Publications

Kim, K., Lee, S.-C., Lee, J., Yu, Y., Yang, K., Choi, B.-S., Koh, H.-J., Waminal, N. E., Choi, H.-I., Kim, N.-H., Jang, W., Park, H.-S., Lee, J., Lee, H. O., Joh, H. J., Lee, H. J., Park, J. Y., Perumal, S., Jayakodi, M., … Yang, T.-J. (2015). Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Scientific Reports, 5(1). https://doi.org/10.1038/srep15655

Wing, R. A. (2015). Harvesting rice’s dispensable genome. Genome Biology, 16(1). https://doi.org/10.1186/s13059-015-0787-x

Muñoz‐Amatriaín, M., Lonardi, S., Luo, M., Madishetty, K., Svensson, J. T., Moscou, M. J., Wanamaker, S., Jiang, T., Kleinhofs, A., Muehlbauer, G. J., Wise, R. P., Stein, N., Ma, Y., Rodriguez, E., Kudrna, D., Bhat, P. R., Chao, S., Condamine, P., Heinen, S., … Close, T. J. (2015). Sequencing of 15 622 gene‐bearing <scp>BAC</scp>s clarifies the gene‐dense regions of the barley genome. The Plant Journal, 84(1), 216–227. https://doi.org/10.1111/tpj.12959

Copetti, D., Zhang, J., El Baidouri, M., Gao, D., Wang, J., Barghini, E., Cossu, R. M., Angelova, A., Maldonado L., C. E., Roffler, S., Ohyanagi, H., Wicker, T., Fan, C., Zuccolo, A., Chen, M., Costa de Oliveira, A., Han, B., Henry, R., Hsing, Y.- ie, … Wing, R. A. (2015). RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-015-1762-3

Gao, D., Jiang, N., Wing, R. A., Jiang, J., & Jackson, S. A. (2015). Transposons play an important role in the evolution and diversification of centromeres among closely related species. Frontiers in Plant Science, 6. https://doi.org/10.3389/fpls.2015.00216

Wang, M., Yu, Y., Haberer, G., Marri, P. R., Fan, C., Goicoechea, J. L., Zuccolo, A., Song, X., Kudrna, D., Ammiraju, J. S. S., Cossu, R. M., Maldonado, C., Chen, J., Lee, S., Sisneros, N., de Baynast, K., Golser, W., Wissotski, M., Kim, W., … Wing, R. A. (2014). The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics, 46(9), 982–988. https://doi.org/10.1038/ng.3044

Shearer, L. A., Anderson, L. K., de Jong, H., Smit, S., Goicoechea, J. L., Roe, B. A., Hua, A., Giovannoni, J. J., & Stack, S. M. (2014). FluorescenceIn SituHybridization and Optical Mapping to Correct Scaffold Arrangement in the Tomato Genome. G3 Genes|Genomes|Genetics, 4(8), 1395–1405. https://doi.org/10.1534/g3.114.011197

Schmutz, J., McClean, P. E., Mamidi, S., Wu, G. A., Cannon, S. B., Grimwood, J., Jenkins, J., Shu, S., Song, Q., Chavarro, C., Torres-Torres, M., Geffroy, V., Moghaddam, S. M., Gao, D., Abernathy, B., Barry, K., Blair, M., Brick, M. A., Chovatia, M., … Jackson, S. A. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics, 46(7), 707–713. https://doi.org/10.1038/ng.3008

Xie, K., Zhang, J., & Yang, Y. (2014). Genome-Wide Prediction of Highly Specific Guide RNA Spacers for CRISPR–Cas9-Mediated Genome Editing in Model Plants and Major Crops. Molecular Plant, 7(5), 923–926. https://doi.org/10.1093/mp/ssu009

Zwickl, D. J., Stein, J. C., Wing, R. A., Ware, D., & Sanderson, M. J. (2014). Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3. Systematic Biology, 63(5), 645–659. https://doi.org/10.1093/sysbio/syu027

Jacquemin, J., Ammiraju, J. S., Haberer, G., Billheimer, D. D., Yu, Y., Liu, L. C., Rivera, L. F., Mayer, K., Chen, M., & Wing, R. A. (2014). Fifteen Million Years of Evolution in the Oryza Genus Shows Extensive Gene Family Expansion. Molecular Plant, 7(4), 642–656. https://doi.org/10.1093/mp/sst149

Wang, X., Kudrna, D. A., Pan, Y., Wang, H., Liu, L., Lin, H., Zhang, J., Song, X., Goicoechea, J. L., Wing, R. A., Zhang, Q., & Luo, M. (2014). Global Genomic Diversity of Oryza sativa Varieties Revealed by Comparative Physical Mapping. Genetics, 196(4), 937–949. https://doi.org/10.1534/genetics.113.159970

Pan, Y., Deng, Y., Lin, H., Kudrna, D. A., Wing, R. A., Li, L., Zhang, Q., & Luo, M. (2014). Comparative <scp>BAC</scp>‐based physical mapping of <scp>O</scp>ryza sativa ssp. indica var. 93–11 and evaluation of the two rice reference sequence assemblies. The Plant Journal, 77(5), 795–805. https://doi.org/10.1111/tpj.12412

Chamala, S., Chanderbali, A. S., Der, J. P., Lan, T., Walts, B., Albert, V. A., dePamphilis, C. W., Leebens-Mack, J., Rounsley, S., Schuster, S. C., Wing, R. A., Xiao, N., Moore, R., Soltis, P. S., Soltis, D. E., & Barbazuk, W. B. (2013). Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella. Science, 342(6165), 1516–1517. https://doi.org/10.1126/science.1241130

Albert, V. A., Barbazuk, W. B., dePamphilis, C. W., Der, J. P., Leebens-Mack, J., Ma, H., Palmer, J. D., Rounsley, S., Sankoff, D., Schuster, S. C., Soltis, D. E., Soltis, P. S., Wessler, S. R., Wing, R. A., Albert, V. A., Ammiraju, J. S. S., Barbazuk, W. B., Chamala, S., Chanderbali, A. S., … Tomsho, L. (2013). The Amborella Genome and the Evolution of Flowering Plants. Science, 342(6165). https://doi.org/10.1126/science.1241089

Wang, C., Shi, X., Liu, L., Li, H., Ammiraju, J. S. S., Kudrna, D. A., Xiong, W., Wang, H., Dai, Z., Zheng, Y., Lai, J., Jin, W., Messing, J., Bennetzen, J. L., Wing, R. A., & Luo, M. (2013). Genomic Resources for Gene Discovery, Functional Genome Annotation, and Evolutionary Studies of Maize and Its Close Relatives. Genetics, 195(3), 723–737. https://doi.org/10.1534/genetics.113.157115

Ortiz, M., Legatzki, A., Neilson, J. W., Fryslie, B., Nelson, W. M., Wing, R. A., Soderlund, C. A., Pryor, B. M., & Maier, R. M. (2013). Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave. The ISME Journal, 8(2), 478–491. https://doi.org/10.1038/ismej.2013.159

Singh, R., Ong-Abdullah, M., Low, E.-T. L., Manaf, M. A. A., Rosli, R., Nookiah, R., Ooi, L. C.-L., Ooi, S., Chan, K.-L., Halim, M. A., Azizi, N., Nagappan, J., Bacher, B., Lakey, N., Smith, S. W., He, D., Hogan, M., Budiman, M. A., Lee, E. K., … Sambanthamurthi, R. (2013). Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature, 500(7462), 335–339. https://doi.org/10.1038/nature12309

Horvath, D. P., Kudrna, D., Talag, J., Anderson, J. V., Chao, W. S., Wing, R., Foley, M. E., & Doğramacı, M. (2013). BAC Library Development and Clone Characterization for Dormancy-Responsive DREB4A, DAM, and FT from Leafy Spurge (Euphorbia esula) Identifies Differential Splicing and Conserved Promoter Motifs. Weed Science, 61(2), 303–309. https://doi.org/10.1614/ws-d-12-00175.1

Matsuba, Y., Nguyen, T. T., Wiegert, K., Falara, V., Gonzales-Vigil, E., Leong, B., Schäfer, P., Kudrna, D., Wing, R. A., Bolger, A. M., Usadel, B., Tissier, A., Fernie, A. R., Barry, C. S., & Pichersky, E. (2013). Evolution of a Complex Locus for Terpene Biosynthesis in Solanum. The Plant Cell, 25(6), 2022–2036. https://doi.org/10.1105/tpc.113.111013

Zhang, C., Wang, J., Marowsky, N. C., Long, M., Wing, R. A., & Fan, C. (2013). High Occurrence of Functional New Chimeric Genes in Survey of Rice Chromosome 3 Short Arm Genome Sequences. Genome Biology and Evolution, 5(5), 1038–1048. https://doi.org/10.1093/gbe/evt071

Jacquemin, J., Bhatia, D., Singh, K., & Wing, R. A. (2013). The International Oryza Map Alignment Project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Current Opinion in Plant Biology, 16(2), 147–156. https://doi.org/10.1016/j.pbi.2013.02.014

Maron, L. G., Guimarães, C. T., Kirst, M., Albert, P. S., Birchler, J. A., Bradbury, P. J., Buckler, E. S., Coluccio, A. E., Danilova, T. V., Kudrna, D., Magalhaes, J. V., Piñeros, M. A., Schatz, M. C., Wing, R. A., & Kochian, L. V. (2013). Aluminum tolerance in maize is associated with higherMATE1gene copy number. Proceedings of the National Academy of Sciences, 110(13), 5241–5246. https://doi.org/10.1073/pnas.1220766110

Chen, J., Huang, Q., Gao, D., Wang, J., Lang, Y., Liu, T., Li, B., Bai, Z., Goicoechea, J. L., Liang, C., Chen, C., Zhang, W., Sun, S., Liao, Y., Zhang, X., Yang, L., Song, C., Wang, M., Shi, J., … Chen, M. (2013). Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Communications, 4(1). https://doi.org/10.1038/ncomms2596

Koo, H., McDowell, E. T., Ma, X., Greer, K. A., Kapteyn, J., Xie, Z., Descour, A., Kim, H., Yu, Y., Kudrna, D., Wing, R. A., Soderlund, C. A., & Gang, D. R. (2013). Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids. BMC Plant Biology, 13(1). https://doi.org/10.1186/1471-2229-13-27