Publications

Harper, J., De Vega, J., Swain, S., Heavens, D., Gasior, D., Thomas, A., Evans, C., Lovatt, A., Lister, S., Thorogood, D., Skøt, L., Hegarty, M., Blackmore, T., Kudrna, D., Byrne, S., Asp, T., Powell, W., Fernandez-Fuentes, N., & Armstead, I. (2019). Integrating a newly developed BAC-based physical mapping resource for Lolium perenne with a genome-wide association study across a L. perenne European ecotype collection identifies genomic contexts associated with agriculturally important traits. Annals of Botany, 123(6), 977–992. https://doi.org/10.1093/aob/mcy230

Lovell, J. T., Jenkins, J., Lowry, D. B., Mamidi, S., Sreedasyam, A., Weng, X., Barry, K., Bonnette, J., Campitelli, B., Daum, C., Gordon, S. P., Gould, B. A., Khasanova, A., Lipzen, A., MacQueen, A., Palacio-Mejía, J. D., Plott, C., Shakirov, E. V., Shu, S., … Juenger, T. E. (2018). The genomic landscape of molecular responses to natural drought stress in Panicum hallii. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-07669-x

Liao, Y., Zhang, X., Li, B., Liu, T., Chen, J., Bai, Z., Wang, M., Shi, J., Walling, J. G., Wing, R. A., Jiang, J., & Chen, M. (2018). Comparison of Oryza sativa and Oryza brachyantha Genomes Reveals Selection-Driven Gene Escape from the Centromeric Regions. The Plant Cell, 30(8), 1729–1744. https://doi.org/10.1105/tpc.18.00163

Lv, S., Wu, W., Wang, M., Meyer, R. S., Ndjiondjop, M.-N., Tan, L., Zhou, H., Zhang, J., Fu, Y., Cai, H., Sun, C., Wing, R. A., & Zhu, Z. (2018). Genetic control of seed shattering during African rice domestication. Nature Plants, 4(6), 331–337. https://doi.org/10.1038/s41477-018-0164-3

Wing, R. A., Purugganan, M. D., & Zhang, Q. (2018). The rice genome revolution: from an ancient grain to Green Super Rice. Nature Reviews Genetics, 19(8), 505–517. https://doi.org/10.1038/s41576-018-0024-z

Kim, N., Jayakodi, M., Lee, S., Choi, B., Jang, W., Lee, J., Kim, H. H., Waminal, N. E., Lakshmanan, M., van Nguyen, B., Lee, Y. S., Park, H., Koo, H. J., Park, J. Y., Perumal, S., Joh, H. J., Lee, H., Kim, J., Kim, I. S., … Yang, T. (2018). Genome and evolution of the shade‐requiring medicinal herb Panax ginseng. Plant Biotechnology Journal, 16(11), 1904–1917. https://doi.org/10.1111/pbi.12926

Wang, W., Mauleon, R., Hu, Z., Chebotarov, D., Tai, S., Wu, Z., Li, M., Zheng, T., Fuentes, R. R., Zhang, F., Mansueto, L., Copetti, D., Sanciangco, M., Palis, K. C., Xu, J., Sun, C., Fu, B., Zhang, H., Gao, Y., … Leung, H. (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557(7703), 43–49. https://doi.org/10.1038/s41586-018-0063-9

Scheben, A., Chan, C.-K. K., Mansueto, L., Mauleon, R., Larmande, P., Alexandrov, N., Wing, R. A., McNally, K. L., Quesneville, H., & Edwards, D. (2018). Progress in single-access information systems for wheat and rice crop improvement. Briefings in Bioinformatics, 20(2), 565–571. https://doi.org/10.1093/bib/bby016

Stein, J. C., Yu, Y., Copetti, D., Zwickl, D. J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J. L., Wei, S., Wang, J., Liao, Y., Wang, M., Jacquemin, J., Becker, C., Kudrna, D., Zhang, J., Londono, C. E. M., … Wing, R. A. (2018). Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics, 50(2), 285–296. https://doi.org/10.1038/s41588-018-0040-0

Bhatia, D., Wing, R. A., Yu, Y., Chougule, K., Kudrna, D., Lee, S., Rang, A., & Singh, K. (2018). Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length. Euphytica, 214(2). https://doi.org/10.1007/s10681-018-2119-1

Wu, W., Liu, X., Wang, M., Meyer, R. S., Luo, X., Ndjiondjop, M.-N., Tan, L., Zhang, J., Wu, J., Cai, H., Sun, C., Wang, X., Wing, R. A., & Zhu, Z. (2017). A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nature Plants, 3(6). https://doi.org/10.1038/nplants.2017.64

Lee, C.-R., Wang, B., Mojica, J. P., Mandáková, T., Prasad, K. V. S. K., Goicoechea, J. L., Perera, N., Hellsten, U., Hundley, H. N., Johnson, J., Grimwood, J., Barry, K., Fairclough, S., Jenkins, J. W., Yu, Y., Kudrna, D., Zhang, J., Talag, J., Golser, W., … Mitchell-Olds, T. (2017). Young inversion with multiple linked QTLs under selection in a hybrid zone. Nature Ecology & Evolution, 1(5). https://doi.org/10.1038/s41559-017-0119

Thakare, D., Zhang, J., Wing, R. A., Cotty, P. J., & Schmidt, M. A. (2017). Aflatoxin-free transgenic maize using host-induced gene silencing. Science Advances, 3(3). https://doi.org/10.1126/sciadv.1602382

Xie, J., Huo, N., Zhou, S., Wang, Y., Guo, G., Deal, K. R., Ouyang, S., Liang, Y., Wang, Z., Xiao, L., Zhu, T., Hu, T., Tiwari, V., Zhang, J., Li, H., Ni, Z., Yao, Y., Peng, H., Zhang, S., … Sun, Q. (2017). Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes. Journal of Genetics and Genomics, 44(1), 51–61. https://doi.org/10.1016/j.jgg.2016.09.005

Brozynska, M., Copetti, D., Furtado, A., Wing, R. A., Crayn, D., Fox, G., Ishikawa, R., & Henry, R. J. (2017). Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. Plant Biotechnology Journal, 15(6), 765–774. https://doi.org/10.1111/pbi.12674

Copetti, D., & Wing, R. A. (2016). The Dark Side of the Genome: Revealing the Native Transposable Element/Repeat Content of Eukaryotic Genomes. Molecular Plant, 9(12), 1664–1666. https://doi.org/10.1016/j.molp.2016.09.006

Gan, X., Hay, A., Kwantes, M., Haberer, G., Hallab, A., Ioio, R. D., Hofhuis, H., Pieper, B., Cartolano, M., Neumann, U., Nikolov, L. A., Song, B., Hajheidari, M., Briskine, R., Kougioumoutzi, E., Vlad, D., Broholm, S., Hein, J., Meksem, K., … Tsiantis, M. (2016). The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nature Plants, 2(11). https://doi.org/10.1038/nplants.2016.167

Zhang, J., Chen, L.-L., Sun, S., Kudrna, D., Copetti, D., Li, W., Mu, T., Jiao, W.-B., Xing, F., Lee, S., Talag, J., Song, J.-M., Du, B., Xie, W., Luo, M., Maldonado, C. E., Goicoechea, J. L., Xiong, L., Wu, C., … Zhang, Q. (2016). Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Scientific Data, 3(1). https://doi.org/10.1038/sdata.2016.76

Wicker, T., Yu, Y., Haberer, G., Mayer, K. F. X., Marri, P. R., Rounsley, S., Chen, M., Zuccolo, A., Panaud, O., Wing, R. A., & Roffler, S. (2016). DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses. Nature Communications, 7(1). https://doi.org/10.1038/ncomms12790

Zhang, J., Chen, L.-L., Xing, F., Kudrna, D. A., Yao, W., Copetti, D., Mu, T., Li, W., Song, J.-M., Xie, W., Lee, S., Talag, J., Shao, L., An, Y., Zhang, C.-L., Ouyang, Y., Sun, S., Jiao, W.-B., Lv, F., … Zhang, Q. (2016). Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proceedings of the National Academy of Sciences, 113(35). https://doi.org/10.1073/pnas.1611012113

Zhang, J., Kudrna, D., Mu, T., Li, W., Copetti, D., Yu, Y., Goicoechea, J. L., Lei, Y., & Wing, R. A. (2016). Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences. Bioinformatics, 32(20), 3058–3064. https://doi.org/10.1093/bioinformatics/btw370

Wang, J., Yu, Y., Tao, F., Zhang, J., Copetti, D., Kudrna, D., Talag, J., Lee, S., Wing, R. A., & Fan, C. (2016). DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. Genome Biology, 17(1). https://doi.org/10.1186/s13059-016-0954-8

Wendel, J. F., Jackson, S. A., Meyers, B. C., & Wing, R. A. (2016). Evolution of plant genome architecture. Genome Biology, 17(1). https://doi.org/10.1186/s13059-016-0908-1

Bai, Z., Chen, J., Liao, Y., Wang, M., Liu, R., Ge, S., Wing, R. A., & Chen, M. (2016). The impact and origin of copy number variations in the Oryza species. BMC Genomics, 17(1). https://doi.org/10.1186/s12864-016-2589-2

Zhang, Y., Zhang, S., Liu, H., Fu, B., Li, L., Xie, M., Song, Y., Li, X., Cai, J., Wan, W., Kui, L., Huang, H., Lyu, J., Dong, Y., Wang, W., Huang, L., Zhang, J., Yang, Q., Shan, Q., … Hu, F. (2015). Genome and Comparative Transcriptomics of African Wild Rice Oryza longistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility. Molecular Plant, 8(11), 1683–1686. https://doi.org/10.1016/j.molp.2015.08.006