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Pan-genome bridges wheat structural variations with habitat and breeding


  • Worldwide Wheat Genome Sequencing Consortium (IWGSC). Shifting the boundaries in wheat analysis and breeding utilizing a totally annotated reference genome. Science 361, eaar7191 (2018).

    Article 

    Google Scholar
     

  • Walkowiak, S. et al. A number of wheat genomes reveal world variation in fashionable breeding. Nature 588, 277–283 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • The Worldwide Wheat Genome Sequencing Consortium (IWGSC). A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345, 1251788 (2014).

    Article 

    Google Scholar
     

  • Feldman, M. & Levy, A. A. Genome evolution attributable to allopolyploidization in wheat. Genetics 192, 763–774 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 

    Google Scholar
     

  • Zhao, X. B. et al. Inhabitants genomics unravels the Holocene historical past of bread wheat and its kinfolk. Nat. Crops 9, 403–419 (2023).

    Article 
    PubMed 

    Google Scholar
     

  • 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).

    Article 

    Google Scholar
     

  • Mcclatchie, M. et al. Neolithic farming in north-western Europe: archaeobotanical proof from Eire. J. Archaeol. Sci. 51, 206–215 (2014).

    Article 

    Google Scholar
     

  • Liu, X. et al. From ecological opportunism to multi-cropping: mapping meals globalisation in prehistory. Quat. Sci. Rev. 206, 21–28 (2019).

    Article 
    ADS 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    ADS 

    Google Scholar
     

  • Fu, D. et al. A kinase-START gene confers temperature-dependent resistance to wheat stripe rust. Science 323, 1357–1360 (2009).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Qin, P. et al. Pan-genome evaluation of 33 genetically various rice accessions reveals hidden genomic variations. Cell 184, 3542–3558.e16 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Track, L. et al. Decreasing brassinosteroid signalling enhances grain yield in semi-dwarf wheat. Nature 617, 118–124 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Németh, A. & Längst, G. Genome group in and across the nucleolus. Tendencies Genet. 27, 149–156 (2011).

    Article 
    PubMed 

    Google Scholar
     

  • Kishii, M. & Mao, L. Artificial hexaploid wheat: yesterday, at this time, and tomorrow. Engineering 4, 552–558 (2018).

    Article 

    Google Scholar
     

  • Guo, W. et al. Origin and adaptation to excessive altitude of Tibetan semi-wild wheat. Nat. Commun. 11, 5085 (2020).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhou, Y. et al. Triticum inhabitants sequencing gives insights into wheat adaptation. Nat. Genet. 52, 1412–1422 (2020).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Athiyannan, N. et al. Lengthy-read genome sequencing of bread wheat facilitates illness resistance gene cloning. Nat. Genet. 54, 227–231 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, B. et al. Wheat centromeric retrotransposons: the brand new ones take a serious function in centromeric construction. Plant J. 73, 952–965 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ahmed, H. I. et al. Einkorn genomics sheds mild on historical past of the oldest domesticated wheat. Nature 620, 830–838 (2023).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, Z. et al. Dispersed emergence and protracted domestication of polyploid wheat uncovered by mosaic ancestral haploblock inference. Nat. Commun. 13, 3891 (2022).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alonge, M. et al. Main impacts of widespread structural variation on gene expression and crop enchancment in tomato. Cell 182, 145–161.e23 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, G. et al. A high-quality genome meeting highlights rye genomic traits and agronomically vital genes. Nat. Genet. 53, 574–584 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhou, Y. et al. Introgressing the Aegilops tauschii genome into wheat as a foundation for cereal enchancment. Nat. Crops 7, 774–786 (2021).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 

    Google Scholar
     

  • Yan, L. L. et al. The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303, 1640–1644 (2004).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yan, L. et al. Positional cloning of the wheat vernalization gene VRN1. Proc. Natl Acad. Sci. USA 100, 6263–6268 (2003).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    ADS 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wingett, S. et al. HiCUP: pipeline for mapping and processing Hello-C knowledge. F1000Res. 4, 1310 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, J. et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nat. Genet. 50, 1565–1573 (2018).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Burton, J. N. et al. Chromosome-scale scaffolding of de novo genome assemblies primarily based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ou, S., Chen, J. & Jiang, N. Assessing genome meeting high quality utilizing the LTR meeting index (LAI). Nucleic Acids Res. 46, e126 (2018).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burkhard, S. et al. The NLR-Annotator software permits annotation of the intracellular immune receptor repertoire. Plant Physiol. 183, 468–482 (2020).

    Article 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Birney, E., Clamp, M. & Durbin, R. GeneWise and Genomewise. Genome Res. 14, 988–995 (2004).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Haas, B. J. et al. Bettering the Arabidopsis genome annotation utilizing maximal transcript alignment assemblies. Nucleic Acids Res. 31, 5654–5666 (2003).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stanke, M. et al. AUGUSTUS: ab initio prediction of other transcripts. Nucleic Acids Res. 34, W435–W439 (2006).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burge, C. & Karlin, S. Prediction of full gene constructions in human genomic DNA. J. Mol. Biol. 268, 78–94 (1997).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Guigo, R. Assembling genes from predicted exons in linear time with dynamic programming. J. Comput. Biol. 5, 681–702 (1998).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open supply ab initio eukaryotic gene-finders. Bioinformatics 20, 2878–2879 (2004).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Korf, I. Gene discovering in novel genomes. BMC Bioinformatics 5, 59 (2004).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim, D. et al. TopHat2: correct alignment of transcriptomes within the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ghosh, S. & Chan, C. Okay. Evaluation of RNA-seq knowledge utilizing TopHat and Cufflinks. Strategies Mol. Biol. 1374, 339–361 (2016).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Haas, B. J. et al. Automated eukaryotic gene construction annotation utilizing EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 9, R7 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hunter, S. et al. InterPro: the integrative protein signature database. Nucleic Acids Res. 37, D211–D215 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27–30 (2000).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Boeckmann, B. et al. The SWISS-PROT protein knowledgebase and its complement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370 (2003).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116–W120 (2005).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tang, H. et al. Synteny and collinearity in plant genomes. Science 320, 486–488 (2008).

    Article 
    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Wu, T. D. & Watanabe, C. Okay. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics 21, 1859–1875 (2005).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li, H. & Durbin, R. Quick and correct brief learn alignment with Burrows–Wheeler remodel. Bioinformatics 25, 1754–1760 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).


    Google Scholar
     

  • McKenna, A. et al. The Genome Evaluation Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing knowledge. Genome Res. 20, 1297–1303 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, Okay., Li, M. & Hakonarson, H. ANNOVAR: useful annotation of genetic variants from high-throughput sequencing knowledge. Nucleic Acids Res. 38, e164 (2010).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marcais, G. et al. MUMmer4: a quick and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chiang, C. et al. SpeedSeq: ultra-fast private genome evaluation and interpretation. Nat. Strategies 12, 966–968 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Huang, W., Li, L., Myers, J. R. & Marth, G. T. ART: a next-generation sequencing learn simulator. Bioinformatics 28, 593–594 (2012).

    Article 
    PubMed 

    Google Scholar
     

  • Laurens, V. D. M. Accelerating t-SNE utilizing tree-based algorithms. J. Mach. Study. Res. 15, 3221–3245 (2014).

    MathSciNet 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Danecek, P. et al. The variant name format and VCFtools. Bioinformatics 27, 2156–2158 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kang, H. M. et al. Variance element mannequin to account for pattern construction in genome-wide affiliation research. Nat. Genet. 42, 348–354 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Katoh, Okay., Asimenos, G. & Toh, H. A number of alignment of DNA sequences with MAFFT. Strategies Mol. Biol. 537, 39–64 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Quinlan, A. R. & Corridor, I. M. BEDTools: a versatile suite of utilities for evaluating genomic options. Bioinformatics 26, 841–842 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

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