Publications

**The chromosome‐scale reference genome of safflower (Carthamus tinctorius) provides insights into linoleic acid and flavonoid biosynthesis**

Zhihua Wu, Hong Liu, Wei Zhan, Zhichao Yu, Erdai Qin, Shuo Liu, Tiange Yang, Niyan Xiang, Dave Kudrna, Yan Chen, Seunghee Lee, Gang Li, Rod A Wing, Jiao Liu, Hairong Xiong, Chunjiao Xia, Yongzhong Xing, Jianwei Zhang, Rui Qin

A route to de novo domestication of wild allotetraploid rice

Hong Yu, Tao Lin, Xiangbing Meng, Huilong Du, Jingkun Zhang, Guifu Liu, Mingjiang Chen, Yanhui Jing, Liquan Kou, Xiuxiu Li, Qiang Gao, Yan Liang, Xiangdong Liu, Zhilan Fan, Yuntao Liang, Zhukuan Cheng, Mingsheng Chen, Zhixi Tian, Yonghong Wang,

Chengcai Chu, Jianru Zuo, Jianmin Wan, Qian Qian, Bin Han, Andrea Zuccolo, Rod A Wing, Caixia Gao, Chengzhi Liang, Jiayang Li

Assembly and Validation of Two Gap-free Reference Genomes for Xian/indica Rice Reveals Insights into Plant Centromere Architecture

Jia-Ming Song, Wen-Zhao Xie, Shuo Wang, Yi-Xiong Guo, Dal-Hoe Koo, Dave Kudrna, Yicheng Huang, Jia-Wu Feng, Wenhui Zhang, Yong Zhou, Andrea Zuccolo, Evan Long, Seunghee Lee, Jayson Talag, Run Zhou, Xi-Tong Zhu, Daojun Yuan, Joshua Udall, Weibo Xie,

Rod A Wing, Qifa Zhang, Jesse Poland, Jianwei Zhang, Ling-Ling Chen

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

John T Lovell, Alice H MacQueen, Sujan Mamidi, Jason Bonnette, Jerry Jenkins, Joseph D Napier, Avinash Sreedasyam, Adam Healey, Adam Session, Shengqiang Shu, Kerrie Barry, Stacy Bonos, LoriBeth Boston, Christopher Daum, Shweta Deshpande, Aren Ewing,

Paul P Grabowski, Taslima Haque, Melanie Harrison, Jiming Jiang, Dave Kudrna, Anna Lipzen, Thomas H Pendergast, Chris Plott, Peng Qi, Christopher A Saski, Eugene V Shakirov, David Sims, Manoj Sharma, Rita Sharma, Ada Stewart, Vasanth R Singan,

Yuhong Tang, Sandra Thibivillier, Jenell Webber, Xiaoyu Weng, Melissa Williams, Guohong Albert Wu, Yuko Yoshinaga, Matthew Zane, Li Zhang, Jiyi Zhang, Kathrine D Behrman, Arvid R Boe, Philip A Fay, Felix B Fritschi, Julie D Jastrow, John Lloyd-Reilley,

Juan Manuel Martínez-Reyna, Roser Matamala, Robert B Mitchell, Francis M Rouquette, Pamela Ronald, Malay Saha, Christian M Tobias, Michael Udvardi, Rod A Wing, Yanqi Wu, Laura E Bartley, Michael Casler, Katrien M Devos, David B Lowry, Daniel S Rokhsar,

Jane Grimwood, Thomas E Juenger, Jeremy Schmutz

Gapless assembly of maize chromosomes using long-read technologies

Jianing Liu, Arun S Seetharam, Kapeel Chougule, Shujun Ou, Kyle W Swentowsky, Jonathan I Gent, Victor Llaca, Margaret R Woodhouse, Nancy Manchanda, Gernot G Presting, David A Kudrna, Magdy Alabady, Candice N Hirsch, Kevin A Fengler, Doreen Ware,

Todd P Michael, Matthew B Hufford, R Kelly Dawe

A willow sex chromosome reveals convergent evolution of complex palindromic repeats

Ran Zhou, David Macaya-Sanz, Craig H Carlson, Jeremy Schmutz, Jerry W Jenkins, David Kudrna, Aditi Sharma, Laura Sandor, Shengqiang Shu, Kerrie Barry, Gerald A Tuskan, Tao Ma, Jianquan Liu, Matthew Olson, Lawrence B Smart, Stephen P DiFazio

Highly accurate long-read HiFi sequencing data for five complex genomes

Ting Hon, Kristin Mars, Greg Young, Yu-Chih Tsai, Joseph W Karalius, Jane M Landolin, Nicholas Maurer, David Kudrna, Michael A Hardigan, Cynthia C Steiner, Steven J Knapp, Doreen Ware, Beth Shapiro, Paul Peluso, David R Rank

The gap-free rice genomes provide insights for centromere structure and function exploration and graph-based pan-genome construction

Jia-Ming Song, Wen-Zhao Xie, Shuo Wang, Yi-Xiong Guo, Jesse Poland, Dal-Hoe Koo, Dave Kudrna, Evan Long, Yicheng Huang, Jia-Wu Feng, Wenhui Zhang, Seunghee Lee, Jayson Talag, Run Zhou, Xi-Tong Zhu, Daojun Yuan, Joshua Udall, Weibo Xie, Rod Anthony Wing,

Qifa Zhang, Jianwei Zhang, Ling-Ling Chen

A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

Brigitte T Hofmeister, Johanna Denkena, Maria Colomé-Tatché, Yadollah Shahryary, Rashmi Hazarika, Jane Grimwood, Sujan Mamidi, Jerry Jenkins, Paul P Grabowski, Avinash Sreedasyam, Shengqiang Shu, Kerrie Barry, Kathleen Lail, Catherine Adam, Anna Lipzen,

Rotem Sorek, Dave Kudrna, Jayson Talag, Rod Wing, David W Hall, Daniel Jacobsen, Gerald A Tuskan, Jeremy Schmutz, Frank Johannes, Robert J Schmitz

Evolution and diversification of reproductive phased small interfering RNAs in Oryza species

Peng Tian, Xuemei Zhang, Rui Xia, Yang Liu, Meijiao Wang, Bo Li, Tieyan Liu, Jinfeng Shi, Rod A Wing, Blake C Meyers, Mingsheng Chen

Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice

Saule Mussurova, Noor Al-Bader, Andrea Zuccolo, Rod A Wing

Platinum-grade soybean reference genome facilitates characterization of genetic underpinnings of traits

Xinxin Yi, Jing Liu, Shengcai Chen, Hao Wu, Min Liu, Qing Xu, Lingshan Lei, Seunghee Lee, Bao Zhang, Dave Kudrna, Wei Fan, Rod Wing, Chunyan Yang, Mengchen Zhang, Jianwei Zhang, Xuelu Wang, Nansheng Chen

Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K)

Guangyi Fan, Yue Song, Liandong Yang, Xiaoyun Huang, Suyu Zhang, Mengqi Zhang, Xianwei Yang, Yue Chang, He Zhang, Yongxin Li, Shanshan Liu, Lili Yu, Jeffery Chu, Inge Seim, Chenguang Feng, Thomas J Near, Rod A Wing, Wen Wang, Kun Wang, Jing Wang, Xun Xu,

Huanming Yang, Xin Liu, Nansheng Chen, Shunping He

SSRG evolution in the genus Oryza

Freitas KEJd, Santos RSd, C Busanello, Victoria FdC, JL Lopes, RA Wing, ACD Oliveira

Evolutionary Dynamics of Abundant 7-bp Satellites in the Genome of Drosophila virilis

Jullien M Flynn, Manyuan Long, Rod A Wing, Andrew G Clark

A platinum standard pan-genome resource that represents the population structure of Asian rice

Yong Zhou, Dmytro Chebotarov, Dave Kudrna, Victor Llaca, Seunghee Lee, Shanmugam Rajasekar, Nahed Mohammed, Noor Al-Bader, Chandler Sobel-Sorenson, Praveena Parakkal, Lady Johanna Arbelaez, Natalia Franco, Nickolai Alexandrov,

N Ruaraidh Sackville Hamilton, Hei Leung, Ramil Mauleon, Mathias Lorieux, Andrea Zuccolo, Kenneth McNally, Jianwei Zhang, Rod A Wing

Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels

Matt Shenton, Masaaki Kobayashi, Shin Terashima, Hajime Ohyanagi, Dario Copetti, Tania Hernández-Hernández, Jianwei Zhang, Nobuko Ohmido, Masahiro Fujita, Atsushi Toyoda, Hiroshi Ikawa, Asao Fujiyama, Hiroyasu Furuumi, Toshie Miyabayashi, Takahiko Kubo,

David Kudrna, Rod Wing, Kentaro Yano, Ken-Ichi Nonomura, Yutaka Sato, Nori Kurata

Mass genome sequencing of crops and wild relatives to accelerate crop breeding: the digital rice genebank

KL McNally, RP Mauleon, D Chebotarov, SP Klassen, A Kohli, G Ye, H Leung, RS Hamilton, RA Wing

Fish10K Pilot Project Data

Guangyi Fan, Yue Song, Liandong Yang, Xiaoyun Huang, Suyu Zhang, Mengqi Zhang, Xianwei Yang, Yue Chang, He Zhang, Yongxin Li, Shanshan Liu, Lili Yu, Jeffery Chu, Inge Seim, Chenguang Feng, Thomas J Near, Rod Anthony Wing, Wen Wang, Kun Wang, Jing Wang,

Xun Xu, Huanming Yang, Xin Liu, Nansheng Chen, Shunping He

Mitochondrial plastid DNA can cause DNA barcoding paradox in plants

Hyun-Seung Park, Murukarthick Jayakodi, Sae Hyun Lee, Jae-Hyeon Jeon, Hyun-Oh Lee, Jee Young Park, Byeong Cheol Moon, Chang-Kug Kim, Rod A Wing, Steven G Newmaster, Ji Yeon Kim, Tae-Jin Yang

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