Journal Articles
Zhang, Li, Ren, Yan, Yang, Tao, Li, Guangwei, Chen, Jianhai, Gschwend, Andrea R., Yu, Yeisoo, Hou, Guixue, Zi, Jin, Zhou, Ruo, Wen, Bo, Zhang, Jianwei, Chougule, Kapeel, Wang, Muhua, Copetti, Dario, Peng, Zhiyu, Zhang, Chengjun, Zhang, Yong, Ouyang, Yidan, Wing, Rod A., Liu, Siqi and Long, Manyuan (2019) Rapid evolution of protein diversity by de novo origination in Oryza. Nature Ecology & Evolution, . doi:10.1038/s41559-019-0822-5
Kim, Nam-Hoon, Jayakodi, Murukarthick, Lee, Sang-Choon, Choi, Beom-Soon, Jang, Woojong, Lee, Junki, Kim, Hyun Hee, Waminal, Nomar E., Lakshmanan, Meiyappan, van Nguyen, Binh, Lee, Yun Sun, Park, Hyun-Seung, Koo, Hyun Jo, Park, Jee Young, Perumal, Sampath, Joh, Ho Jun, Lee, Hana, Kim, Jinkyung, Kim, In Seo, Kim, Kyunghee, Koduru, Lokanand, Kang, Kyo Bin, Sung, Sang Hyun, Yu, Yeisoo, Park, Daniel S., Choi, Doil, Seo, Eunyoung, Kim, Seungill, Kim, Young-Chang, Hyun, Dong Yun, Park, Youn-Il, Kim, Changsoo, Lee, Tae-Ho, Kim, Hyun Uk, Soh, Moon Soo, Lee, Yi, In, Jun Gyo, Kim, Heui-Soo, Kim, Yong-Min, Yang, Deok-Chun, Wing, Rod A., Lee, Dong-Yup, Paterson, Andrew H. and Yang, Tae-Jin (2018) Genome and evolution of the shade-requiring medicinal herb Panax ginseng. Plant Biotechnology Journal, 16 11: 1904-1917. doi:10.1111/pbi.12926
Stein, Joshua C., Yu, Yeisoo, Copetti, Dario, Zwickl, Derrick J., Zhang, Li, Zhang, Chengjun, Chougule, Kapeel, Gao, Dongying, Iwata, Aiko, Goicoechea, Jose Luis, Wei, Sharon, Wang, Jun, Liao, Yi, Wang, Muhua, Jacquemin, Julie, Becker, Claude, Kudrna, Dave, Zhang, Jianwei, Londono, Carlos E. M., Song, Xiang, Lee, Seunghee, Sanchez, Paul, Zuccolo, Andrea, Ammiraju, Jetty S. S., Talag, Jayson, Danowitz, Ann, Rivera, Luis F., Gschwend, Andrea R., Noutsos, Christos, Wu, Cheng-chieh, Kao, Shu-min, Zeng, Jhih-wun, Wei, Fu-jin, Zhao, Qiang, Feng, Qi, El Baidouri, Moaine, Carpentier, Marie-Christine, Lasserre, Eric, Cooke, Richard, da Rosa Farias, Daniel, da Maia, Luciano Carlos, dos Santos, Railson S., Nyberg, Kevin G., McNally, Kenneth L., Mauleon, Ramil, Alexandrov, Nickolai, Schmutz, Jeremy, Flowers, Dave, Fan, Chuanzhu, Weigel, Detlef, Jena, Kshirod K., Wicker, Thomas, Chen, Mingsheng, Han, Bin, Henry, Robert, Hsing, Yue-ie C., Kurata, Nori, de Oliveira, Antonio Costa, Panaud, Olivier, Jackson, Scott A., Machado, Carlos A., Sanderson, Michael J., Long, Manyuan, Ware, Doreen and Wing, Rod A. (2018) Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics, 50 11: 1618-1618. doi:10.1038/s41588-018-0261-2
Wing, Rod A., Purugganan, Michael D. and Zhang, Qifa (2018) The rice genome revolution: from an ancient grain to Green Super Rice. Nature Reviews Genetics, 19 8: 505-517. doi:10.1038/s41576-018-0024-z
Liao, Yi, Zhang, Xuemei, Li, Bo, Liu, Tieyan, Chen, Jinfeng, Bai, Zetao, Wang, Meijiao, Shi, Jinfeng, Walling, Jason G., Wing, Rod A., Jiang, Jiming and Chen, Mingsheng (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. doi:10.1105/tpc.18.00163
Lv, Shuwei, Wu, Wenguang, Wang, Muhua, Meyer, Rachel S., Ndjiondjop, Marie-Noelle, Tan, Lubin, Zhou, Haiying, Zhang, Jianwei, Fu, Yongcai, Cai, Hongwei, Sun, Chuanqing, Wing, Rod A. and Zhu, Zuofeng (2018) Genetic control of seed shattering during African rice domestication. Nature Plants, 4 6: 331-337. doi:10.1038/s41477-018-0164-3
Wang, Wensheng, Mauleon, Ramil, Hu, Zhiqiang, Chebotarov, Dmytro, Tai, Shuaishuai, Wu, Zhichao, Li, Min, Zheng, Tianqing, Fuentes, Roven Rommel, Zhang, Fan, Mansueto, Locedie, Copetti, Dario, Sanciangco, Millicent, Palis, Kevin Christian, Xu, Jianlong, Sun, Chen, Fu, Binying, Zhang, Hongliang, Gao, Yongming, Zhao, Xiuqin, Shen, Fei, Cui, Xiao, Yu, Hong, Li, Zichao, Chen, Miaolin, Detras, Jeffrey, Zhou, Yongli, Zhang, Xinyuan, Zhao, Yue, Kudrna, Dave, Wang, Chunchao, Li, Rui, Jia, Ben, Lu, Jinyuan, He, Xianchang, Dong, Zhaotong, Xu, Jiabao, Li, Yanhong, Wang, Miao, Shi, Jianxin, Li, Jing, Zhang, Dabing, Lee, Seunghee, Hu, Wushu, Poliakov, Alexander, Dubchak, Inna, Ulat, Victor Jun, Borja, Frances Nikki, Mendoza, John Robert, Ali, Jauhar, Gao, Qiang, Niu, Yongchao, Yue, Zhen, Naredo, Ma. Elizabeth B., Talag, Jayson, Wang, Xueqiang, Li, Jinjie, Fang, Xiaodong, Yin, Ye, Glaszmann, Jean-Christophe, Zhang, Jianwei, Li, Jiayang, Hamilton, Ruaraidh Sackville, Wing, Rod A., Ruan, Jue, Zhang, Gengyun, Wei, Chaochun, Alexandrov, Nickolai, McNally, Kenneth L., Li, Zhikang and Leung, Hei (2018) Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557 7703: 43-49. doi:10.1038/s41586-018-0063-9
Bhatia, Dharminder, Wing, Rod A., Yu, Yeisoo, Chougule, Kapeel, Kudrna, Dave, Lee, Seunghee, Rang, Allah and Singh, Kuldeep (2018) Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length. Euphytica, 214 2: . doi:10.1007/s10681-018-2119-1
Stein, Joshua C., Yu, Yeisoo, Copetti, Dario, Zwickl, Derrick J., Zhang, Li, Zhang, Chengjun, Chougule, Kapeel, Gao, Dongying, Iwata, Aiko, Goicoechea, Jose Luis, Wei, Sharon, Wang, Jun, Liao, Yi, Wang, Muhua, Jacquemin, Julie, Becker, Claude, Kudrna, Dave, Zhang, Jianwei, Londono, Carlos E. M., Song, Xiang, Lee, Seunghee, Sanchez, Paul, Zuccolo, Andrea, Ammiraju, Jetty S. S., Talag, Jayson, Danowitz, Ann, Rivera, Luis F., Gschwend, Andrea R., Noutsos, Christos, Wu, Cheng-chieh, Kao, Shu-min, Zeng, Jhih-wun, Wei, Fu-jin, Zhao, Qiang, Feng, Qi, El Baidouri, Moaine, Carpentier, Marie-Christine, Lasserre, Eric, Cooke, Richard, Rosa Farias, Daniel Da, da Maia, Luciano Carlos, Dos Santos, Railson S., Nyberg, Kevin G., McNally, Kenneth L., Mauleon, Ramil, Alexandrov, Nickolai, Schmutz, Jeremy, Flowers, Dave, Fan, Chuanzhu, Weigel, Detlef, Jena, Kshirod K., Wicker, Thomas, Chen, Mingsheng, Han, Bin, Henry, Robert, Hsing, Yue-ie C., Kurata, Nori, de Oliveira, Antonio Costa, Panaud, Olivier, Jackson, Scott A., Machado, Carlos A., Sanderson, Michael J., Long, Manyuan, Ware, Doreen and Wing, Rod 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. doi:10.1038/s41588-018-0040-0
dos Santos, Railson Schreinert, Farias, Daniel da Rosa, Pegoraro, Camila, Rombaldi, Cesar Valmor, Fukao, Takeshi, Wing, Rod A. and de Oliveira, Antonio Costa (2017) Evolutionary analysis of the SUB1 locus across the Oryza genomes. Rice, 10 1: . doi:10.1186/s12284-016-0140-3
Copetti, Dario, Búrquez, Alberto, Bustamante, Enriquena, Charboneau, Joseph L. M., Childs, Kevin L., Eguiarte, Luis E., Lee, Seunghee, Liu, Tiffany L., McMahon, Michelle M., Whiteman, Noah K., Wing, Rod A., Wojciechowski, Martin F. and Sanderson, Michael J. (2017) Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. Proceedings of the National Academy of Sciences of the United States of America, 114 45: 12003-12008. doi:10.1073/pnas.1706367114
Harkess, Alex, Zhou, Jinsong, Xu, Chunyan, Bowers, John E, Van der Hulst, Ron, Ayyampalayam, Saravanaraj, Mercati, Francesco, Riccardi, Paolo, McKain, Michael R, Kakrana, Atul, Tang, Haibao, Ray, Jeremy, Groenendijk, John, Arikit, Siwaret, Mathioni, Sandra M, Nakano, Mayumi, Shan, Hongyan, Telgmann-Rauber, Alexa, Kanno, Akira, Yue, Zhen, Chen, Haixin, Li, Wenqi, Chen, Yanling, Xu, Xiangyang, Zhang, Yueping, Luo, Shaochun, Chen, Helong, Gao, Jianming, Mao, Zichao, Pires, J Chris, Luo, Meizhong, Kudrna, Dave, Wing, Rod A, Meyers, Blake C, Yi, Kexian, Kong, Hongzhi, Lavrijsen, Pierre, Sunseri, Francesco, Falavigna, Agostino, Ye, Yin, Leebens-Mack, James H and Chen, Guangyu (2017) The asparagus genome sheds light on the origin and evolution of a young Y chromosome. Nature Communications, 8 1: 1279. doi:10.1038/s41467-017-01064-8
Eizenga, G. C., Sanchez, P. L., Jackson, A. K., Edwards, J. D., Hurwitz, B. L., Wing, R. A. and Kudrna, D. (2017) Genetic variation for domestication-related traits revealed in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) × ancestral rice, O. nivara, mapping population. Molecular Breeding, 37 11: . doi:10.1007/s11032-017-0734-5
Brozynska, Marta, Copetti, Dario, Furtado, Agnelo, Wing, Rod A., Crayn, Darren, Fox, Glen, Ishikawa, Ryuji and Henry, Robert J. (2017) Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. Plant Biotechnology Journal, 15 6: 765-774. doi:10.1111/pbi.12674
Wu, Wenguang, Liu, Xiaoyun, Wang, Muhua, Meyer, Rachel S., Luo, Xiaojin, Ndjiondjop, Marie-Noelle, Tan, Lubin, Zhang, Jianwei, Wu, Jianzhong, Cai, Hongwei, Sun, Chuanqing, Wang, Xiangkun, Wing, Rod A. and Zhu, Zuofeng (2017) A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nature Plants, 3 . doi:10.1038/nplants.2017.64
Lee, Cheng-Ruei, Wang, Baosheng, Mojica, Julius P., Mandáková, Terezie, Prasad, Kasavajhala V. S. K., Goicoechea, Jose Luis, Perera, Nadeesha, Hellsten, Uffe, Hundley, Hope N., Johnson, Jenifer, Grimwood, Jane, Barry, Kerrie, Fairclough, Tephen, Jenkins, Jerry W., Yu, Yeisoo, Kudrna, Dave, Zhang, Jianwei, Talag, Jayson, Golser, Wolfgang, Ghattas, Kathryn, Schranz, M. Eric, Wing, Rod, Lysak, Martin A., Schmutz, Jeremy, Rokhsar, Daniel S. and Mitchell-Olds, Thomas (2017) Young inversion with multiple linked QTLs under selection in a hybrid zone. Nature Ecology and Evolution, 1 5: . doi:10.1038/s41559-017-0119
Choi, Jae Young, Platts, Adrian E., Fuller, Dorian Q., Hsing, Yue-Ie, Wing, Rod A., Purugganan, Michael D. and Kim, Yuseob (2017) The rice paradox: multiple origins but single domestication in Asian Rice. Molecular Biology and Evolution, 34 4: 969-979. doi:10.1093/molbev/msx049
Thakare, Dhiraj, Zhang, Jianwei, Wing, Rod A., Cotty, Peter J. and Schmidt, Monica A. (2017) Aflatoxin-free transgenic maize using host-induced gene silencing. Science Advances, 3 3: e1602382. doi:10.1126/sciadv.1602382
Mansueto, Locedie, Fuentes, Roven Rommel, Borja, Frances Nikki, Detras, Jeffery, Abrio-Santos, Juan Miguel, Chebotarov, Dmytro, Sanciangco, Millicent, Palis, Kevin, Copetti, Dario, Poliakov, Alexandre, Dubchak, Inna, Solovyev, Victor, Wing, Rod A., Hamilton, Ruaraidh Sackville, Mauleon, Ramil, McNally, Kenneth L. and Alexandrov, Nickolai (2017) Rice SNP-seek database update: New SNPs, indels, and queries. Nucleic Acids Research, 45 D1: D1075-D1081. doi:10.1093/nar/gkw1135
Copetti, Dario and Wing, Rod A. (2016) The dark side of the genome: revealing the native transposable element/repeat content of Eukaryotic genomes. Molecular Plant, 9 12: 1664-1666. doi:10.1016/j.molp.2016.09.006
Gan, Xiangchao, Hay, Angela, Kwantes, Michiel, Haberer, Georg, Hallab, Asis, Ioio, Raffaele Dello, Hofhuis, Hugo, Pieper, Bjorn, Cartolano, Maria, Neumann, Ulla, Nikolov, Lachezar A., Song, Baoxing, Hajheidari, Mohsen, Briskine, Roman, Kougioumoutzi, Evangelia, Vlad, Daniela, Broholm, Suvi, Hein, Jotun, Meksem, Khalid, Lightfoot, David, Shimizu, Kentaro K., Shimizu-Inatsugi, Rie, Imprialou, Martha, Kudrna, David, Wing, Rod, Sato, Shusei, Huijser, Peter, Filatov, Dmitry, Mayer, Klaus F. X., Mott, Richard and Tsiantis, Miltos (2016) The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nature Plants, 2 . doi:10.1038/nplants.2016.167
Zhang, Jianwei, Kudrna, Dave, Mu, Ting, Li, Weiming, Copetti, Dario, Yu, Yeisoo, Goicoechea, Jose Luis, Lei, Yang and Wing, Rod A. (2016) Genome puzzle master (GPM): An integrated pipeline for building and editing pseudomolecules from fragmented sequences. Bioinformatics, 32 20: 3058-3064. doi:10.1093/bioinformatics/btw370
Van Andel, Tinde R., Meyer, Rachel S., Aflitos, Saulo A., Carney, Judith A., Veltman, Margaretha A., Copetti, Dario, Flowers, Jonathan M., Havinga, Reinout M., Maat, Harro, Purugganan, Michael D., Wing, Rod A. and Schranz, M. Eric (2016) Tracing ancestor rice of Suriname Maroons back to its African origin. Nature Plants, 2 10: . doi:10.1038/nplants.2016.149
Zhang, Jianwei, Chen, Ling-Ling, Sun, Shuai, Kudrna, Dave, Copetti, Dario, Li, Weiming, Mu, Ting, Jiao, Wen-Biao, Xing, Feng, Lee, Seunghee, Talag, Jayson, Song, Jia-Ming, Du, Bogu, Xie, Weibo, Luo, Meizhong, Maldonado, Carlos Ernesto, Goicoechea, Jose Luis, Xiong, Lizhong, Wu, Changyin, Xing, Yongzhong, Zhou, Dao-Xiu, Yu, Sibin, Zhao, Yu, Wang, Gongwei, Yu, Yeisoo, Luo, Yijie, Hurtado, Beatriz Elena Padilla, Danowitz, Ann, Wing, Rod A. and Zhang, Qifa (2016) Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Scientific Data, 3 . doi:10.1038/sdata.2016.76
Wicker, Thomas, Yu, Yeisoo, Haberer, Georg, Mayer, Klaus F. X., Marri, Pradeep Reddy, Rounsley, Steve, Chen, Mingsheng, Zuccolo, Andrea, Panaud, Olivier, Wing, Rod A. and Roffler, Stefan (2016) DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses. Nature Communications, 7 . doi:10.1038/ncomms12790
Zhang, Jianwei, Chen, Ling-Ling, Xing, Feng, Kudrna, David A., Yao, Wen, Copetti, Dario, Mu, Ting, Li, Weiming, Song, Jia-Ming, Xie, Weibo, Lee, Seunghee, Talag, Jayson, Shao, Lin, An, Yue, Zhang, Chun-Liu, Ouyang, Yidan, Sun, Shuai, Jiao, Wen-Biao, Lv, Fang, Du, Bogu, Luo, Meizhong, Maldonado, Carlos Ernesto, Goicoechea, Jose Luis, Xiong, Lizhong, Wu, Changyin, Xing, Yongzhong, Zhou, Dao-Xiu, Yu, Sibin, Zhao, Yu, Wang, Gongwei, Yu, Yeisoo, Luo, Yijie, Zhou, Zhi-Wei, Hurtado, Beatriz Elena Padilla, Danowitz, Ann, Wing, Rod A. and Zhang, Qifa (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: E5163-E5171. doi:10.1073/pnas.1611012113
Ray, Soham, Bose, Lotan K., Ray, Joshitha, Ngangkham, Umakanta, Katara, Jawahar L., Samantaray, Sanghamitra, Behera, Lambodar, Anumalla, Mahender, Singh, Onkar N., Chen, Meingsheng, Wing, Rod A. and Mohapatra, Trilochan (2016) Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha. Molecular Genetics and Genomics, 291 4: 1783-1794. doi:10.1007/s00438-016-1214-z
Wang, Jun, Yu, Yeisoo, Tao, Feng, Zhang, Jianwei, Copetti, Dario, Kudrna, Dave, Talag, Jayson, Lee, Seunghee, Wing, Rod A. and Fan, Chuanzhu (2016) DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. Genome Biology, 17 1: . doi:10.1186/s13059-016-0954-8
Wendel, Jonathan F., Jackson, Scott A., Meyers, Blake C. and Wing, Rod A. (2016) Evolution of plant genome architecture. Genome Biology, 17 37: . doi:10.1186/s13059-016-0908-1
De Vega, Jose J., Ayling, Sarah, Hegarty, Matthew, Kudrna, Dave, Goicoechea, Jose L., Ergon, Åshild, Rognli, Odd A., Jones, Charlotte, Swain, Martin, Geurts, Rene, Lang, Chunting, Mayer, Klaus F. X., Rössner, Stephan, Yates, Steven, Webb, Kathleen J., Donnison, Iain S., Oldroyd, Giles E. D., Wing, Rod A., Caccamo, Mario, Powell, Wayne, Abberton, Michael T. and Skøt, Leif (2015) Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Scientific Reports, 5 . doi:10.1038/srep17394
Zhang, Yesheng, Zhang, Shilai, Liu, Hui, Fu, Binying, Li, Lijuan, Xie, Min, Song, Yue, Li, Xin, Cai, Jing, Wan, Wenting, Kui, Ling, Huang, Hui, Lyu, Jun, Dong, Yang, Wang, Wensheng, Huang, Liyu, Zhang, Jing, Yang, Qinzhong, Shan, Qinli, Li, Qiong, Huang, Wangqi, Tao, Dayun, Wang, Muhua, Chen, Mingsheng, Yu, Yeisoo, Wing, Rod A., Wang, Wen and Hu, Fengyi (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. doi:10.1016/j.molp.2015.08.006
Kim, Kyunghee, Lee, Sang-Choon, Lee, Junki, Yu, Yeisoo, Yang, Kiwoung, Choi, Beom-Soon, Koh, Hee-Jong, Waminal, Nomar Espinosa, Choi, Hong-Il, Kim, Nam-Hoon, Jang, Woojong, Park, Hyun-Seung, Lee, Jonghoon, Lee, Hyun Oh, Joh, Ho Jun, Lee, Hyeon Ju, Park, Jee Young, Perumal, Sampath, Jayakodi, Murukarthick, Lee, Yun Sun, Kim, Backki, Copetti, Dario, Kim, Soonok, Kim, Sunggil, Lim, Ki-Byung, Kim, Young-Dong, Lee, Jungho, Cho, Kwang-Su, Park, Beom-Seok, Wing, Rod A. and Yang, Tae-Jin (2015) Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Scientific Reports, 5 . doi:10.1038/srep15655
Copetti, Dario, Zhang, Jianwei, El Baidouri, Moaine, Gao, Dongying, Wang, Jun, Barghini, Elena, Cossu, Rosa M., Angelova, Angelina, Maldonado L., Carlos E., Roffler, Stefan, Ohyanagi, Hajime, Wicker, Thomas, Fan, Chuanzhu, Zuccolo, Andrea, Chen, Mingsheng, Costa de Oliveira, Antonio, Han, Bin, Henry, Robert, Hsing, Yue-ie, Kurata, Nor, Wang, Wen, Jackson, Scott A., Panaud, Olivier and Wing, Rod A. (2015) RiTE database: A resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics, 16 1: 538-538. doi:10.1186/s12864-015-1762-3
Sanderson, Michael J., Copetti, Dario, Búrquez, Alberto, Bustamante, Enriquena, Charboneau, Joseph L. M., Eguiarte, Luis E., Kumar, Sudhir, Lee, Hyun Oh, Lee, Junki, McMahon, Michelle, Steele, Kelly, Wing, Rod, Yang, Tae-Jin, Zwickl, Derrick and Wojciechowski, Martin F. (2015) Exceptional reduction of the plastid genome of saguaro cactus (Carnegiea gigantea): loss of the ndh gene suite and inverted repeat 1. American Journal of Botany, 102 7: 1115-1127. doi:10.3732/ajb.1500184
Gao, Dongying, Jiang, Ning, Wing, Rod A., Jiang, Jiming and Jackson, Scott A. (2015) Transposons play an important role in the evolution and diversification of centromeres among closely related species. Frontiers in Plant Science, 6 APR: . doi:10.3389/fpls.2015.00216
Muñoz-Amatriaín, María, Lonardi, Stefano, Luo, Mingcheng, Madishetty, Kavitha, Svensson, Jan T., Moscou, Matthew J., Wanamaker, Steve, Jiang, Tao, Kleinhofs, Andris, Muehlbauer, Gary J., Wise, Roger P., Stein, Nils, Ma, Yaqin, Rodriguez, Edmundo, Kudrna, Dave, Bhat, Prasanna R., Chao, Shiaoman, Condamine, Pascal, Heinen, Shane, Resnik, Josh, Wing, Rod, Witt, Heather N., Alpert, Matthew, Beccuti, Marco, Bozdag, Serdar, Cordero, Francesca, Mirebrahim, Hamid, Ounit, Rachid, Wu, Yonghui, You, Frank, Zheng, Jie, Simková, Hana, Dolezel, Jaroslav, Grimwood, Jane, Schmutz, Jeremy, Duma, Denisa, Altschmied, Lothar, Blake, Tom, Bregitzer, Phil, Cooper, Laurel, Dilbirligi, Muharrem, Falk, Anders, Feiz, Leila, Graner, Andreas, Gustafson, Perry, Hayes, Patrick M., Lemaux, Peggy, Mammadov, Jafar and Close, Timothy J. (2015) Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant Journal, 84 1: 216-227. doi:10.1111/tpj.12959
Geering, Andrew D. W., Maumus, Florian, Copetti, Dario, Choisne, Nathalie, Zwickl, Derrick J., Zytnicki, Matthias, McTaggart, Alistair R., Scalabrin, Simone, Vezzulli, Silvia, Wing, Rod A., Quesneville, Hadi and Teycheney, Pierre-Yves (2014) Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nature Communications, 5 1: 5269.1-5269.11. doi:10.1038/ncomms6269
Wang, Muhua, Yu, Yeisoo, Haberer, Georg, Marri, Pradeep Reddy, Fan, Chuanzhu, Goicoechea, Jose Luis, Zuccolo, Andrea, Song, Xiang, Kudrna, Dave, Ammiraju, Jetty S.S., Cossu, Rosa Maria, Maldonado, Carlos, Chen, Jinfeng, Lee, Seunghee, Sisneros, Nick, De Baynast, Kristi, Golser, Wolfgang, Wissotski, Marina, Kim, Woojin, Sanchez, Paul, Ndjiondjop, Marie-Noelle, Sanni, Kayode, Long, Manyuan, Carney, Judith, Panaud, Olivier, Wicker, Thomas, MacHado, Carlos A., Chen, Mingsheng, Mayer, Klaus F.X., Rounsley, Steve and Wing, Rod A. (2014) The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics, 46 9: 982-988. doi:10.1038/ng.3044
Schmutz, Jeremy, McClean, Phillip E., Mamidi, Sujan, Wu, G Albert, Cannon, Steven B., Grimwood, Jane, Jenkins, Jerry, Shu, Shengqiang, Song, Qijian, Chavarro, Carolina, Torres-Torres, Mirayda, Geffroy, Valerie, Moghaddam, Samira Mafi, Gao, Dongying, Abernathy, Brian, Barry, Kerrie, Blair, Matthew, Brick, Mark A., Chovatia, Mansi, Gepts, Paul, Goodstein, David M., Gonzales, Michael, Hellsten, Uffe, Hyten, David L., Jia, Gaofeng, Kelly, James D., Kudrna, Dave, Lee, Rian, Richard, Manon M. S., Miklas, Phillip N., Osorno, Juan M., Rodrigues, Josiane, Thareau, Vincent, Urrea, Carlos A., Wang, Mei, Yu, Yeisoo, Zhang, Ming, Wing, Rod A., Cregan, Perry B., Rokhsar, Daniel S. and Jackson, Scott A. (2014) A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics, 46 7: 707-713. doi:10.1038/ng.3008
Jacquemin, Julie, Ammiraju, Jetty S.S., Haberer, Georg, Billheimer, Dean D., Yu, Yeisoo, Liu, Liana C., Rivera, Luis F., Mayer, Klaus, Chen, Mingsheng and Wing, Rod A. (2014) Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion. Molecular Plant, 7 4: 642-656. doi:10.1093/mp/sst149
Wang, Xiaoming, Kudrna, David A., Pan, Yonglong, Wang, Hao, Liu, Lin, Lin, Haiyan, Zhang, Jianwei, Song, Xiang, Goicoechea, Jose Luis, Wing, Rod A., Zhang, Qifa and Luo, Meizhong (2014) Global genomic diversity of Oryza sativa varieties revealed by comparative physical mapping. Genetics, 196 4: 937-949. doi:10.1534/genetics.113.159970
Pan, Yonglong, Deng, Ying, Lin, Haiyan, Kudrna, David A., Wing, Rod A., Li, Lijia, Zhang, Qifa and Luo, Meizhong (2014) Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies. Plant Journal, 77 5: 795-805. doi:10.1111/tpj.12412
Ortiz, Marianyoly, Legatzki, Antje, Neilson, Julia W., Fryslie, Brandon, Nelson, William M., Wing, Rod A., Soderlund, Carol A., Pryor, Barry M. and Maier, Raina M. (2014) Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave. ISME Journal, 8 2: 478-491. doi:10.1038/ismej.2013.159
Chamala, Srikar, Chanderbali, Andre S., Der, Joshua P., Lan, Tianying, Walts, Brandon, Albert, Victor A., DePamphilis, Claude W., Leebens-Mack, Jim, Rounsley, Steve, Schuster, Stephan C., Wing, Rod A., Xiao, Nianqing, Moore, Richard, Soltis, Pamela S., Soltis, Douglas E. and Barbazuk, W. Brad (2013) Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science, 342 6165: 1516-1517. doi:10.1126/science.1241130
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Wang, Chao, Shi, Xue, Liu, Lin, Li, Haiyan, Ammiraju, Jetty S.S., Kudrna, David A., Xiong, Wentao, Wang, Hao, Dai, Zhaozhao, Zheng, Yonglian, Lai, Jinsheng, Jin, Weiwei, Messing, Joachim, Bennetzen, Jeffrey L., Wing, Rod A. and Luo, Meizhong (2013) Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives. Genetics, 195 3: 723-737. doi:10.1534/genetics.113.157115
Dereeper, Alexis, Guyot, Romain, Tranchant-Dubreuil, Christine, Anthony, François, Argout, Xavier, de Bellis, Fabien, Combes, Marie-Christine, Gavory, Frederick, de Kochko, Alexandre, Kudrna, Dave, Leroy, Thierry, Poulain, Julie, Rondeau, Myriam, Song, Xiang, Wing, Rod and Lashermes, Philippe (2013) BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution. Plant Molecular Biology, 83 3: 177-189. doi:10.1007/s11103-013-0077-5
Singh, Rajinder, Ong-Abdullah, Meilina, Low, Eng-Ti Leslie, Manaf, Mohamad Arif Abdul, Rosli, Rozana, Nookiah, Rajanaidu, Ooi, Leslie Cheng-Li, Ooi, Siew-Eng, Chan, Kuang-Lim, Halim, Mohd Amin, Azizi, Norazah, Nagappan, Jayanthi, Bacher, Blaire, Lakey, Nathan, Smith, Steven W., He, Dong, Hogan, Michael, Budiman, Muhammad A., Lee, Ernest K., Desalle, Rob, Kudrna, David, Goicoechea, Jose Luis, Wing, Rod A., Wilson, Richard K., Fulton, Robert S., Ordway, Jared M., Martienssen, Robert A. and Sambanthamurthi, Ravigadevi (2013) Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature, 500 7462: 335-339. doi:10.1038/nature12309
Matsuba, Yuki, Nguyen, Thuong T.H., Wiegert, Krystle, Falara, Vasiliki, Gonzales-Vigil, Eliana, Leong, Bryan, Schäfer, Petra, Kudrna, David, Wing, Rod A., Bolger, Anthony M., Usadel, Björn, Tissier, Alain, Fernie, Alisdair R., Barry, Cornelius S. and Pichersky, Eran (2013) Evolution of a complex locus for terpene biosynthesis in Solanum. Plant Cell, 25 6: 2022-2036. doi:10.1105/tpc.113.111013
Zhang, Chengjun, Wang, Jun, Marowsky, Nicholas C., Long, Manyuan, Wing, Rod A. and Fan, Chuanzhu (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. doi:10.1093/gbe/evt071
Yang, Ruolin, Jarvis, David E., Chen, Hao, Beilstein, Mark A., Grimwood, Jane, Jenkins, Jerry, Shu, ShengQiang, Prochnik, Simon, Xin, Mingming, Ma, Chuang, Schmutz, Jeremy, Wing, Rod A., Mitchell-Olds, Thomas, Schumaker, Karen S. and Wang, Xiangfeng (2013) The reference genome of the halophytic plant Eutrema salsugineum. Frontiers in Plant Science, 4 MAR: . doi:10.3389/fpls.2013.00046
Chen, Jinfeng, Huang, Quanfei, Gao, Dongying, Wang, Junyi, Lang, Yongshan, Liu, Tieyan, Li, Bo, Bai, Zetao, Luis Goicoechea, Jose, Liang, Chengzhi, Chen, Chengbin, Zhang, Wenli, Sun, Shouhong, Liao, Yi, Zhang, Xuemei, Yang, Lu, Song, Chengli, Wang, Meijiao, Shi, Jinfeng, Liu, Geng, Liu, Junjie, Zhou, Heling, Zhou, Weili, Yu, Qiulin, An, Na, Chen, Yan, Cai, Qingle, Wang, Bo, Liu, Binghang, Min, Jiumeng, Huang, Ying, Wu, Honglong, Li, Zhenyu, Zhang, Yong, Yin, Ye, Song, Wenqin, Jiang, Jiming, Jackson, Scott A., Wing, Rod A., Waang, Jun and Chen, Mingsheng (2013) Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Communications, 4 1: . doi:10.1038/ncomms2596
Koo, Hyun Jo, McDowell, Eric T., Ma, Xiaoqiang, Greer, Kevin A., Kapteyn, Jeremy, Xie, Zhengzhi, Descour, Anne, Kim, HyeRan, Yu, Yeisoo, Kudrna, David, Wing, Rod A., Soderlund, Carol A. and Gang, David 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: . doi:10.1186/1471-2229-13-27
Mayer, Klaus F. X., Waugh, Robbie, Langridge, Peter, Close, Timothy J., Wise, Roger P., Graner, Andreas, Matsumoto, Takashi, Sato, Kazuhiro, Schulman, Alan, Ariyadasa, Ruvini, Schulte, Daniela, Poursarebani, Naser, Zhou, Ruonan, Steuernagel, Burkhard, Mascher, Martin, Scholz, Uwe, Shi, Bujun, Madishetty, Kavitha, Svensson, Jan T., Bhat, Prasanna, Moscou, Matthew, Resnik, Josh, Muehlbauer, Gary J., Hedley, Pete, Liu, Hui, Morris, Jenny, Frenkel, Zeev, Korol, Avraham, Bergès, Hélène, Taudien, Stefan, Felder, Marius, Groth, Marco, Platzer, Matthias, Himmelbach, Axel, Lonardi, Stefano, Duma, Denisa, Alpert, Matthew, Cordero, Francesa, Beccuti, Marco, Ciardo, Gianfranco, Ma, Yaqin, Wanamaker, Steve, Cattonaro, Federica, Vendramin, Vera, Scalabrin, Simone, Radovic, Slobodanka, Wing, Rod, Morgante, Michele, Nussbaumer, Thomas, Gundlach, Heidrun, Martis, Mihaela, Poland, Jesse, Pfeifer, Matthias, Moisy, Cédric, Tanskanen, Jaakko, Zuccolo, Andrea, Spannagl, Manuel, Russell, Joanne, Druka, Arnis, Marshall, David, Bayer, Micha, Swarbreck, David, Sampath, Dharanya, Ayling, Sarah, Febrer, Melanie, Caccamo, Mario, Tanaka, Tsuyoshi, Wannamaker, Steve, Schmutzer, Thomas, Brown, John W. S., Fincher, Geoffrey B. and Stein, Nils (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature, 491 7426: 711-716. doi:10.1038/nature11543
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Ha, Jungmin, Abernathy, Brian, Nelson, William, Grant, David, Wu, Xiaolei, Nguyen, Henry T., Stacey, Gary, Yu, Yeisoo, Wing, Rod A., Shoemaker, Randy C. and Jackson, Scott A. (2012) Integration of the draft sequence and physical map as a framework for genomic research in soybean (Glycine max (l.) merr.) and wild soybean (Glycine soja Sieb. and Zucc.). G3: Genes, Genomes, Genetics, 2 3: 321-329. doi:10.1534/g3.111.001834
Lin, Haiyan, Xia, Peng, Wing, Rod A., Zhang, Qifa and Luo, Meizhong (2012) Dynamic intra-japonica subspecies variation and resource application. Molecular Plant, 5 1: 218-230. doi:10.1093/mp/ssr085
Jacquemin, J., Chaparro, C., Laudié, M., Berger, A., Gavory, F., Goicoechea, J. L., Wing, R. A. and Cooke, R. (2011) Long-range and targeted ectopic recombination between the two homeologous chromosomes 11 and 12 in Oryza species. Molecular Biology and Evolution, 28 11: 3139-3150. doi:10.1093/molbev/msr144
Fan, Chuanzhu, Walling, Jason G., Zhang, Jianwei, Hirsch, Cory D., Jiang, Jiming and Wing, Rod A. (2011) Conservation and purifying selection of transcribed genes located in a rice centromere. Plant Cell, 23 8: 2821-2830. doi:10.1105/tpc.111.085605
Zuccolo, Andrea, Bowers, John E., Estill, James C., Xiong, Zhiyong, Luo, Meizhong, Sebastian, Aswathy, Goicoechea, José L., Collura, Kristi, Yu, Yeisoo, Jiao, Yuannian, Duarte, Jill, Tang, Haibao, Ayyampalayam, Saravanaraj, Rounsley, Steve, Kudrna, Dave, Paterson, Andrew H., Pires, J C., Chanderbali, Andre, Soltis, Douglas E., Chamala, Srikar, Barbazuk, Brad, Soltis, Pamela S., Albert, Victor A., Ma, Hong, Mandoli, Dina, Banks, Jody, Carlson, John E., Tomkins, Jeffrey, dePamphilis, Claude W., Wing, Rod A. and Leebens-Mack, Jim (2011) A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biology, 12 5: . doi:10.1186/gb-2011-12-5-r48
Wing, Rod A., Lin, Jinke and Kudrna, Dave (2011) Construction, characterization, and preliminary BAC-end sequence analysis of a bacterial artificial chromosome library of the tea plant (Camellia sinensis). Journal of Biomedicine and Biotechnology, 2011 . doi:10.1155/2011/476723
Tian, Zhixi, Yu, Yanjun, Lin, Feng, Yu, Yeisoo, SanMiguel, Phillip J., Wing, Rod A., McCouch, Susan R., Ma, Jianxin and Jackson, Scott A. (2011) Exceptional lability of a genomic complex in rice and its close relatives revealed by interspecific and intraspecific comparison and population analysis. BMC Genomics, 12 . doi:10.1186/1471-2164-12-142
Paiva, Jorge A. P., Prat, Elisa, Vautrin, Sonia, Santos, Mauro D., San-Clemente, Hélène, Brommonschenkel, Sérgio, Fonseca, Paulo G. S., Grattapaglia, Dario, Song, Xiang, Ammiraju, Jetty S. S., Kudrna, David, Wing, Rod A., Freitas, Ana T., Bergès, Hélène and Grima-Pettenati, Jacqueline (2011) Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries. BMC Genomics, 12 . doi:10.1186/1471-2164-12-137
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Zuccolo, Andrea, Sebastian, Aswathy, Yu, Yeisoo, Jackson, Scott, Rounsley, Steve, Billheimer, Dean and Wing, Rod A. (2010) Assessing the extent of substitution rate variation of retrotransposon Long Terminal Repeat sequences in Oryza sativa and Oryza glaberrima. Rice, 3 4: 242-250. doi:10.1007/s12284-010-9046-7
Henry, Robert J., Rice, Nicole, Waters, Daniel L. E., Kasem, Shabana, Ishikawa, Ryuji, Hao, Yin, Dillon, Sally, Crayn, Darren, Wing, Rod and Vaughan, Duncan (2010) Australian Oryza: utility and conservation. Rice, 3 4: 235-241. doi:10.1007/s12284-009-9034-y
Ammiraju, Jetty S.S., Song, Xiang, Luo, Meizhong, Sisneros, Nicholas, Angelova, Angelina, Kudrna, David, Kim, Hyeran, Yu, Yeisoo, Goicoechea, Jose Luis, Lorieux, Mathias, Kurata, Nori, Brar, Darshan, Ware, Doreen, Jackson, Scott and Wing, Rod A. (2010) The Oryza BAC resource: A genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives. Breeding Science, 60 5: 536-543. doi:10.1270/jsbbs.60.536
Febrer, Melanie, Goicoechea, Jose Luis, Wright, Jonathan, McKenzie, Neil, Song, Xiang, Lin, Jinke, Collura, Kristi, Wissotski, Marina, Yu, Yeisoo, Ammiraju, Jetty S. S., Wolny, Elzbieta, Idziak, Dominika, Betekhtin, Alexander, Kudrna, Dave, Hasterok, Robert, Wing, Rod A. and Bevan, Michael W. (2010) An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research. PLoS ONE, 5 10: e13461. doi:10.1371/journal.pone.0013461
Geraldes, Armando, Rambo, Teri, Wing, Rod A., Ferrand, Nuno and Nachman, Michael W. (2010) Extensive gene conversion drives the concerted evolution of paralogous copies of the SRY gene in European rabbits. Molecular Biology and Evolution, 27 11: 2437-2440. doi:10.1093/molbev/msq139
Sanyal, Abhijit, Ammiraju, Jetty S.S., Lu, Fei, Yu, Yeisoo, Rambo, Teri, Currie, Jennifer, Kollura, Kristi, Kim, Hye-Ran, Chen, Jinfeng, Ma, Jianxin, San Miguel, Phillip, Mingsheng, Chen, Wing, Rod A. and Jackson, Scott A. (2010) Orthologous comparisons of the Hd1 region across genera reveal hd1 gene lability within diploid oryza species and disruptions to microsynteny in sorghum. Molecular Biology and Evolution, 27 11: 2487-2506. doi:10.1093/molbev/msq133
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Yang, Tae-Jin, Yu, Yeisoo, Chang, Song-Bin, De Jong, Hans, Oh, Chang-Sik, Ahn, Sang-Nag, Fang, Eric and Wing, Rod A. (2005) Toward closing rice telomere gaps: Mapping and sequence characterization of rice subtelomere regions. Theoretical and Applied Genetics, 111 3: 467-478. doi:10.1007/s00122-005-2034-4
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Conference Paper
Adema, Coen M., Luo, Mei-Zhong, Hanelt, Ben, Hertel, Lynn A., Marshall, Jennifer J., Zhang, Si-Ming, DeJong, Randall J., Kim, Hye-Ran, Kudrna, David, Wing, Rod A., Soderlund, Cari, Knight, Matty, Lewis, Fred A., Caldeira, Roberta Lima, Jannotti-Passos, Liana K., Carvalho, Omar Dos Santos and Loker, Eric S. (2006). A bacterial artificial chromosome library for Biomphalaria glabrata, intermediate snail host of Schistosoma mansoni. In: , , (167-177). . doi:10.1590/S0074-02762006000900027