Publications

2020

Tian, P., Zhang, X., Xia, R., Liu, Y., Wang, M., Li, B., Liu, T., Shi, J., Wing, R. A., Meyers, B. C., & Chen, M. (2020). Evolution and diversification of reproductive phased small interfering RNAs in Oryza species. New Phytologist, 229(5), 2970–2983. https://doi.org/10.1111/nph.17035

Hofmeister, B. T., Denkena, J., Colomé-Tatché, M., Shahryary, Y., Hazarika, R., Grimwood, J., Mamidi, S., Jenkins, J., Grabowski, P. P., Sreedasyam, A., Shu, S., Barry, K., Lail, K., Adam, C., Lipzen, A., Sorek, R., Kudrna, D., Talag, J., Wing, R., … Schmitz, R. J. (2020). A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biology, 21(1). https://doi.org/10.1186/s13059-020-02162-5

Mussurova, S., Al-Bader, N., Zuccolo, A., & Wing, R. A. (2020). Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice. Frontiers in Plant Science, 11. https://doi.org/10.3389/fpls.2020.579980

Fan, G., Song, Y., Yang, L., Huang, X., Zhang, S., Zhang, M., Yang, X., Chang, Y., Zhang, H., Li, Y., Liu, S., Yu, L., Chu, J., Seim, I., Feng, C., Near, T. J., Wing, R. A., Wang, W., Wang, K., … He, S. (2020). Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K). GigaScience, 9(8). https://doi.org/10.1093/gigascience/giaa080

Yi, X., Liu, J., Chen, S., Wu, H., Liu, M., Xu, Q., Lei, L., Lee, S., Zhang, B., Kudrna, D., Fan, W., Wing, R., Yang, C., Zhang, M., Zhang, J., Wang, X., & Chen, N. (2020). Platinum-grade soybean reference genome facilitates characterization of genetic underpinnings of traits. https://doi.org/10.21203/rs.3.rs-57915/v1

Freitas, K. E. J. de, dos Santos, R. S., Busanello, C., de Carvalho Victoria, F., Lopes, J. L., Wing, R. A., & Costa de Oliveira, A. (2020). SSRG evolution in the genus Oryza. https://doi.org/10.21203/rs.3.rs-45627/v1

Hon, T., Mars, K., Young, G., Tsai, Y.-C., Karalius, J. W., Landolin, J. M., Maurer, N., Kudrna, D., Hardigan, M. A., Steiner, C. C., Knapp, S. J., Ware, D., Shapiro, B., Peluso, P., & Rank, D. R. (2020). Highly accurate long-read HiFi sequencing data for five complex genomes. https://doi.org/10.1101/2020.05.04.077180

Zhou, Y., Chebotarov, D., Kudrna, D., Llaca, V., Lee, S., Rajasekar, S., Mohammed, N., Al-Bader, N., Sobel-Sorenson, C., Parakkal, P., Arbelaez, L. J., Franco, N., Alexandrov, N., Hamilton, N. R. S., Leung, H., Mauleon, R., Lorieux, M., Zuccolo, A., McNally, K., … Wing, R. A. (2020). A platinum standard pan-genome resource that represents the population structure of Asian rice. Scientific Data, 7(1). https://doi.org/10.1038/s41597-020-0438-2

Park, H.-S., Jayakodi, M., Lee, S. H., Jeon, J.-H., Lee, H.-O., Park, J. Y., Moon, B. C., Kim, C.-K., Wing, R. A., Newmaster, S. G., Kim, J. Y., & Yang, T.-J. (2020). Mitochondrial plastid DNA can cause DNA barcoding paradox in plants. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-63233-y

Shenton, M., Kobayashi, M., Terashima, S., Ohyanagi, H., Copetti, D., Hernández-Hernández, T., Zhang, J., Ohmido, N., Fujita, M., Toyoda, A., Ikawa, H., Fujiyama, A., Furuumi, H., Miyabayashi, T., Kubo, T., Kudrna, D., Wing, R., Yano, K., Nonomura, K.- ichi, … Kurata, N. (2020). Evolution and diversity of the wild rice Oryza officinalis complex, across continents genome types, and ploidy levels. Genome Biology and Evolution. https://doi.org/10.1093/gbe/evaa037

McNally, K. L., Mauleon, R. P., Chebotarov, D., Klassen, S. P., Kohli, A., Ye, G., Leung, H., Hamilton, R. S., & Wing, R. A. (2020). Mass genome sequencing of crops and wild relatives to accelerate crop breeding: the digital rice genebank. IOP Conference Series: Earth and Environmental Science, 482(1), 012005. https://doi.org/10.1088/1755-1315/482/1/012005

Liu, J., Seetharam, A. S., Chougule, K., Ou, S., Swentowsky, K. W., Gent, J. I., Llaca, V., Woodhouse, M. R., Manchanda, N., Presting, G. G., Kudrna, D. A., Alabady, M., Hirsch, C. N., Fengler, K. A., Ware, D., Michael, T. P., Hufford, M. B., & Dawe, R. K. (2020). Gapless assembly of maize chromosomes using long read technologies. https://doi.org/10.1101/2020.01.14.906230

2019

Hofmeister, B. T., Denkena, J., Colomé-Tatché, M., Shahryary, Y., Hazarika, R., Grimwood, J., Mamidi, S., Jenkins, J., Grabowski, P. P., Sreedasyam, A., Shu, S., Barry, K., Lail, K., Adam, C., Lipzen, A., Sorek, R., Kudrna, D., Talag, J., Wing, R., … Schmitz, R. J. (2019). The somatic genetic and epigenetic mutation rate in a wild long-lived perennialPopulus trichocarpa. https://doi.org/10.1101/862623

Zhou, Y., Chebotarov, D., Kudrna, D., Llaca, V., Lee, S., Rajasekar, S., Mohammed, N., Al-Bader, N., Sobel-Sorenson, C., Parakkal, P., Arbelaez, L. J., Franco, N., Alexandrov, N., Hamilton, N. R. S., Leung, H., Mauleon, R., Lorieux, M., Zuccolo, A., McNally, K., … Wing, R. A. (2019). Twelve Platinum-Standard Reference Genomes Sequences (PSRefSeq) that complete the full range of genetic diversity of Asian rice. https://doi.org/10.1101/2019.12.29.888347

Ohyanagi, H., Goto, K., Negrão, S., Wing, R. A., Tester, M. A., McNally, K. L., Bajic, V. B., Mineta, K., & Gojobori, T. (2019). High-resolution Introgressive Region Map Reveals Spatiotemporal Genome Evolution in Asian Rice Domestication. https://doi.org/10.1101/829168

Hazzouri, K. M., Gros-Balthazard, M., Flowers, J. M., Copetti, D., Lemansour, A., Lebrun, M., Masmoudi, K., Ferrand, S., Dhar, M. I., Fresquez, Z. A., Rosas, U., Zhang, J., Talag, J., Lee, S., Kudrna, D., Powell, R. F., Leitch, I. J., Krueger, R. R., Wing, R. A., … Purugganan, M. D. (2019). Genome-wide association mapping of date palm fruit traits. Nature Communications, 10(1). https://doi.org/10.1038/s41467-019-12604-9

Jain, R., Jenkins, J., Shu, S., Chern, M., Martin, J. A., Copetti, D., Duong, P. Q., Pham, N. T., Kudrna, D. A., Talag, J., Schackwitz, W. S., Lipzen, A. M., Dilworth, D., Bauer, D., Grimwood, J., Nelson, C. R., Xing, F., Xie, W., Barry, K. W., … Ronald, P. C. (2019). Genome sequence of the model rice variety KitaakeX. https://doi.org/10.21203/rs.2.10528/v2

Zhou, R., Macaya-Sanz, D., Carlson, C. H., Schmutz, J., Jenkins, J. W., Kudrna, D., Sharma, A., Sandor, L., Shu, S., Barry, K., Tuskan, G. A., Ma, T., Liu, J., Olson, M., Smart, L. B., & DiFazio, S. P. (2019). A Willow Sex Chromosome Reveals Convergent Evolution of Complex Palindromic Repeats. https://doi.org/10.1101/710046

Flynn, J. M., Long, M., Wing, R. A., & Clark, A. G. (2019). Evolutionary dynamics of abundant 7 bp satellites in the genome ofDrosophila virilis. https://doi.org/10.1101/693077

Paritosh, K., Yadava, S. K., Singh, P., Bhayana, L., Mukhopadhyay, A., Gupta, V., Bisht, N. C., Zhang, J., Kudrna, D., Copetti, D., Wing, R. A., Lachagari, V. B. R., Pradhan, A. K., & Pental, D. (2019). A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes. https://doi.org/10.1101/681080

Mangu, V. R., Ratnasekera, D., Yabes, J. C., Wing, R. A., & Baisakh, N. (2019). Functional screening of genes from a halophyte wild rice relative Porteresia coarctata in Arabidopsis model identifies candidate genes involved in salt tolerance. Current Plant Biology, 18, 100107. https://doi.org/10.1016/j.cpb.2019.100107

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., Mauleon, R., & Alexandrov, N. (2019). Structural variants in 3000 rice genomes. Genome Research, 29(5), 870–880. https://doi.org/10.1101/gr.241240.118

Chen, E., Huang, X., Tian, Z., Wing, R. A., & Han, B. (2019). The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis. Annual Review of Plant Biology, 70(1), 639–665. https://doi.org/10.1146/annurev-arplant-050718-100320

Zhang, L., Ren, Y., Yang, T., Li, G., Chen, J., Gschwend, A. R., Yu, Y., Hou, G., Zi, J., Zhou, R., Wen, B., Zhang, J., Chougule, K., Wang, M., Copetti, D., Peng, Z., Zhang, C., Zhang, Y., Ouyang, Y., … Long, M. (2019). Rapid evolution of protein diversity by de novo origination in Oryza. Nature Ecology & Evolution, 3(4), 679–690. https://doi.org/10.1038/s41559-019-0822-5