Worldwide Wheat Genome Sequencing Consortium (IWGSC). Shifting the boundaries in wheat analysis and breeding utilizing a totally annotated reference genome. Science 361, eaar7191 (2018).
Walkowiak, S. et al. A number of wheat genomes reveal world variation in fashionable breeding. Nature 588, 277–283 (2020).
Salamini, F., Zkan, H., Brandolini, A., Schfer-Pregl, R. & Martin, W. Genetics and geography of untamed cereal domestication within the close to east. Nat. Rev. Genet. 3, 429–441 (2002).
The Worldwide Wheat Genome Sequencing Consortium (IWGSC). A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345, 1251788 (2014).
Feldman, M. & Levy, A. A. Genome evolution attributable to allopolyploidization in wheat. Genetics 192, 763–774 (2012).
Biehl, P. F. et al. Historic DNA from 8400 year-old catalhöyük wheat: implications for the origin of neolithic agriculture. PLoS ONE 11, e0151974 (2016).
Zhao, X. B. et al. Inhabitants genomics unravels the Holocene historical past of bread wheat and its kinfolk. Nat. Crops 9, 403–419 (2023).
Michael F, S. et al. A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication historical past. Nat. Crops 5, 1120–1128 (2019).
Mcclatchie, M. et al. Neolithic farming in north-western Europe: archaeobotanical proof from Eire. J. Archaeol. Sci. 51, 206–215 (2014).
Liu, X. et al. From ecological opportunism to multi-cropping: mapping meals globalisation in prehistory. Quat. Sci. Rev. 206, 21–28 (2019).
Hao, C. et al. Resequencing of 145 landmark cultivars reveals uneven sub-genome choice and powerful founder genotype results on wheat breeding in China. Mol. Plant 13, 1733–1751 (2020).
Zhuang, Q. S. Chinese language Wheat Enchancment and Pedigree Evaluation [Chinese] (Agricultural Press, 2003).
Murukarthick, J., Mona, S., Nils, S. & Martin, M. Constructing pan-genome infrastructures for crop crops and their use in affiliation genetics. DNA Res. 28, dsaa030 (2021).
Lei, L., Goltsman, E., Goodstein, D., Wu, G. A. & Vogel, J. P. Plant pan-genomics comes of age. Annu. Rev. Plant Biol. 72, 411–435 (2021).
Mona, S., Murukarthick, J., Nils, S. & Martin, M. Plant pangenomes for crop enchancment, biodiversity and evolution. Nat. Rev. Genet. https://doi.org/10.1038/s41576-024-00691-4 (2024).
Zhang, X. Y. & Appels, R. in The Wheat Genome (eds Appels, R. et al.) 93–111 (Springer, 2023).
Castillo, F. A. The Oxford Handbook of the Archaeology of Weight-reduction plan (Oxford Univ. Press, 2015).
Simon G, Okay. et al. A putative ABC transporter confers sturdy resistance to a number of fungal pathogens in wheat. Science 323, 1360–1363 (2009).
Fu, D. et al. A kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science 323, 1357–1360 (2009).
Wang, B. et al. De novo genome meeting and analyses of 12 founder inbred traces present insights into maize heterosis. Nat. Genet. 55, 312–323 (2023).
Qin, P. et al. Pan-genome evaluation of 33 genetically various rice accessions reveals hidden genomic variations. Cell 184, 3542–3558.e16 (2021).
Track, L. et al. Decreasing brassinosteroid signalling enhances grain yield in semi-dwarf wheat. Nature 617, 118–124 (2023).
Németh, A. & Längst, G. Genome group in and across the nucleolus. Tendencies Genet. 27, 149–156 (2011).
Kishii, M. & Mao, L. Artificial hexaploid wheat: yesterday, at this time, and tomorrow. Engineering 4, 552–558 (2018).
Guo, W. et al. Origin and adaptation to excessive altitude of Tibetan semi-wild wheat. Nat. Commun. 11, 5085 (2020).
Zhou, Y. et al. Triticum inhabitants sequencing gives insights into wheat adaptation. Nat. Genet. 52, 1412–1422 (2020).
Monat, C., Padmarasu, S., Lux, T., Wicker, T. & Mascher, M. TRITEX: chromosome-scale sequence meeting of Triticeae genomes with open-source instruments. Genome Biol. 20, 284 (2019).
Athiyannan, N. et al. Lengthy-read genome sequencing of bread wheat facilitates illness resistance gene cloning. Nat. Genet. 54, 227–231 (2022).
Kale, S. M. et al. A listing of resistance gene homologs and a chromosome-scale reference sequence assist resistance gene mapping in winter wheat. Plant Biotechnol. J. 20, 1730–1742 (2022).
Li, B. et al. Wheat centromeric retrotransposons: the brand new ones take a serious function in centromeric construction. Plant J. 73, 952–965 (2013).
Ahmed, H. I. et al. Einkorn genomics sheds mild on historical past of the oldest domesticated wheat. Nature 620, 830–838 (2023).
Wang, Z. et al. Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference. Nat. Commun. 13, 3891 (2022).
Cheng, H., Liu, J., Wen, J., Nie, X. & Jiang, Y. Frequent intra- and inter-species introgression shapes the panorama of genetic variation in bread wheat. Genome Biol. 20, 136 (2019).
Oliver, S. N., Finnegan, E. J., Dennis, E. S., Peacock, W. J. & Trevaskis, B. Vernalization-induced flowering in cereals is related to modifications in histone methylation on the VERNALIZATION1 gene. Proc. Natl Acad. Sci. USA 106, 8386–8391 (2009).
Alonge, M. et al. Main impacts of widespread structural variation on gene expression and crop enchancment in tomato. Cell 182, 145–161.e23 (2020).
Li, G. et al. A high-quality genome meeting highlights rye genomic traits and agronomically vital genes. Nat. Genet. 53, 574–584 (2021).
Rabanus-Wallace, M. T. et al. Chromosome-scale genome meeting gives insights into rye biology, evolution and agronomic potential. Nat. Genet. 53, 564–573 (2021).
Gabay, G., Zhang, J., Burguener, G. F., Howell, T. & Dubcovsky, J. Structural rearrangements in wheat (1BS)–rye (1RS) recombinant chromosomes have an effect on gene dosage and root size. Plant Genome 14, e20079 (2021).
Zhou, Y. et al. Introgressing the Aegilops tauschii genome into wheat as a foundation for cereal enchancment. Nat. Crops 7, 774–786 (2021).
Track, J. M. et al. Eight high-quality genomes reveal pan-genome structure and ecotype differentiation of Brassica napus. Nat. Crops 6, 34–45 (2020).
Saayman, X., Graham, E., Nathan, W. J., Nussenzweig, A. & Esashi, F. Centromeres as common hotspots of DNA breakage, driving RAD51-mediated recombination throughout quiescence. Mol. Cell 83, 523–538.e7 (2023).
Nambiar, M. & Smith, G. R. Pericentromere-Particular cohesin advanced prevents meiotic pericentric DNA double-strand breaks and deadly crossovers. Mol. Cell 71, 540–553.e4 (2018).
He, F. et al. Exome sequencing highlights the function of wild-relative introgression in shaping the adaptive panorama of the wheat genome. Nat. Genet. https://doi.org/10.1038/s41588-019-0382-2 (2019).
Zhao, J. et al. Centromere repositioning and shifts in wheat evolution. Plant Commun. 4, 100556 (2023).
Scott A, B. et al. Ppd-1 is a key regulator of inflorescence structure and paired spikelet growth in wheat. Nat. Crops 1, 14016 (2015).
Yan, L. L. et al. The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303, 1640–1644 (2004).
Yan, L. et al. Positional cloning of the wheat vernalization gene VRN1. Proc. Natl Acad. Sci. USA 100, 6263–6268 (2003).
Hazen, S. P. et al. Copy quantity variation affecting the Photoperiod-B1 and Vernalization-A1 genes is related to altered flowering time in wheat (Triticum aestivum). PLoS ONE https://doi.org/10.1371/journal.pone.0033234 (2012).
Würschum, T., Boeven, P. H. G., Langer, S. M., Longin, C. F. H. & Leiser, W. L. Multiply to beat: copy quantity variations at Ppd-B1 and Vrn-A1 facilitate world adaptation in wheat. BMC Genet. 16, 96 (2015).
Giroux, M. J. & Morris, C. F. Wheat grain hardness outcomes from extremely conserved mutations within the friabilin elements puroindoline a and b. Proc. Natl Acad. Sci. USA 11, 6262–6266 (1998).
Xie, T. et al. De novo plant genome meeting primarily based on chromatin interactions: a case research of Arabidopsis thaliana. Mol. Plant 8, 489–492 (2015).
Cheng, H., Concepcion, G. T., Feng, X., Zhang, H. & Li, H. Haplotype-resolved de novo meeting utilizing phased meeting graphs with hifiasm. Nat. Strategies 18, 170–175 (2021).
Wingett, S. et al. HiCUP: pipeline for mapping and processing Hello-C knowledge. F1000Res. 4, 1310 (2015).
Zhang, J. et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat. Genet. 50, 1565–1573 (2018).
Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies primarily based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013).
Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. BUSCO: assessing genome meeting and annotation completeness with single-copy orthologs. Bioinformatics 31, 3210–3212 (2015).
Ou, S., Chen, J. & Jiang, N. Assessing genome meeting high quality utilizing the LTR meeting index (LAI). Nucleic Acids Res. 46, e126 (2018).
Burkhard, S. et al. The NLR-Annotator software permits annotation of the intracellular immune receptor repertoire. Plant Physiol. 183, 468–482 (2020).
Tarailo-Graovac, M. & Chen, N. Utilizing RepeatMasker to determine repetitive parts in genomic sequences. Curr. Protoc. Bioinformatics https://doi.org/10.1002/0471250953.bi0410s05 (2009).
Benson, G. Tandem repeats finder: a program to investigate DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).
Yu, X. J., Zheng, H. Okay., Wang, J., Wang, W. & Su, B. Detecting lineage-specific adaptive evolution of brain-expressed genes in human utilizing rhesus macaque as outgroup. Genomics 88, 745–751 (2006).
Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–995 (2004).
Haas, B. J. et al. Bettering the Arabidopsis genome annotation utilizing maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).
Stanke, M. et al. AUGUSTUS: ab initio prediction of other transcripts. Nucleic Acids Res. 34, W435–W439 (2006).
Burge, C. & Karlin, S. Prediction of full gene constructions in human genomic DNA. J. Mol. Biol. 268, 78–94 (1997).
Guigo, R. Assembling genes from predicted exons in linear time with dynamic programming. J. Comput. Biol. 5, 681–702 (1998).
Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open supply ab initio eukaryotic gene-finders. Bioinformatics 20, 2878–2879 (2004).
Korf, I. Gene discovering in novel genomes. BMC Bioinformatics 5, 59 (2004).
Kim, D. et al. TopHat2: correct alignment of transcriptomes within the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
Ghosh, S. & Chan, C. Okay. Evaluation of RNA-seq knowledge utilizing TopHat and Cufflinks. Strategies Mol. Biol. 1374, 339–361 (2016).
Haas, B. J. et al. Automated eukaryotic gene construction annotation utilizing EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008).
Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Primary native alignment search software. J. Mol. Biol. 215, 403–410 (1990).
Pruitt, Okay. D., Tatusova, T. & Maglott, D. R. NCBI Reference Sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61–D65 (2007).
Hunter, S. et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 37, D211–D215 (2009).
Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000).
Boeckmann, B. et al. The SWISS-PROT protein knowledgebase and its complement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370 (2003).
Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116–W120 (2005).
Tang, H. et al. Synteny and collinearity in plant genomes. Science 320, 486–488 (2008).
Wu, T. D. & Watanabe, C. Okay. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859–1875 (2005).
Li, H. & Durbin, R. Quick and correct brief learn alignment with Burrows–Wheeler remodel. Bioinformatics 25, 1754–1760 (2009).
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Weber, J. A., Aldana, R., Gallagher, B. D. & Edwards, J. S. Sentieon DNA pipeline for variant detection-Software program-only resolution, over 20× sooner than GATK 3.3 with similar outcomes. PeerJ PrePrints 4, e1672v1672 (2016).
McKenna, A. et al. The Genome Evaluation Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing knowledge. Genome Res. 20, 1297–1303 (2010).
Wang, Okay., Li, M. & Hakonarson, H. ANNOVAR: useful annotation of genetic variants from high-throughput sequencing knowledge. Nucleic Acids Res. 38, e164 (2010).
Marcais, G. et al. MUMmer4: a quick and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944 (2018).
Goel, M., Solar, H., Jiao, W. B. & Schneeberger, Okay. SyRI: discovering genomic rearrangements and native sequence variations from whole-genome assemblies. Genome Biol. 20, 277 (2019).
Jeffares, D. C. et al. Transient structural variations have robust results on quantitative traits and reproductive isolation in fission yeast. Nat. Commun. 8, 14061 (2017).
Chiang, C. et al. SpeedSeq: ultra-fast private genome evaluation and interpretation. Nat. Strategies 12, 966–968 (2015).
Huang, W., Li, L., Myers, J. R. & Marth, G. T. ART: a next-generation sequencing learn simulator. Bioinformatics 28, 593–594 (2012).
Laurens, V. D. M. Accelerating t-SNE utilizing tree-based algorithms. J. Mach. Study. Res. 15, 3221–3245 (2014).
Yang, Z. et al. ggComp permits dissection of germplasm sources and building of a multiscale germplasm community in wheat. Plant Physiol. 188, 1950–1965 (2022).
Gao, F., Ming, C., Hu, W. & Li, H. New software program for the quick estimation of inhabitants recombination charges (FastEPRR) within the genomic period. G3 6, 1563–1571 (2016).
Danecek, P. et al. The variant name format and VCFtools. Bioinformatics 27, 2156–2158 (2011).
Kang, H. M. et al. Variance element mannequin to account for pattern construction in genome-wide affiliation research. Nat. Genet. 42, 348–354 (2010).
Katoh, Okay., Asimenos, G. & Toh, H. A number of alignment of DNA sequences with MAFFT. Strategies Mol. Biol. 537, 39–64 (2009).
Worth, M. N., Dehal, P. S. & Arkin, A. P. FastTree: computing massive minimal evolution bushes with profiles as an alternative of a distance matrix. Mol. Biol. Evol. 26, 1641–1650 (2009).
Quinlan, A. R. & Corridor, I. M. BEDTools: a versatile suite of utilities for evaluating genomic options. Bioinformatics 26, 841–842 (2010).
Scrucca, L., Fop, M., Murphy, T. B. & Raftery, A. E. mclust 5: Clustering, classification and density estimation utilizing Gaussian finite combination fashions. R J. 8, 289–317 (2016).
Chen, Y. et al. A collinearity-incorporating homology inference technique for connecting rising assemblies within the Triticeae tribe as a pilot observe within the plant pangenomic period. Mol. Plant 13, 1694–1708 (2020).
Ma, S. et al. WheatOmics: a platform combining a number of omics knowledge to speed up useful genomics research in wheat. Mol. Plant 14, 1965–1968 (2021).
He, W. et al. NGenomeSyn: an easy-to-use and versatile software for publication-ready visualization of syntenic relationships throughout a number of genomes. Bioinformatics 39, btad121 (2023).
Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Han, F., Lamb, J. C. & Birchler, J. A. Excessive frequency of centromere inactivation leading to steady dicentric chromosomes of maize. Proc. Natl Acad. Sci. USA 103, 3238–3243 (2006).
Fu, S., Chen, L., Wang, Y., Li, M. & Tang, Z. Oligonucleotide probes for ND-FISH evaluation to determine rye and wheat chromosomes. Sci. Rep. 5, 10552 (2015).
Tang, Z., Yang, Z. & Fu, S. Oligonucleotides changing the roles of repetitive sequences pAs1, pSc119.2, pTa-535, pTa71, CCS1, and pAWRC.1 for FISH evaluation. J. Appl. Genet. 55, 313–318 (2014).