Origin and evolution of the bread wheat D genome.

Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
14 Aug 2024
Historique:
received: 15 11 2023
accepted: 10 07 2024
medline: 15 8 2024
pubmed: 15 8 2024
entrez: 14 8 2024
Statut: aheadofprint

Résumé

Bread wheat (Triticum aestivum) is a globally dominant crop and major source of calories and proteins for the human diet. Compared with its wild ancestors, modern bread wheat shows lower genetic diversity, caused by polyploidisation, domestication and breeding bottlenecks

Identifiants

DOI: 10.1038/s41586-024-07808-z PMID: 39143210
pubmed: 39143210
doi: 10.1038/s41586-024-07808-z
pii: 10.1038/s41586-024-07808-z
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

© 2024. The Author(s).

Références

Dubcovsky, J. & Dvorak, J. Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316, 1862–1866 (2007).
pubmed: 17600208 pmcid: 4737438 doi: 10.1126/science.1143986
Zhou, Y. et al. Triticum population sequencing provides insights into wheat adaptation. Nat. Genet. 52, 1412–1422 (2020).
pubmed: 33106631 doi: 10.1038/s41588-020-00722-w
Tadesse, W. et al. Genetic gains in wheat breeding and its role in feeding the world. Crop Breed. Genet. Genom. 1, e190005 (2019).
Marcussen, T. et al. Ancient hybridizations among the ancestral genomes of bread wheat. Science 345, 1250092 (2014).
pubmed: 25035499 doi: 10.1126/science.1250092
Wang, J. et al. Aegilops tauschii single nucleotide polymorphisms shed light on the origins of wheat D‐genome genetic diversity and pinpoint the geographic origin of hexaploid wheat. New Phytol. 198, 925–937 (2013).
pubmed: 23374069 doi: 10.1111/nph.12164
Zhao, X. et al. Population genomics unravels the Holocene history of bread wheat and its relatives. Nat. Plants 9, 403–419 (2023).
pubmed: 36928772 doi: 10.1038/s41477-023-01367-3
Gaut, B. S., Seymour, D. K., Liu, Q. & Zhou, Y. Demography and its effects on genomic variation in crop domestication. Nat. Plants 4, 512–520 (2018).
pubmed: 30061748 doi: 10.1038/s41477-018-0210-1
Leal‐Bertioli, S. C. et al. Segmental allopolyploidy in action: increasing diversity through polyploid hybridization and homoeologous recombination. Am. J. Bot. 105, 1053–1066 (2018).
pubmed: 29985538 doi: 10.1002/ajb2.1112
Cheng, H. et al. Frequent intra- and inter-species introgression shapes the landscape of genetic variation in bread wheat. Genome Biol. 20, 136 (2019).
pubmed: 31300020 pmcid: 6624984 doi: 10.1186/s13059-019-1744-x
He, F. et al. Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat. Genet. 51, 1194–1194 (2019).
pubmed: 31197271 doi: 10.1038/s41588-019-0463-2
Walkowiak, S. et al. Multiple wheat genomes reveal global variation in modern breeding. Nature 588, 277–283 (2020).
pubmed: 33239791 pmcid: 7759465 doi: 10.1038/s41586-020-2961-x
Keilwagen, J. et al. Detecting major introgressions in wheat and their putative origins using coverage analysis. Sci. Rep. 12, 1908 (2022).
pubmed: 35115645 pmcid: 8813953 doi: 10.1038/s41598-022-05865-w
Ahmed, H. I. et al. Einkorn genomics sheds light on history of the oldest domesticated wheat. Nature 620, 830–838 (2023).
pubmed: 37532937 pmcid: 10447253 doi: 10.1038/s41586-023-06389-7
Gaurav, K. et al. Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. Nat. Biotechnol. 40, 422–431 (2022).
pubmed: 34725503 doi: 10.1038/s41587-021-01058-4
Zhou, Y. et al. Introgressing the Aegilops tauschii genome into wheat as a basis for cereal improvement. Nat. Plants 7, 774–786 (2021).
pubmed: 34045708 doi: 10.1038/s41477-021-00934-w
Wenger, A. M. et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat. Biotechnol. 37, 1155–1162 (2019).
pubmed: 31406327 pmcid: 6776680 doi: 10.1038/s41587-019-0217-9
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A. & Zdobnov, E. M. BUSCO update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol. Biol. Evol. 38, 4647–4654 (2021).
pubmed: 34320186 pmcid: 8476166 doi: 10.1093/molbev/msab199
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
pubmed: 19815776 pmcid: 2858594 doi: 10.1126/science.1181369
Wang, L. et al. Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation. G3 11, jkab325 (2021).
pubmed: 34515796 pmcid: 8664484 doi: 10.1093/g3journal/jkab325
Zhu, T. et al. Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly. Plant J. 107, 303–314 (2021).
pubmed: 33893684 pmcid: 8360199 doi: 10.1111/tpj.15289
Mizuno, N., Yamasaki, M., Matsuoka, Y., Kawahara, T. & Takumi, S. Population structure of wild wheat D‐genome progenitor Aegilops tauschii Coss.: implications for intraspecific lineage diversification and evolution of common wheat. Mol. Ecol. 19, 999–1013 (2010).
pubmed: 20149088 doi: 10.1111/j.1365-294X.2010.04537.x
Savary, S. et al. The global burden of pathogens and pests on major food crops. Nat. Ecol. Evol. 3, 430–439 (2019).
pubmed: 30718852 doi: 10.1038/s41559-018-0793-y
Olson, E. L. et al. Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat. Theor. Appl. Genet. 126, 1179–1188 (2013).
pubmed: 23377571 doi: 10.1007/s00122-013-2045-5
Periyannan, S. et al. The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science 341, 786–788 (2013).
pubmed: 23811228 doi: 10.1126/science.1239028
Arora, S. et al. Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat. Biotechnol. 37, 139–143 (2019).
pubmed: 30718880 doi: 10.1038/s41587-018-0007-9
Boden, S. et al. Updated guidelines for gene nomenclature in wheat. Theor. Appl. Genet. 136, 72 (2023).
pubmed: 36952017 pmcid: 10036449 doi: 10.1007/s00122-023-04253-w
Raupp, W., Brown-Guedira, G. & Gill, B. Cytogenetic and molecular mapping of the leaf rust resistance gene Lr39 in wheat. Theor. Appl. Genet. 102, 347–352 (2001).
doi: 10.1007/s001220051652
Singh, S. et al. Lr41, Lr39, and a leaf rust resistance gene from Aegilops cylindrica may be allelic and are located on wheat chromosome 2DS. Theor. Appl. Genet. 108, 586–591 (2004).
pubmed: 14534751 doi: 10.1007/s00122-003-1477-8
Kolmer, J. A. & Fajolu, O. Virulence phenotypes of the wheat leaf rust pathogen, Puccinia triticina, in the United States from 2018 to 2020. Plant Dis. 106, 1723–1729 (2022).
pubmed: 34978866 doi: 10.1094/PDIS-10-21-2321-RE
Athiyannan, N. Molecular Genetic Characterisation of Triple Rust Resistance in Aegilops tauschii. PhD thesis, Univ. of Queensland (2018).
Wang, Y. et al. An unusual tandem kinase fusion protein confers leaf rust resistance in wheat. Nat. Genet. 55, 914–920 (2023).
pubmed: 37217716 pmcid: 10260399 doi: 10.1038/s41588-023-01401-2
Yu, G. et al. The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase. Nat. Genet. 55, 921–926 (2023).
pubmed: 37217714 pmcid: 10260397 doi: 10.1038/s41588-023-01402-1
Klymiuk, V., Coaker, G., Fahima, T. & Pozniak, C. J. Tandem protein kinases emerge as new regulators of plant immunity. Mol. Plant Microbe Interact. 34, 1094–1102 (2021).
pubmed: 34096764 pmcid: 8761531 doi: 10.1094/MPMI-03-21-0073-CR
Athiyannan, N. et al. Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nat. Genet. 54, 227–231 (2022).
pubmed: 35288708 pmcid: 8920886 doi: 10.1038/s41588-022-01022-1
Sansaloni, C. et al. Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Nat. Commun. 11, 4572 (2020).
pubmed: 32917907 pmcid: 7486412 doi: 10.1038/s41467-020-18404-w
Beridze, R. K., Hanelt, P., Kandelaki, V. N., Sakvarelidze, I. M. & Schultze-Motel, J. A further mission to the Georgian SSR 1984 for collecting indigenous material of cultivated plants. Kulturpflanze 33, 199–212 (1985).
doi: 10.1007/BF01997272
Rosyara, U. et al. Genetic contribution of synthetic hexaploid wheat to CIMMYT’s spring bread wheat breeding germplasm. Sci. Rep. 9, 12355 (2019).
pubmed: 31451719 pmcid: 6710277 doi: 10.1038/s41598-019-47936-5
Cheng, S. et al. Harnessing landrace diversity empowers wheat breeding. Nature https://doi.org/10.1038/s41586-024-07682-9 (2024).
Delorean, E. et al. High molecular weight glutenin gene diversity in Aegilops tauschii demonstrates unique origin of superior wheat quality. Commun. Biol. 4, 1242 (2021).
pubmed: 34725451 pmcid: 8560932 doi: 10.1038/s42003-021-02563-7
Sato, K. et al. Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’. DNA Res. 28, dsab008 (2021).
pubmed: 34254113 pmcid: 8320877 doi: 10.1093/dnares/dsab008
Kale, S. M. et al. A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat. Plant Biotechnol. J. 20, 1730–1742 (2022).
pubmed: 35562859 pmcid: 9398310 doi: 10.1111/pbi.13843
Wang, Z. Y. et al. Helitron and CACTA DNA transposons actively reshape the common wheat-AK58 genome. Genomics 114, 110288 (2022).
pubmed: 35124171 doi: 10.1016/j.ygeno.2022.110288
Guo, W. et al. Origin and adaptation to high altitude of Tibetan semi-wild wheat. Nat. Commun. 11, 5085 (2020).
pubmed: 33033250 pmcid: 7545183 doi: 10.1038/s41467-020-18738-5
Gonçalves-Dias, J., Singh, A., Graf, C. & Stetter, M. G. Genetic incompatibilities and evolutionary rescue by wild relatives shaped grain amaranth domestication. Mol. Biol. Evol. 40, msad177 (2023).
pubmed: 37552934 pmcid: 10439364 doi: 10.1093/molbev/msad177
Weide, A., Riehl, S., Zeidi, M. & Conard, N. J. A systematic review of wild grass exploitation in relation to emerging cereal cultivation throughout the Epipalaeolithic and aceramic Neolithic of the Fertile Crescent. PLoS ONE 13, e0189811 (2018).
pubmed: 29293519 pmcid: 5749723 doi: 10.1371/journal.pone.0189811
Singh, N. et al. Genomic analysis confirms population structure and identifies inter-lineage hybrids in Aegilops tauschii. Front. Plant Sci. 10, 9 (2019).
pubmed: 30740115 pmcid: 6357674 doi: 10.3389/fpls.2019.00009
Abrouk, M. et al. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nat. Commun. 11, 4488 (2020).
pubmed: 32901040 pmcid: 7479619 doi: 10.1038/s41467-020-18329-4
Thachuk, C. et al. Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures. BMC Bioinformatics 10, 243 (2009).
pubmed: 19660135 pmcid: 2734557 doi: 10.1186/1471-2105-10-243
Driguez, P. et al. LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology. Genome Biol. 22, 256 (2021).
pubmed: 34479618 pmcid: 8414726 doi: 10.1186/s13059-021-02475-z
Cheng, H. Y., Concepcion, G. T., Feng, X. W., Zhang, H. W. & Li, H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat. Methods 18, 170–175 (2021).
pubmed: 33526886 pmcid: 7961889 doi: 10.1038/s41592-020-01056-5
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).
pubmed: 23422339 pmcid: 3624806 doi: 10.1093/bioinformatics/btt086
Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020).
pubmed: 32928274 pmcid: 7488777 doi: 10.1186/s13059-020-02134-9
Bankevich, A., Bzikadze, A. V., Kolmogorov, M., Antipov, D. & Pevzner, P. A. Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads. Nat. Biotechnol. 40, 1075–1081 (2022).
pubmed: 35228706 doi: 10.1038/s41587-022-01220-6
Padmarasu, S., Himmelbach, A., Mascher, M. & Stein, N. in Plant Long Non-Coding RNAs: Methods and Protocols, Vol. 1933 (eds Chekanova, J. A. & Wang, H.-L. V.) 441–472 (Springer, 2019).
Himmelbach, A., Walde, I., Mascher, M. & Stein, N. Tethered chromosome conformation capture sequencing in Triticeae: a valuable tool for genome assembly. Bio Protoc. 8, e2955 (2018).
pubmed: 34395764 pmcid: 8328666 doi: 10.21769/BioProtoc.2955
Durand, N. C. et al. Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments. Cell Syst. 3, 95–98 (2016).
pubmed: 27467249 pmcid: 5846465 doi: 10.1016/j.cels.2016.07.002
Dudchenko, O. et al. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356, 92–95 (2017).
pubmed: 28336562 pmcid: 5635820 doi: 10.1126/science.aal3327
Durand, N. C. et al. Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Cell Syst. 3, 99–101 (2016).
pubmed: 27467250 pmcid: 5596920 doi: 10.1016/j.cels.2015.07.012
Alonge, M. et al. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biol. 23, 258 (2022).
pubmed: 36522651 pmcid: 9753292 doi: 10.1186/s13059-022-02823-7
Jain, C., Koren, S., Dilthey, A., Phillippy, A. M. & Aluru, S. A fast adaptive algorithm for computing whole-genome homology maps. Bioinformatics 34, i748–i756 (2018).
pubmed: 30423094 pmcid: 6129286 doi: 10.1093/bioinformatics/bty597
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
pubmed: 24695404 pmcid: 4103590 doi: 10.1093/bioinformatics/btu170
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
pubmed: 23104886 doi: 10.1093/bioinformatics/bts635
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
pubmed: 33590861 pmcid: 7931819 doi: 10.1093/gigascience/giab008
Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M. & Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genom. Bioinformatics 3, lqaa108 (2021).
doi: 10.1093/nargab/lqaa108
Hoff, K. J., Lange, S., Lomsadze, A., Borodovsky, M. & Stanke, M. BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS. Bioinformatics 32, 767–769 (2016).
pubmed: 26559507 doi: 10.1093/bioinformatics/btv661
Hoff, K. J., Lomsadze, A., Borodovsky, M. & Stanke, M. in Gene Prediction: Methods and Protocols, Vol. 1962 (ed. Kollmar, M.) 65–95 (Springer, 2019).
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
pubmed: 20003500 pmcid: 2803857 doi: 10.1186/1471-2105-10-421
Blum, M. et al. The InterPro protein families and domains database: 20 years on. Nucleic Acids Res. 49, D344–D354 (2021).
pubmed: 33156333 doi: 10.1093/nar/gkaa977
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).
pubmed: 24451626 pmcid: 3998142 doi: 10.1093/bioinformatics/btu031
Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 238 (2019).
pubmed: 31727128 pmcid: 6857279 doi: 10.1186/s13059-019-1832-y
Smit, A., Hubley, R. & Green, P. RepeatMasker Open-4.0 http://www.repeatmasker.org (2015).
Contreras‐Moreira, B. et al. K‐mer counting and curated libraries drive efficient annotation of repeats in plant genomes. Plant Genome 14, e20143 (2021).
pubmed: 34562304 pmcid: 7614178 doi: 10.1002/tpg2.20143
Abrouk, M. et al. Chromosome-scale assembly of the wild wheat relative Aegilops umbellulata. Sci. Data 10, 739 (2023).
pubmed: 37880246 pmcid: 10600132 doi: 10.1038/s41597-023-02658-2
Shumate, A. & Salzberg, S. L. Liftoff: accurate mapping of gene annotations. Bioinformatics 37, 1639–1643 (2021).
pubmed: 33320174 pmcid: 8289374 doi: 10.1093/bioinformatics/btaa1016
Pertea, G. & Pertea, M. GFF utilities: GffRead and GffCompare. F1000Research 9, 304 (2020).
doi: 10.12688/f1000research.23297.1
Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).
pubmed: 33828273 pmcid: 8026399 doi: 10.1038/s41592-021-01101-x
Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).
pubmed: 32015543 pmcid: 7056644 doi: 10.1038/s41592-019-0686-2
Waskom, M. L. Seaborn: statistical data visualization. J. Op. Source Softw. 6, 3021 (2021).
doi: 10.21105/joss.03021
Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at arXiv https://doi.org/10.48550/arXiv.1303.3997 (2013).
Cook, D. E. & Andersen, E. C. VCF-kit: assorted utilities for the variant call format. Bioinformatics 33, 1581–1582 (2017).
pubmed: 28093408 pmcid: 5423453 doi: 10.1093/bioinformatics/btx011
Gain, C. & François, O. LEA 3: Factor models in population genetics and ecological genomics with R. Mol. Ecol. Resour. 21, 2738–2748 (2021).
pubmed: 33638893 doi: 10.1111/1755-0998.13366
Danecek, P. et al. The variant call format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
pubmed: 21653522 pmcid: 3137218 doi: 10.1093/bioinformatics/btr330
Wei, F., Wing, R. A. & Wise, R. P. Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. Plant Cell 14, 1903–1917 (2002).
pubmed: 12172030 pmcid: 151473 doi: 10.1105/tpc.002238
Stecher, G., Tamura, K. & Kumar, S. Molecular Evolutionary Genetics Analysis (MEGA) for macOS. Mol. Biol. Evol. 37, 1237–1239 (2020).
pubmed: 31904846 pmcid: 7086165 doi: 10.1093/molbev/msz312
Tamura, K., Stecher, G. & Kumar, S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol. Biol. Evol. 38, 3022–3027 (2021).
pubmed: 33892491 pmcid: 8233496 doi: 10.1093/molbev/msab120
Kolmer, J., Bajgain, P., Rouse, M., Li, J. & Zhang, P. Mapping and characterization of the recessive leaf rust resistance gene Lr83 on wheat chromosome arm 1DS. Theor. Appl. Genet. 136, 115 (2023).
pubmed: 37083869 doi: 10.1007/s00122-023-04361-7
Long, D. & Kolmer, J. A North American system of nomenclature for Puccinia recondita f. sp. tritici. Phytopathology 79, 525–529 (1989).
doi: 10.1094/Phyto-79-525
Wang, S. et al. Characterization of polyploid wheat genomic diversity using a high‐density 90,000 single nucleotide polymorphism array. Plant Biotechnol. J. 12, 787–796 (2014).
pubmed: 24646323 pmcid: 4265271 doi: 10.1111/pbi.12183
Pestsova, E., Ganal, M. & Röder, M. Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome 43, 689–697 (2000).
pubmed: 10984182 doi: 10.1139/g00-042
Heffelfinger, C., Fragoso, C. A. & Lorieux, M. Constructing linkage maps in the genomics era with MapDisto 2.0. Bioinformatics 33, 2224–2225 (2017).
pubmed: 28369214 pmcid: 5870660 doi: 10.1093/bioinformatics/btx177
Voorrips, R. E. MapChart: software for the graphical presentation of linkage maps and QTLs. J. Heredity 93, 77–78 (2002).
doi: 10.1093/jhered/93.1.77
Lück, S. et al. siRNA-Finder (si-Fi) software for RNAi-target design and off-target prediction. Front. Plant Sci. 10, 1023 (2019).
pubmed: 31475020 pmcid: 6704232 doi: 10.3389/fpls.2019.01023
Barnes, C. W. & Szabo, L. J. Detection and identification of four common rust pathogens of cereals and grasses using real-time polymerase chain reaction. Phytopathology 97, 717–727 (2007).
pubmed: 18943603 doi: 10.1094/PHYTO-97-6-0717
Chang, Q. et al. A unique invertase is important for sugar absorption of an obligate biotrophic pathogen during infection. New Phytol. 215, 1548–1561 (2017).
pubmed: 28744865 doi: 10.1111/nph.14666
Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).
pubmed: 21217122 pmcid: 3051319 doi: 10.1093/bioinformatics/btr011
Kokot, M., Długosz, M. & Deorowicz, S. KMC 3: counting and manipulating k-mer statistics. Bioinformatics 33, 2759–2761 (2017).
pubmed: 28472236 doi: 10.1093/bioinformatics/btx304
Gel, B. & Serra, E. karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics 33, 3088–3090 (2017).
pubmed: 28575171 pmcid: 5870550 doi: 10.1093/bioinformatics/btx346
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer-Verlag, 2016).
Cavalet-Giorsa, E. et al. Population genomics of the wild wheat Aegilops tauschii (Open wild wheat consortium phase II) [Dataset]. Dryad https://doi.org/10.5061/dryad.vmcvdnd0d (2024).
Cavalet-Giorsa, E. et al. k-mer matrix Aegilops tauschii diversity panel (Open wild wheat consortium phase II) Part 3/3 [Dataset]. Dryad https://doi.org/10.5061/dryad.wm37pvmvd (2024).
Cavalet-Giorsa, E. et al. k-mer matrix Aegilops tauschii diversity panel (Open wild wheat consortium phase II) Part 2/3 [Dataset]. Dryad https://doi.org/10.5061/dryad.wpzgmsbvm (2024).
Cavalet-Giorsa, E. et al. k-mer matrix Aegilops tauschii diversity panel (Open wild wheat consortium phase II) Part 1/3 [Dataset]. Dryad https://doi.org/10.5061/dryad.p5hqbzkvx (2024).

Auteurs

Emile Cavalet-Giorsa (E)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
ORCID: 0000-0001-6619-5996

Andrea González-Muñoz (A)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

Naveenkumar Athiyannan (N)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
ORCID: 0000-0002-9232-4680

Samuel Holden (S)

Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada.

Adil Salhi (A)

Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

Catherine Gardener (C)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

Jesús Quiroz-Chávez (J)

John Innes Centre, Norwich Research Park, Norwich, UK.
ORCID: 0000-0001-5935-2578

Samira M Rustamova (SM)

Institute of Molecular Biology and Biotechnologies, Ministry of Science and Education of the Republic of Azerbaijan, Baku, Azerbaijan.
ORCID: 0000-0001-5337-7109

Ahmed Fawzy Elkot (AF)

Wheat Research Department, Field Crops Research Institute, Agricultural Research Center (ARC), Giza, Egypt.
ORCID: 0000-0003-2967-2137

Mehran Patpour (M)

Department of Agroecology, Aarhus University, Slagelse, Denmark.
ORCID: 0000-0002-4914-2697

Awais Rasheed (A)

Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
International Maize and Wheat Improvement Centre (CIMMYT), c/o CAAS, Beijing, China.

Long Mao (L)

State Key Laboratory of Crop Gene Resources and Breeding and National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
ORCID: 0000-0002-3377-4040

Evans S Lagudah (ES)

Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Canberra, New South Wales, Australia.
ORCID: 0000-0002-6234-1789

Sambasivam K Periyannan (SK)

Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Canberra, New South Wales, Australia.
Centre for Crop Health School of Agriculture and Environmental Science, University of Southern Queensland, Toowoomba, Queensland, Australia.
ORCID: 0000-0002-5421-2872

Amir Sharon (A)

Institute for Cereal Crops Improvement, School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
ORCID: 0000-0002-6045-9169

Axel Himmelbach (A)

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.

Jochen C Reif (JC)

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
ORCID: 0000-0002-6742-265X

Manuela Knauft (M)

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.

Martin Mascher (M)

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
ORCID: 0000-0001-6373-6013

Nils Stein (N)

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany.
Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany.
ORCID: 0000-0003-3011-8731

Noam Chayut (N)

John Innes Centre, Norwich Research Park, Norwich, UK.

Sreya Ghosh (S)

John Innes Centre, Norwich Research Park, Norwich, UK.
ORCID: 0000-0002-7271-8914

Dragan Perovic (D)

Julius Kuehn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany.

Alexander Putra (A)

Bioscience Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
ORCID: 0000-0002-4864-9744

Ana B Perera (AB)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

Chia-Yi Hu (CY)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

Guotai Yu (G)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

Hanin Ibrahim Ahmed (HI)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
Centre d'anthropobiologie et de génomique de Toulouse (CAGT), Laboratoire d'Anthropobiologie et d'Imagerie de Synthèse, CNRS UMR 5288, Faculté de Médecine de Purpan, Toulouse, France.
ORCID: 0000-0001-9078-183X

Konstanze D Laquai (KD)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

Luis F Rivera (LF)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

Renjie Chen (R)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

Yajun Wang (Y)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.

Xin Gao (X)

Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
ORCID: 0000-0002-7108-3574

Sanzhen Liu (S)

Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
ORCID: 0000-0002-9513-855X

W John Raupp (WJ)

Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, Manhattan, KS, USA.
ORCID: 0000-0002-0135-3911

Eric L Olson (EL)

Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.

Jong-Yeol Lee (JY)

National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea.
ORCID: 0000-0002-0090-7193

Parveen Chhuneja (P)

School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.

Satinder Kaur (S)

School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.

Peng Zhang (P)

Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, New South Wales, Australia.
ORCID: 0000-0002-4191-1068

Robert F Park (RF)

Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, New South Wales, Australia.

Yi Ding (Y)

Plant Breeding Institute, School of Life and Environmental Sciences, University of Sydney, Cobbitty, New South Wales, Australia.

Deng-Cai Liu (DC)

Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.

Wanlong Li (W)

Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.

Firuza Y Nasyrova (FY)

Institute of Botany, Plant Physiology and Genetics, Tajik National Academy of Sciences, Dushanbe, Tajikistan.

Jan Dvorak (J)

Department of Plant Sciences, University of California, Davis, CA, USA.
ORCID: 0000-0002-0427-6528

Mehrdad Abbasi (M)

Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada.

Meng Li (M)

Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada.

Naveen Kumar (N)

Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada.

Wilku B Meyer (WB)

Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa.

Willem H P Boshoff (WHP)

Department of Plant Sciences, University of the Free State, Bloemfontein, South Africa.
ORCID: 0000-0003-2769-5546

Brian J Steffenson (BJ)

Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA.
ORCID: 0000-0001-7961-5363

Oadi Matny (O)

Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA.
ORCID: 0000-0002-8447-2886

Parva K Sharma (PK)

Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
ORCID: 0000-0002-0393-6432

Vijay K Tiwari (VK)

Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
ORCID: 0000-0001-7297-4048

Surbhi Grewal (S)

Nottingham Wheat Research Centre, School of Biosciences, University of Nottingham, Loughborough, UK.
ORCID: 0000-0002-0707-2504

Curtis J Pozniak (CJ)

University of Saskatchewan, Crop Development Centre, Agriculture Building, Saskatoon, Saskatchewan, Canada.
ORCID: 0000-0002-7536-3856

Harmeet Singh Chawla (HS)

University of Saskatchewan, Crop Development Centre, Agriculture Building, Saskatoon, Saskatchewan, Canada.
Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada.

Jennifer Ens (J)

University of Saskatchewan, Crop Development Centre, Agriculture Building, Saskatoon, Saskatchewan, Canada.
ORCID: 0000-0003-2663-1006

Luke T Dunning (LT)

Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Western Bank, Sheffield, UK.

James A Kolmer (JA)

Cereal Disease Laboratory, USDA-ARS, St Paul, MN, USA.

Gerard R Lazo (GR)

Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA.
ORCID: 0000-0002-9160-2052

Steven S Xu (SS)

Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA.

Yong Q Gu (YQ)

Crop Improvement and Genetics Research Unit, Western Regional Research Center, USDA-ARS, Albany, CA, USA.

Xianyang Xu (X)

Peanut and Small Grains Research Unit, USDA-ARS, Stillwater, OK, USA.

Cristobal Uauy (C)

John Innes Centre, Norwich Research Park, Norwich, UK.
ORCID: 0000-0002-9814-1770

Michael Abrouk (M)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
ORCID: 0000-0001-9082-1432

Salim Bougouffa (S)

Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
ORCID: 0000-0001-9218-6452

Gurcharn S Brar (GS)

Faculty of Land and Food Systems, The University of British Columbia (UBC), Vancouver, British Columbia, Canada.
Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, Canada.

Brande B H Wulff (BBH)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. brande.wulff@kaust.edu.sa.
ORCID: 0000-0003-4044-4346

Simon G Krattinger (SG)

Plant Science Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. simon.krattinger@kaust.edu.sa.
ORCID: 0000-0001-6912-7411

Classifications MeSH