References
Bush, S.J., Castillo-Morales, A., Tovar-Corona, J.M., Chen, L., Kover, P. X., and Urrutia, A.O. (2014). Presence-absence variation in A. thaliana is primarily associated with genomic signatures consistent with relaxed selective constraints. Mol Biol Evol 31, 59–69.
Cao, J., Yu, Y., Huang, J., Liu, R., Chen, Y., Li, S., and Liu, J. (2017). Genome re-sequencing analysis uncovers pathogenecity-related genes undergoing positive selection in Magnaporthe oryzae. Sci China Life Sci 60, 880–890.
Chiang, C., Scott, A.J., Davis, J.R., Tsang, E.K., Li, X., Kim, Y., Hadzic, T., Damani, F.N., Ganel, L., Montgomery, S.B., et al. (2017). The impact of structural variation on human gene expression. Nat Genet 49, 692–699.
Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., and Ren, B. (2012). Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380.
Editorial. (2018). A reference standard for genome biology. Nat Biotechnol 36, 1121.
English, A.C., Salerno, W.J., Hampton, O.A., Gonzaga-Jauregui, C., Ambreth, S., Ritter, D.I., Beck, C.R., Davis, C.F., Dahdouli, M., Ma, S., et al. (2015). Assessing structural variation in a personal genome—towards a human reference diploid genome. BMC Genomics 16, 286.
Fuentes, R.R., Chebotarov, D., Duitama, J., Smith, S., De la Hoz, J.F., Mohiyuddin, M., Wing, R.A., McNally, K.L., Tatarinova, T., Grigoriev, A., et al. (2019). Structural variants in 3000 rice genomes. Genome Res 29, 870–880.
Garrison, E., Sirén, J., Novak, A.M., Hickey, G., Eizenga, J.M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M.F., et al. (2018). Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol 36, 875–879.
Guan, P., and Sung, W.K. (2016). Structural variation detection using nextgeneration sequencing data. Methods 102, 36–49.
Kronenberg, Z.N., Fiddes, I.T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O.S., Underwood, J.G., Nelson, B.J., Chaisson, M.J.P., Dougherty, M.L., et al. (2018). High-resolution comparative analysis of great ape genomes. Science 360, eaar6343.
Li, E., Liu, H., Huang, L., Zhang, X., Dong, X., Song, W., Zhao, H., and Lai, J. (2019). Long-range interactions between proximal and distal regulatory regions in maize. Nat Commun 10, 2633.
Lupianez, D.G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J.M., Laxova, R., et al. (2015). Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell 161, 1012–1025.
Morgante, M., Brunner, S., Pea, G., Fengler, K., Zuccolo, A., and Rafalski, A. (2005). Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 37, 997–1002.
Navarro, C. (2017). The mobile world of transposable elements. Trends Genet 33, 771–772.
Peng, Y., Xiong, D., Zhao, L., Ouyang, W., Wang, S., Sun, J., Zhang, Q., Guan, P., Xie, L., Li, W., et al. (2019). Chromatin interaction maps reveal genetic regulation for quantitative traits in maize. Nat Commun 10, 2632.
Pyhäjärvi, T., Hufford, M.B., Mezmouk, S., and Ross-Ibarra, J. (2013). Complex patterns of local adaptation in teosinte. Genome Biol Evol 5, 1594–1609.
Ranz, J., and Clifton, B. (2019). Characterization and evolutionary dynamics of complex regions in eukaryotic genomes. Sci China Life Sci 62, 467–488.
Sibbesen, J.A., Maretty, L., Maretty, L., and Krogh, A. (2018). Accurate genotyping across variant classes and lengths using variant graphs. Nat Genet 50, 1054–1059.
Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., et al. (2018). Extensive intraspecific gene order and gene structural variations between Mol7 and other maize genomes. Nat Genet 50, 1289–1295.
Sedlazeck, F.J., Dhroso, A., Bodian, D.L., Paschall, J., Hermes, F., and Zook, J.M. (2017). Tools for annotation and comparison of structural variation. F1000 Res 6, 1795.
Shen, Y., Liu, J., Geng, H., Zhang, J., Liu, Y., Zhang, H., Xing, S., Du, J., Ma, S., and Tian, Z. (2018). De novo assembly of a Chinese soybean genome. Sci China Life Sci 61, 871–884.
Song, X., and Cao, X. (2017). Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice. Curr Opin Plant Biol 36, 111–118.
Studer, A., Zhao, Q., Ross-Ibarra, J., and Doebley, J. (2011). Identification of a functional transposon insertion in the maize domestication gene tbl. Nat Genet 43, 1160–1163.
Sudmant, PH., Rausch, T., Gardner, E.J., Handsaker, R.E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015). An integrated map of structural variation in 2,504 human genomes. Nature 526, 75–81.
The 3000 rice genomes project. (2014). The 3,000 rice genomes project. GigaScience 3, 7.
Torkamaneh, D., Laroche, J., Tardivel, A., O' Donoughue, L., Cober, E., Rajcan, I., and Belzile, F. (2018). Comprehensive description of genomewide nucleotide and structural variation in short-season soya bean. Plant Biotechnol J 16, 749–759.
Xue, W., Xing, Y., Weng, X., Zhao, Y., Tang, W., Wang, L., Zhou, H., Yu, S., Xu, C., Li, X., et al. (2008). Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40, 761–767.
Yang, N., Liu, J., Gao, Q., Gui, S., Chen, L., Yang, L., Huang, J., Deng, T., Luo, J., He, L., et al. (2019). Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nat Genet 51, 1052–1059.
Zuo, W., Chao, Q., Zhang, N., Ye, J., Tan, G., Li, B., Xing, Y., Zhang, B., Liu, H., Fengler, K.A., et al. (2015). A maize wall-associated kinase confers quantitative resistance to head smut. Nat Genet 47, 151–157.
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Yang, N., Wu, S. & Yan, J. Structural variation in complex genome: detection, integration and function. Sci. China Life Sci. 62, 1098–1100 (2019). https://doi.org/10.1007/s11427-019-9664-4
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DOI: https://doi.org/10.1007/s11427-019-9664-4