Publications

2023

Thathapalli Prakash, P., Chebotarov, D., Zhang, J., Kudrna, D. A., Torres, R. O., Natividad, M. A., Quintana, M. R., Song, J., Maldonado, C. E., Hechanova, S. L., Jena, K., Wing, R. A., & Henry, A. (2023). Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice. Plant Physiology, 193(4), 2381–2397. https://doi.org/10.1093/plphys/kiad485

Ntakirutimana, F., Tranchant-Dubreuil, C., Cubry, P., Chougule, K., Zhang, J., Wing, R. A., Adam, H., Lorieux, M., & Jouannic, S. (2023). Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3: Genes, Genomes, Genetics, 13(10). https://doi.org/10.1093/g3journal/jkad174

Zhou, Y., Kathiresan, N., Yu, Z., Rivera, L. F., Thimma, M., Manickam, K., Chebotarov, D., Mauleon, R., Chougule, K., Wei, S., Gao, T., Green, C. D., Zuccolo, A., Ware, D., Zhang, J., McNally, K. L., & Wing, R. A. (2023). HPC-based genome variant calling workflow (HPC-GVCW). https://doi.org/10.1101/2023.06.25.546420

Sedeek, K., Zuccolo, A., Fornasiero, A., Weber, A. M., Sanikommu, K., Sampathkumar, S., Rivera, L. F., Butt, H., Mussurova, S., Alhabsi, A., Nurmansyah, N., Ryan, E. P., Wing, R. A., & Mahfouz, M. M. (2023). Multi-omics resources for targeted agronomic improvement of pigmented rice. Nature Food, 4(5), 366–371. https://doi.org/10.1038/s43016-023-00742-9

Zhou, Y., Yu, Z., Chebotarov, D., Chougule, K., Lu, Z., Rivera, L. F., Kathiresan, N., Al-Bader, N., Mohammed, N., Alsantely, A., Mussurova, S., Santos, J., Thimma, M., Troukhan, M., Fornasiero, A., Green, C. D., Copetti, D., Kudrna, D., Llaca, V., … Wing, R. A. (2023). Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-37004-y

Yu, Z., Chen, Y., Zhou, Y., Zhang, Y., Li, M., Ouyang, Y., Chebotarov, D., Mauleon, R., Zhao, H., Xie, W., McNally, K. L., Wing, R. A., Guo, W., & Zhang, J. (2023). (preprint) Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice. https://doi.org/10.1101/2023.02.14.528456

Peñuela, M., Riccio-Rengifo, C., Finke, J., Rocha, C., Gkanogiannis, A., Wing, R. A., & Lorieux, M. (2023). Prediction of crossover recombination using parental genomes. PLOS ONE, 18(2), e0281804. https://doi.org/10.1371/journal.pone.0281804

Yu, Z., Chen, Y., Zhou, Y., Zhang, Y., Li, M., Ouyang, Y., Chebotarov, D., Mauleon, R., Zhao, H., Xie, W., McNally, K. L., Wing, R. A., Guo, W., & Zhang, J. (2023). Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice. https://doi.org/10.1101/2023.02.14.528456

Zuccolo, A., Mfarrej, S., Celii, M., Mussurova, S., Rivera, L. F., Llaca, V., Mohammed, N., Pain, A., Alrefaei, A. F., Alrefaei, A. F., & Wing, R. A. (2023). The gyrfalcon (Falco rusticolus) genome. G3: Genes, Genomes, Genetics, 13(3). https://doi.org/10.1093/g3journal/jkad001

2022

Alsantely, A., Gutaker, R., Navarrete Rodríguez, M. E., Arrieta-Espinoza, G., Fuchs, E. J., Costa de Oliveira, A., Tohme, J., Zuccolo, A., Wing, R. A., & Fornasiero, A. (2022). The InternationalOryzaMap Alignment Project (IOMAP): the Americas—past achievements and future directions. Journal of Experimental Botany, 74(5), 1331–1342. https://doi.org/10.1093/jxb/erac490

Gros‐Balthazard, M., Battesti, V., Flowers, J. M., Ferrand, S., Breil, M., Ivorra, S., Terral, J., Purugganan, M. D., Wing, R. A., Mohammed, N., & Bourgeois, Y. (2022). What lies behind a fruit crop variety name? A case study of the barnī date palm from al‐‘Ulā oasis, Saudi Arabia. PLANTS, PEOPLE, PLANET, 5(1), 82–97. https://doi.org/10.1002/ppp3.10326

Zhou, Y., Zhang, C., Zhang, L., Ye, Q., Liu, N., Wang, M., Long, G., Fan, W., Long, M., & Wing, R. A. (2022). Gene fusion as an important mechanism to generate new genes in the genus Oryza. Genome Biology, 23(1). https://doi.org/10.1186/s13059-022-02696-w

Athiyannan, N., Abrouk, M., Boshoff, W. H. P., Cauet, S., Rodde, N., Kudrna, D., Mohammed, N., Bettgenhaeuser, J., Botha, K. S., Derman, S. S., Wing, R. A., Prins, R., & Krattinger, S. G. (2022). Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning. Nature Genetics, 54(3), 227–231. https://doi.org/10.1038/s41588-022-01022-1

Fornasiero, A., Wing, R. A., & Ronald, P. (2022). Rice domestication. Current Biology, 32(1), R20–R24. https://doi.org/10.1016/j.cub.2021.11.025

2021

Song, J.-M., Xie, W.-Z., Wang, S., Guo, Y.-X., Koo, D.-H., Kudrna, D., Gong, C., Huang, Y., Feng, J.-W., Zhang, W., Zhou, Y., Zuccolo, A., Long, E., Lee, S., Talag, J., Zhou, R., Zhu, X.-T., Yuan, D., Udall, J., … Chen, L.-L. (2021). Two gap-free reference genomes and a global view of the centromere architecture in rice. Molecular Plant, 14(10), 1757–1767. https://doi.org/10.1016/j.molp.2021.06.018

Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., Chougule, K. M., Ou, S., Liu, J., Ricci, W. A., Guo, T., Olson, A., Qiu, Y., Della Coletta, R., Tittes, S., Hudson, A. I., Marand, A. P., Wei, S., Lu, Z., Wang, B., Tello-Ruiz, M. K., Piri, R. D., … Dawe, R. K. (2021). De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science, 373(6555), 655–662. https://doi.org/10.1126/science.abg5289

Li, H., Hu, X., Lovell, J. T., Grabowski, P. P., Mamidi, S., Chen, C., Amirebrahimi, M., Kahanda, I., Mumey, B., Barry, K., Kudrna, D., Schmutz, J., Lachowiec, J., & Lu, C. (2021). Genetic dissection of natural variation in oilseed traits of camelina by whole-genome resequencing and QTL mapping. The Plant Genome, 14(2). https://doi.org/10.1002/tpg2.20110

de Freitas, K. E. J., dos Santos, R. S., Busanello, C., de Carvalho Victoria, F., Lopes, J. L., Wing, R. A., & Costa de Oliveira, A. (2021). Starch Synthesis-Related Genes (SSRG) Evolution in the Genus Oryza. Plants, 10(6), 1057. https://doi.org/10.3390/plants10061057

Ma, X., Olsen, J. L., Reusch, T. B., Procaccini, G., Kudrna, D., Williams, M., Grimwood, J., Rajasekar, S., Jenkins, J., Schmutz, J., & Van de Peer, Y. (2021). Improved chromosome-level genome assembly and annotation of the seagrass, Zostera marina (eelgrass). F1000Research, 10, 289. https://doi.org/10.12688/f1000research.38156.1

Wu, Z., Liu, H., Zhan, W., Yu, Z., Qin, E., Liu, S., Yang, T., Xiang, N., Kudrna, D., Chen, Y., Lee, S., Li, G., Wing, R. A., Liu, J., Xiong, H., Xia, C., Xing, Y., Zhang, J., & Qin, R. (2021). The chromosome‐scale reference genome of safflower (Carthamus tinctorius) provides insights into linoleic acid and flavonoid biosynthesis. Plant Biotechnology Journal, 19(9), 1725–1742. https://doi.org/10.1111/pbi.13586

Yu, H., Lin, T., Meng, X., Du, H., Zhang, J., Liu, G., Chen, M., Jing, Y., Kou, L., Li, X., Gao, Q., Liang, Y., Liu, X., Fan, Z., Liang, Y., Cheng, Z., Chen, M., Tian, Z., Wang, Y., … Li, J. (2021). A route to de novo domestication of wild allotetraploid rice. Cell, 184(5), 1156-1170.e14. https://doi.org/10.1016/j.cell.2021.01.013

Lovell, J. T., MacQueen, A. H., Mamidi, S., Bonnette, J., Jenkins, J., Napier, J. D., Sreedasyam, A., Healey, A., Session, A., Shu, S., Barry, K., Bonos, S., Boston, L., Daum, C., Deshpande, S., Ewing, A., Grabowski, P. P., Haque, T., Harrison, M., … Schmutz, J. (2021). Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass. Nature, 590(7846), 438–444. https://doi.org/10.1038/s41586-020-03127-1

2020

Song, J.-M., Xie, W.-Z., Wang, S., Guo, Y.-X., Koo, D.-H., Kudrna, D., Huang, Y., Feng, J.-W., Zhang, W., Zhou, Y., Zuccolo, A., Long, E., Lee, S., Talag, J., Zhou, R., Zhu, X.-T., Yuan, D., Udall, J., Xie, W., … Chen, L.-L. (2020). Assembly and Validation of Two Gap-free Reference Genomes forXian/indicaRice Reveals Insights into Plant Centromere Architecture. https://doi.org/10.1101/2020.12.24.424073

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