budak, H., NLR gene family:, Steuernagel, B., Jones, J. D. G., Witek, K., Wulff, B. B. H., Yu, G., PPR gene family:, Small, I., Melonek, J., Zhou, R., Prolamin gene family:, Juhasz, A., Belova, T., Appels, R., Olsen, O.-A., WAK gene family:, Kanyuka, K., King, R., Stem solidness (SSt1) QTL team:, Nilsen, K., Walkowiak, S., Pozniak, C. J., Cuthbert, R., Datla, R., Knox, R., Wiebe, K., Xiang, D., Flowering locus C (FLC) gene team:, Rohde, A., Golds, T., Genome size analysis:, Dolezel, J., Cizkova, J., Tibbits, J., Micro; RNA and t; RNA annotation:, Budak, H., Akpinar, B. A., Biyiklioglu, S., Genetic maps and mapping:, Muehlbauer, G., Poland, J., Gao, L., Gutierrez-Gonzalez, J., NDaiye, A., BAC libraries and chromosome sorting:, Dolezel, J., Simkova, H., Cihalikova, J., Kubalakova, M., Safar, J., Vrana, J., BAC pooling, BAC library repository, and access:, Berges, H., Bellec, A., Vautrin, S., IWGSC sequence and data repository and access:, Alaux, M., Alfama, F., Adam-Blondon, A.-F., Flores, R., Guerche, C., Letellier, T., Loaec, M., Quesneville, H., Physical maps and BAC-based sequences:, 1; A BAC sequencing and assembly:, Pozniak, C. J., Sharpe, A. G., Walkowiak, S., Budak, H., Condie, J., Ens, J., Koh, C., Maclachlan, R., Tan, Y., Wicker, T., 1; B BAC sequencing and assembly:, Choulet, F., Paux, E., Alberti, A., Aury, J.-M., Balfourier, F., Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., 1; D, 4; D, and 6; D physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 2; AL physical mapping:, Singh, K., Chhuneja, P., Gupta, O. P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., 2; AS physical mapping:, Singh, N. K., Khurana, J., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R. S., 2; B, 2; D, 4; B, 5; BL, and 5; DL IWGSC-Bayer Whole-Genome Profiling (WGP) physical maps:, Rogers, J., Jacobs, J., Alaux, M., Bellec, A., Berges, H., Dolezel, J., Feuillet, C., Frenkel, Z., Gill, B., Korol, A., van der Vossen, E., Vautrin, S., 3; AL physical mapping:, Gill, B., Kaur, G., Luo, M., Sehgal, S., 3; DS physical mapping and BAC sequencing and assembly:, Bartos, J., Holusova, K., Plihal, O., 3; DL BAC sequencing and assembly:, Clark, M. D., Heavens, D., Kettleborough, G., Wright, J., 4; A physical mapping, BAC sequencing, assembly, and annotation:, Valarik, M., Abrouk, M., Balcarkova, B., Holusova, K., Hu, Y., Luo, M., 5; BS BAC sequencing and assembly:, Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., 6; B BAC sequencing and assembly:, Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., 7; A physical mapping and BAC sequencing:, Appels, R., Hayden, M., Keeble-Gagnere, G., Rigault, P., Tibbits, J., 7; B physical mapping, BAC sequencing, and assembly:, Olsen, O.-A., Belova, T., Cattonaro, F., Jiumeng, M., Kugler, K., Mayer, K. F. X., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., 7; DS BAC sequencing and assembly:, Simkova, H., Abrouk, M., Batley, J., Bayer, P. E., Edwards, D., Hayashi, S., Toegelova, H., Tulpova, Z., Visendi, P., 7; DL physical mapping and BAC sequencing:, Weining, S., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Figures:, Borrill, P., Gundlach, H., Galvez, S., Kaithakottil, G., Lang, D., Lux, T., Mascher, M., Ormanbekova, D., Prade, V., Ramirez-Gonzalez, R. H., Spannagl, M., Stein, N., Uauy, C., Venturini, L., Manuscript writing team:, Stein, N., Appels, R., Eversole, K., Rogers, J., Borrill, P., Cattivelli, L., Choulet, F., Hernandez, P., Kanyuka, K., Lang, D., Mascher, M., Nilsen, K., Paux, E., Pozniak, C. J., Ramirez-Gonzalez, R. H., Simkova, H., Small, I., Spannagl, M., Swarbreck, D., Uauy, C. American Association for the Advancement of Science (AAAS) 0036-8075 00368075 1095-9203 10959203 |
shingle_title_1 | Shifting the limits in wheat research and breeding using a fully annotated reference genome |
shingle_title_2 | Shifting the limits in wheat research and breeding using a fully annotated reference genome |
shingle_title_3 | Shifting the limits in wheat research and breeding using a fully annotated reference genome |
shingle_title_4 | Shifting the limits in wheat research and breeding using a fully annotated reference genome |
timestamp | 2025-06-30T23:36:29.681Z |
titel | Shifting the limits in wheat research and breeding using a fully annotated reference genome |
titel_suche | Shifting the limits in wheat research and breeding using a fully annotated reference genome |
topic | W V TE-TZ SQ-SU WW-YZ TA-TD U |
uid | ipn_articles_6320909 |