Kang Zhang#; Xiang Wang#; Shunmin Chen#; Yuanhang Liu; Lingkui Zhang; Xiaolong Yang; Hailong Yu; Yacong Cao; Lei Zhang; Chengcheng Cai; Jue Ruan; Lihao Wang*; Feng Cheng*. The Gap-free Genome of Pepper Reveals the Transposable Element-driven Expansion and Rapid Evolution of Pericentromeres. Plant Communications (2024). Accept.

Guo Zhongwei#, Zhang Kang, Cai Chengcheng, Zhang Lingkui, Li Xing, Wang Xiang, Yang Yinqing, Zhang Lei, Chen Shumin, Cheng Feng*. Deep learning can predict subgenome dominance in ancient but not in neo/synthetic polyploidized genomes. The Plant Journal (2024). https://onlinelibrary.wiley.com/doi/10.1111/tpj.16979.

Chengcheng Cai#, Yinqing Yang#, Lei Zhang#, Yinan Cui, Jian Wu, Jianli Liang, Xing Li, Lingkui Zhang, Xin Zhang, Yiyue Zhang, Zhongwei Guo, Shumin Chen, Kang Zhang*, Michael Freeling*, Xiaowu Wang*, Feng Cheng*. Regional Active Transcription Associates with Homoeologous Exchange Breakpoints in Synthetic Brassica Tetraploids. Plant Physiology (2024). https://doi.org/10.1093/plphys/kiae434.

Yinqing Yang#, Lei Zhang, Qi Tang, Lingkui Zhang, Xing Li, Shumin Chen, Kang Zhang, Ying Li*, Xilin Hou*, Feng Cheng*. Improved Genome Annotation of Brassica oleracea Highlights the Importance of Alternative Splicing. Horticultural Plant Journal (2024). https://doi.org/10.1016/j.hpj.2024.03.005.

Hongbing She#, Zhiyuan Liu#, Zhaosheng Xu, Helong Zhang, Jian Wu, Xiaowu Wang, Feng Cheng*, Deborah Charlesworth*, Wei Qian*. Insights into spinach domestication from genome sequences of two wild spinach progenitors, Spinacia turkestanica and Spinacia tetrandra. New Phytologist (2024). https://doi.org/10.1111/nph.19799.

Lingkui Zhang#; Yanfeng Duan#; Zewei Zhang; Lei Zhang; Shumin Chen; Chengcheng Cai; Shaoguang Duan; Kang Zhang; Guangcun Li*; Feng Cheng*. OcBSA: an NGS-based Bulk Segregant Analysis Tool for Outcross Populations. Molecular Plant (2024). https://doi.org/10.1016/j.molp.2024.02.011.

Xing Li#, Yong Wang#, Chengcheng Cai#, Jialei Ji#, Fengqing Han#, Lei Zhang#, Shumin Chen, Lingkui Zhang, Yinqing Yang, Qi Tang, Johan Bucher, Xuelin Wang, Limei Yang, Mu Zhuang, Kang Zhang*, Honghao Lv*, Guusje Bonnema*, Yangyong Zhang*, Feng Cheng*. Large-scale Gene Expression Variation Introduced by Structural Variation Drives Morphotype Diversification in Brassica oleracea. Nature Genetics (2024). https://doi.org/10.1038/s41588-024-01655-4.

Kang Zhang#, Lingkui Zhang#, Yinan Cui#, Yinqing Yang, Jian Wu, Jianli Liang, Xing Li, Xin Zhang, Yiyue Zhang, Zhongwei Guo, Lei Zhang, Shumin Chen, Jue Ruan, Michael Freeling*, Xiaowu Wang*, Feng Cheng*. The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids. PNAS (2023). https://doi.org/10.1073/pnas.2305208120.

Yile Huang,# Xinyi Guo#, Kang Zhang, Terezie Mandáková, Feng Cheng*, Martin A. Lysak*. The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora. The Plant Journal (2023). https://doi.org/10.1111/tpj.16383.

Xiaohui Yang#, Lingkui Zhang#, Xiao Guo, Jianfei Xu, Kang Zhang, Yinqing Yang, Yu Yang, Yinqiao Jian, Daofeng Dong, Sanwen Huang, Feng Cheng*, Guangcun Li*. The gap-free potato genome reveals large tandem gene clusters of agronomical importance in highly repeated genomic regions. Molecular Plant (2022). https://doi.org/10.1016/j.molp.2022.12.010.

Yacong Cao#, Kang Zhang#, Hailong Yu#, Shumin Chen#, Donghui Xu#, Hong Zhao, Zhenghai Zhang, Yinqing Yang, Xiaozhen Gu, Xinyan Liu, Haiping Wang, Yaxin Jing, Yajie Mei, Xiang Wang, Véronique Lefebvre, Weili Zhang, Yuan Jin, Dongliang An, Risheng Wang, Paul Bosland, Xixiang Li, Ilan Paran, Baoxi Zhang, Giovanni Giuliano*, Lihao Wang*, Feng Cheng*. Pepper variome reveals the history and key loci associated with fruit domestication and diversification. Molecular Plant (2022). https://doi.org/10.1016/j.molp.2022.09.021.

Kang Zhang#, Yinqing Yang#, Xin Zhang#, Lingkui Zhang, Yu Fu, Zhongwei Guo, Shumin Chen, Jian Wu, James C. Schnable*, Keke Yi*, Xiaowu Wang*, and Feng Cheng*. The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits. PLANT COMMUNICATIONS (2022). https://doi.org/10.1016/j.xplc.2022.100431.

Yinqing Yang#, Kang Zhang#, Ya Xiao, Lingkui Zhang, Yile Huang, Xing Li, Shumin Chen, Yansong Peng, Shuhua Yang*, Yongbo Liu*, and Feng Cheng*. Genome Assembly and Population Resequencing Reveal the Geographical Divergence of Shanmei (Rubus corchorifolius). Genomics, Proteomics & Bioinformatics (2022). https://doi.org/10.1101/2021.11.22.469527.

Zheng Wang#, Jinghua Yang#, Feng Cheng#, Peirong Li, Xiaoyun Xin, Weihong Wang, Yangjun Yu, Deshuang Zhang, Xiuyun Zhao, Shuancang Yu, Fenglan Zhang, Yang Dong*, and Tongbing Su*. Subgenome dominance and its evolutionary implications in crop domestication and breeding. Horticulture Research (2022). https://doi.org/10.1093/hr/uhac090.

Peng Wu#, Lingkui Zhang#, Kang Zhang#, Yulai Yin#, Ailian Liu, Yue Zhu, Yu Fu, Fangfang Sun, Shuping Zhao, Kai Feng, Xuewen Xu, Xuehao Chen*, Feng Cheng*, Liangjun Li*. The adaptive evolution of Euryale ferox to the aquatic environment through paleo-hexaploidization. The Plant Journal (2022). https://doi.org/10.1111/tpj.15717.

Xiaoxue Sun#, Xing Li#, Yin Lu#, Shan Wang#, Xiaomeng Zhang#, Kang Zhang#, Xiangjie Su, Mengyang Liu, Daling Feng, Shuangxia Luo, Aixia Gu, Yu Fu, Xueping Chen, Shuxin Xuan, Yanhua Wang, Donghui Xu, Shumin Chen, Wei Ma*, Shuxing Shen*, Feng Cheng*, Jianjun Zhao*. Construction of a high-density mutant population of Chinese cabbage facilitates the genetic dissection of agronomic traits. Molecular Plant (2022), https://doi.org/10.1016/j.molp.2022.02.006.

Kang Zhang#, Yinqing Yang#, Jian Wu, Jianli Liang, Shumin Chen, Lei Zhang, Honghao Lv, Xiaona Yin, Xin Zhang, Yiyue Zhang, Lingkui Zhang, Yangyong Zhang, Michael Freeling*, Xiaowu Wang*, Feng Cheng*. A cluster of transcripts identifies a transition stage initiating leafy head growth in heading morphotypes of Brassica. The Plant Journal (2022). https://doi.org/10.1111/tpj.15695.

Lei Liu#, Kang Zhang#, Jin Rui Bai, Jinghua Lu, Xiaoxiao Lu, Junling Hu, Chunyang Pan, Shumin He, Jiale Yuan, Yiyue Zhang, Min Zhang, Yanmei Guo, Xiaoxuan Wang, Zejun Huang, Yongchen Du, Feng Cheng*, Junming Li*. All-flesh fruit in tomato is controlled by reduced expression dosage of AFF through a structural variant mutation in the promoter. Journal of Experimental Botany (2021). https://doi.org/10.1093/jxb/erab401.

Yile Huang#, Lingkui Zhang, Kang Zhang, Shumin Chen, Jianbin Hu*, Feng Cheng*. The impact of tandem duplication on gene evolution in Solanaceae species. Journal of Integrative Agriculture (2021). https://doi.org/10.1016/S2095-3119(21)63698-5.

Feng An#, Kang Zhang#, Ling-kui Zhang, Xing Li, Shu-min Chen, Hua-sen Wang*, Feng Cheng*. Genome-wide identification, evolutionary selection, and genetic variation of DNA methylation-related genes in Brassica rapa and Brassica oleracea. Journal of Integrative Agriculture (2021). https://doi.org/10.1016/S2095-3119(21)63827-3.

Weifeng Xu#*, Qian Zhang*, Wei Yuan, Feiyun Xu, Mehtab Muhammad Aslam, Rui Miao, Ying Li, Qianwen Wang, Xing Li, Xin Zhang, Kang Zhang, Tianyu Xia*, Feng Cheng*. The genome evolution and low-phosphorus adaptation in white lupin. Nature Communications (2020). https://doi.org/10.1038/s41467-020-14891-z.

Yinan Cui#, Mu Zhuang#, Jian Wu, Jisheng Liu, Yiyue Zhang, Lingkui Zhang, Yile Huang, Xu Cai, Jianli Liang, Kang Zhang, Xiaowu Wang*, Feng Cheng*. Segmental Translocation Contributed to the Origin of the Brassica S-locus. Horticultural Plant Journal (2020). https://doi.org/10.1016/j.hpj.2020.04.005.

Xin Zhang#, Kang Zhang#, Jian Wu, Ning Guo, Jianli Liang, Xiaowu Wang*, Feng Cheng*. QTL-Seq and Sequence Assembly Rapidly Mapped the Gene BrMYBL2.1 for the Purple Trait in Brassica rapa. Scientific Reports (2020). https://doi.org/10.1038/s41598-020-58916-5.

Kang Zhang#, Xiaowu Wang, Feng Cheng*.Plant Polyploidy: Origin, Evolution, and Its Influence on Crop Domestication. Horticultural Plant Journal (2019). https://doi.org/10.1016/j.hpj.2019.11.003.
.

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Feng Cheng#, Jian Wu, Xu Cai, Jianli Liang, Michael Freeling*, Xiaowu Wang*. Gene retention, fractionation and subgenome differences in polyploid plants. Nature Plants (2018). https://doi.org/10.1038/s41477-018-0136-7.

Feng Cheng#, Rifei Sun#, Xilin Hou#, Hongkun Zheng#, Fenglan Zhang#, Yangyong Zhang, Bo Liu, Jianli Liang, Mu Zhuang, Yunxia Liu, Dongyuan Liu, Xiaobo Wang, Pingxia Li, Yumei Liu, Ke Lin, Johan Bucher, Ningwen Zhang, Yan Wang, Hui Wang, Jie Deng, Yongcui Liao, Keyun Wei, Xueming Zhang, Lixia Fu, Yunyan Hu, Jisheng Liu, Chengcheng Cai, Shujiang Zhang, Shifan Zhang, Fei Li, Hui Zhang, Jifang Zhang, Ning Guo, Zhiyuan Liu, Jin Liu, Chao Sun, Yuan Ma, Haijiao Zhang, Yang Cui, Micheal R Freeling, Theo Borm, Guusje Bonnema*, Jian Wu*, Xiaowu Wang*. Sub-genome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nature Genetics (2016). https://doi.org/10.1038/ng.3634.

Jinghua Yang#, Dongyuan Liu#, Xiaowu Wang#, Changmian Ji#, Feng Cheng#, Baoning Liu, Zhongyuan Hu, Sheng Chen, Deepak Penta, Youhui Ju, Pu Yao, Xuming Li, Kun Xie, Jianhui Zhang, Jianlin Wang, Fan Liu, Weiwei Ma, Jannat Shopan, Hongkun Zheng, Sally A Mackenzie*, Mingfang Zhang*. The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nature Genetics (2016). https://doi.org/10.1038/ng.3657.

Feng Cheng#, Terezie Mandakova, Jian Wu, Qi Xie, Martin A. Lysak, Xiaowu Wang*, Deciphering the Diploid Ancestral Genome of the Mesohexaploid Brassica rapa, Plant Cell, 2013, 25(5): 1541-1554.

Margaret R.#, Feng Cheng#, Chris J. Pires, Damon Lisch, Michael Freeling*, Xiaowu Wang*, Origin, inheritance, and gene regulatory consequences of genome dominance in polyploids, PNAS, 2014, 111(14): 5283-5288.

Feng Cheng#*, Chao Sun#, Jian Wu, James Schnable, Margaret R. Woodhouse, Jianli Liang, Chengcheng Cai, Michael Freeling, Xiaowu Wang*, Epigenetic Regulation of Subgenome Dominance Following Whole Genome Triplication in Brassica rapa, New Phytologist, 2016, 211(1): 288-299.

Feng Cheng#, Jianli Liang#, Chengcheng Cai, Xu Cai, Jian Wu, Xiaowu Wang*. Genome sequencing supports a multi-vertex model for Brassiceae species, Current Opinion in Plant Biology, 2017, 36: 79-87.

Chengcheng Cai#, Xiaobo Wang#, Bo Liu, Jian Wu, Jianli Liang, Yinan Cui, Feng Cheng*, and Xiaowu Wang*, Brassica rapa Genome 2.0: the reference upgrade through sequence re-assembly and gene re-annotation, Molecular Plant, 2017, 10(4): 649-651.

Huanan Zhang#, Feng Cheng#, Yuguo Xiao#, Xiaojun Kang#, Xiaowu Wang, Rui Kaung*, Min Ni*, Global analysis of canola genes targeted by SHORT HYPOCOTYL UNDER BLUE 1 during endosperm and embryo development, Plant Journal, 2017, 91(1): 158-171.

Xu Cai#, Yinan Cui, Lei Zhang, Jian Wu, Jianli Liang, Xiaowu Wang*, Feng Cheng*, Hotspots of Independent and Multiple Rounds of LTR-retrotransposon Bursts in Brassica Species, Horticultural Plant Journal, 2018, 4(4): 165-174.

Feng Cheng#, Jian Wu, Chengcheng Cai, Lixia Fu, Jianli Liang, Theo Borm, Mu Zhuang, Yangyong Zhang, Fenglan Zhang, Guusje Bonnema*, Xiaowu Wang*, Genome resequencing and comparative variome analysis in a Brassica rapa and Brassica oleracea collection. Scientific Data, 2016, doi:10.1038/sdata.2016.119.

Xiaobo Wang#, Jian Wu, Jianli Liang, Feng Cheng*, Xiaowu Wang*, Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources, Database (Oxford), 2015 (bav093): 1-8.

Chao Sun#, Jian Wu, Jianli Liang, James C Schnable, Wencai Yang, Feng Cheng*, Xiaowu Wang*, Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa, Genome Biology and Evolution, 2015, 7(11): 3085-3096.

Lixia Fu#, Chengcheng Cai#, Yinan Cui, Jian Wu, Jianli Liang, Feng Cheng*, Xiaowu Wang*, Pooled Mapping: An Efficient Method of Calling Variations for Population Samples with Low-depth Resequencing Data, Molecular Breeding, 2016, 36:48.

Feng Cheng#, Jian Wu, Xiaowu Wang*, Genome triplication drove the diversification of Brassica plants, Horticulture Research, 2014, 1: 14024.

Feng Cheng#, Jian Wu, Lu Fang, Silong Sun, Bo Liu, Ke Lin, Guusje Bonnema, Xiaowu Wang*, Biased Gene Fractionation and Dominant Gene Expression among the Subgenomes of Brassica rapa, PLoS ONE, 2012, 7(5).

Feng Cheng#, Jian Wu, Lu Fang, Xiaowu Wang*, Syntenic gene analysis between Brassica rapa and other Brassicaceae species, Front Plant Sci, 2012, 3: 198.

Feng Cheng#, Shengyi Liu, Jian Wu, Lu Fang, Silong Sun, Bo Liu, Pingxia Li, Wei Hua, Xiaowu Wang*, BRAD, the genetics and genomics database for Brassica plants, BMC Plant Biology, 2011, 11.

Feng Cheng#, Xianglong Zhang, Yinan Zhang, Chaohua Li, Changqing Zeng*, Haplo2Ped: a tool using haplotypes as markers for linkage analysis, BMC Bioinformatics, 2011, 12.

Feng Cheng#, Ke X., Lv M., Zhang F., Li C., Zhang X., Zhang Y., Zhao X., Wang X., Liu B., Han J., Li Y., Zeng C.*, and Li S.*, A novel frame-shift mutation of GLI3 causes non-syndromic and complex digital anomalies in a Chinese family. Clinica Chimica Acta, 2011, 412, 1012-1017.

Feng Cheng#, Chen W, Richards E, Deng L, and Zeng C.*, SNP@Evolution: a hierarchical database of positive selection on the human genome. BMC Evolutionary Biology, 2009, 9, 221.

Zeshi He#, Feng Cheng#, Li Y, Wang X, Parkin IA, Chalhoub B, Liu S, Bancroft I.*, Construction of Brassica a and c genome-based ordered pan-transcriptomes for use in rapeseed genomic research. Data Brief, 2015, 4: 357-362.

Xiaowu Wang#*, Hanzhong Wang*, Jun Wang*, Rifei Sun*, Jian Wu#, Shengyi Liu#, Yinqi Bai#, Jeong-Hwan Mun#, Ian Bancroft#, Feng Cheng (group leader), Sanwen Huang, Xixiang Li, Wei Hua, Junyi Wang, Xiyin Wang, Michael Freeling, J Chris Pires, Andrew H Paterson, Boulos Chalhoub, Bo Wang, Alice Hayward, Andrew G Sharpe, Beom-Seok Park, Bernd Weisshaar, Binghang Liu, Bo Li, Bo Liu, Chaobo Tong, Chi Song, Christopher Duran, Chunfang Peng, Chunyu Geng, Chushin Koh, Chuyu Lin, David Edwards, Desheng Mu, Di Shen, Eleni Soumpourou, Fei Li, Fiona Fraser, Gavin Conant, Gilles Lassalle, Graham J King, Guusje Bonnema, Haibao Tang, Haiping Wang, Harry Belcram, Heling Zhou, Hideki Hirakawa, Hiroshi Abe, Hui Guo, Hui Wang, Huizhe Jin, Isobel A P Parkin, Jacqueline Batley, Jeong-Sun Kim, Jérémy Just, Jianwen Li, Jiaohui Xu, Jie Deng, Jin A Kim, Jingping Li, Jingyin Yu, Jinling Meng, Jinpeng Wang, Jiumeng Min, Julie Poulain, Jun Wang, Katsunori Hatakeyama, Kui Wu, Li Wang, Lu Fang, Martin Trick, Matthew G Links, Meixia Zhao, Mina Jin, Nirala Ramchiary, Nizar Drou, Paul J Berkman, Qingle Cai, Quanfei Huang, Ruiqiang Li, Satoshi Tabata, Shifeng Cheng, Shu Zhang, Shujiang Zhang, Shunmou Huang, Shusei Sato, Silong Sun, Soo-Jin Kwon, Su-Ryun Choi, Tae-Ho Lee, Wei Fan, Xiang Zhao, Xu Tan, Xun Xu, Yan Wang, Yang Qiu, Ye Yin, Yingrui Li, Yongchen Du, Yongcui Liao, Yongpyo Lim, Yoshihiro Narusaka, Yupeng Wang, Zhenyi Wang, Zhenyu Li, Zhiwen Wang, Zhiyong Xiong and Zhonghua Zhang, The genome of the mesopolyploid crop species Brassica rapa, Nature Genetics, 2011, 43(10): 1035-1039.

Shengyi Liu#*, Yumei Liu#, Xinhua Yang#, Chaobo Tong#, David Edwards#, Isobel A. P. Parkin#, Meixia Zhao, Jianxin Ma, Jingyin Yu, Shunmou Huang, Xiyin Wang, Junyi Wang, Kun Lu, Zhiyuan Fang, Ian Bancroft, Tae-Jin Yang, Qiong Hu, Xinfa Wang, Zhen Yue, Haojie Li, Linfeng Yang, Jian Wu, Qing Zhou, Wanxin Wang, Graham J King, J. Chris Pires, Changxin Lu, Zhangyan Wu, Perumal Sampath, Zhuo Wang, Hui Guo, Shengkai Pan, Limei Yang, Jiumeng Min, Dong Zhang, Dianchuan Jin, Wanshun Li, Harry Belcram, Jinxing Tu, Mei Guan, Cunkou Qi, Dezhi Du, Jiana Li, Liangcai Jiang, Jacqueline Batley, Andrew G Sharpe, Beom-Seok Park, Pradeep Ruperao, Feng Cheng, Nomar Espinosa Waminal, Yin Huang, Caihua Dong, Li Wang, Jingping Li, Zhiyong Hu, Mu Zhuang, Yi Huang, Junyan Huang, Jiaqin Shi, Desheng Mei, Jing Liu, Tae-Ho Lee, Jinpeng Wang, Huizhe Jin, Zaiyun Li, Xun Li, Jiefu Zhang, Lu Xiao, Yongming Zhou, Zhongsong Liu, Xuequn Liu, Rui Qin, Xu Tang, Wenbin Liu, Yupeng Wang, Yangyong Zhang, Jonghoon Lee, Hyun Hee Kim, France Denoeud, Xun Xu, Xinming Liang, Wei Hua, Xiaowu Wang, Jun Wang, Boulos Chalhoub and Andrew H. Paterson, The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes, Nature Communications, 5, 2014/5.

Xiaohui Zhang#, Zhen Yue#, Shiyong Mei#, Yang Qiu, Xinhua Yang, Xiaohua Chen, Feng Cheng, Zhangyan Wu, Yuyan Sun, Yi Jing, Bo Liu, Di Shen, haiping Wang, Na Cui, Yundan Duan, Jian Wu, Jinglei Wang, Caixia Gan, Jun Wang, Xiaowu Wang*, Xixiang Li*, A de novo Genome of a Chinese Radish Cultivar, Horticultural Plant Journal, 2015, (03): 155-164.