22 results on '"Wu Zhangyan"'
Search Results
2. A de novo Genome of a Chinese Radish Cultivar
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Zhang Xiaohui, Yue Zhen, Mei Shiyong, Qiu Yang, Yang Xinhua, Chen Xiaohua, Cheng Feng, Wu Zhangyan, Sun Yuyan, Jing Yi, Liu Bo, Shen Di, Wang Haiping, Cui Na, Duan Yundan, Wu Jian, Wang Jinglei, Gan Caixia, Wang Jun, Wang Xiaowu, and Li Xixiang more...
- Subjects
Raphanus sativus ,genome ,sequencing ,Plant culture ,SB1-1110 - Abstract
Here, we report a high-quality draft genome of a Chinese radish (Raphanus sativus) cultivar. This draft contains 387.73 Mb of assembled scaffolds, 83.93% of the scaffolds were anchored onto nine pseudochromosomes and 95.09% of 43 240 protein-coding genes were functionally annotated. 184.75 Mb (47.65%) of repeat sequences was identified in the assembled genome. By comparative analyses of the radish genome against 10 other plant genomes, 2 275 genes in 780 gene families were found unique to R. sativus. This genome is a good reference for genomic study and of great value for genetic improvement of radish. more...
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- 2015
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3. High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation
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Tong, Xiaoling, Han, Min-Jin, Lu, Kunpeng, Tai, Shuaishuai, Liang, Shubo, Liu, Yucheng, Hu, Hai, Shen, Jianghong, Long, Anxing, Zhan, Chengyu, Ding, Xin, Liu, Shuo, Gao, Qiang, Zhang, Bili, Zhou, Linli, Tan, Duan, Yuan, Yajie, Guo, Nangkuo, Li, Yan-Hong, Wu, Zhangyan, Liu, Lulu, Li, Chunlin, Lu, Yaru, Gai, Tingting, Zhang, Yahui, Yang, Renkui, Qian, Heying, Liu, Yanqun, Luo, Jiangwen, Zheng, Lu, Lou, Jinghou, Peng, Yunwu, Zuo, Weidong, Song, Jiangbo, He, Songzhen, Wu, Songyuan, Zou, Yunlong, Zhou, Lei, Cheng, Lan, Tang, Yuxia, Cheng, Guotao, Yuan, Lianwei, He, Weiming, Xu, Jiabao, Fu, Tao, Xiao, Yang, Lei, Ting, Xu, Anying, Yin, Ye, Wang, Jian, Monteiro, Antónia, Westhof, Eric, Lu, Cheng, Tian, Zhixi, Wang, Wen, Xiang, Zhonghuai, and Dai, Fangyin more...
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- 2022
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4. Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii
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Yuan, Junhui, Jiang, Sanjie, Jian, Jianbo, Liu, Mingyu, Yue, Zhen, Xu, Jiabao, Li, Juan, Xu, Chunyan, Lin, Lihong, Jing, Yi, Zhang, Xiaoxiao, Chen, Haixin, Zhang, Linjuan, Fu, Tao, Yu, Shuiyan, Wu, Zhangyan, Zhang, Ying, Wang, Chongzhi, Zhang, Xiao, Huang, Liangbo, Wang, Hongqi, Hong, Deyuan, Chen, Xiao-Ya, and Hu, Yonghong more...
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- 2022
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5. Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum
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Jian, Jianbo, Wu, Zhangyan, Silva-Núñez, Arisbe, Liu, Yun, Li, Xiaohui, Zheng, Xiaomin, Luo, Bei, Fang, Xiaodong, Workman, Christopher T., Larsen, Thomas Ostenfeld, Hansen, Per Juel, Sonnenschein, Eva C., Jian, Jianbo, Wu, Zhangyan, Silva-Núñez, Arisbe, Liu, Yun, Li, Xiaohui, Zheng, Xiaomin, Luo, Bei, Fang, Xiaodong, Workman, Christopher T., Larsen, Thomas Ostenfeld, Hansen, Per Juel, and Sonnenschein, Eva C. more...
- Abstract
Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKSs) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Repeat expanded and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future. more...
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- 2024
6. Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum
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Jian, Jianbo, primary, Wu, Zhangyan, additional, Silva-Núñez, Arisbe, additional, Li, Xiaohui, additional, Zheng, Xiaomin, additional, Luo, Bei, additional, Liu, Yun, additional, Fang, Xiaodong, additional, Workman, Christopher T., additional, Larsen, Thomas Ostenfeld, additional, Hansen, Per Juel, additional, and Sonnenschein, Eva C., additional more...
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- 2023
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7. Musa balbisiana genome reveals subgenome evolution and functional divergence
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Wang, Zhuo, Miao, Hongxia, Liu, Juhua, Xu, Biyu, Yao, Xiaoming, Xu, Chunyan, Zhao, Shancen, Fang, Xiaodong, Jia, Caihong, Wang, Jingyi, Zhang, Jianbin, Li, Jingyang, Xu, Yi, Wang, Jiashui, Ma, Weihong, Wu, Zhangyan, Yu, Lili, Yang, Yulan, Liu, Chun, Guo, Yu, Sun, Silong, Baurens, Franc-Christophe, Martin, Guillaume, Salmon, Frederic, Garsmeur, Olivier, Yahiaoui, Nabila, Hervouet, Catherine, Rouard, Mathieu, Laboureau, Nathalie, Habas, Remy, Ricci, Sebastien, Peng, Ming, Guo, Anping, Xie, Jianghui, Li, Yin, Ding, Zehong, Yan, Yan, Tie, Weiwei, D’Hont, Angélique, Hu, Wei, and Jin, Zhiqiang more...
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- 2019
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8. Genome of wild olive and the evolution of oil biosynthesis
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Unver, Turgay, Wu, Zhangyan, Sterck, Lieven, Turktas, Mine, Lohaus, Rolf, Li, Zhen, Yang, Ming, He, Lijuan, Deng, Tianquan, Escalante, Francisco Javier, Llorens, Carlos, Roig, Francisco J., Parmaksiz, Iskender, Dundar, Ekrem, Xie, Fuliang, Zhang, Baohong, Ipek, Arif, Uranbey, Serkan, Erayman, Mustafa, Ilhan, Emre, Badad, Oussama, Ghazal, Hassan, Lightfoot, David A., Kasarla, Pavan, Colantonio, Vincent, Tombuloglu, Huseyin, Hernandez, Pilar, Mete, Nurengin, Cetin, Oznur, Van Montagu, Marc, Yang, Huanming, Gao, Qiang, Dorado, Gabriel, and Van de Peer, Yves more...
- Published
- 2017
9. Variation among 532 genomes unveils the origin and evolutionary history of a global insect herbivore
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You, Minsheng, Ke, Fushi, You, Shijun, Wu, Zhangyan, Liu, Qingfeng, He, Weiyi, Baxter, Simon W., Yuchi, Zhiguang, Vasseur, Liette, Gurr, Geoff M., Ward, Christopher M., Cerda, Hugo, Yang, Guang, Peng, Lu, Jin, Yuanchun, Xie, Miao, Cai, Lijun, Douglas, Carl J., Isman, Murray B., Goettel, Mark S., Song, Qisheng, Fan, Qinghai, Wang-Pruski, Gefu, Lees, David C., Yue, Zhen, Bai, Jianlin, Liu, Tiansheng, Lin, Lianyun, Zheng, Yunkai, Zeng, Zhaohua, Lin, Sheng, Wang, Yue, Zhao, Qian, Xia, Xiaofeng, Chen, Wenbin, Chen, Lilin, Zou, Mingmin, Liao, Jinying, Gao, Qiang, Fang, Xiaodong, Yin, Ye, Yang, Huanming, Wang, Jian, Han, Liwei, Lin, Yingjun, Lu, Yanping, and Zhuang, Mousheng more...
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- 2020
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10. Reference genomes of 545 silkworms enable high-throughput exploring genotype-phenotype relationships
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Tong, Xiaoling, primary, Han, Min-Jin, additional, Lu, Kunpeng, additional, Tai, Shuaishuai, additional, Liang, Shubo, additional, Liu, Yucheng, additional, Hu, Hai, additional, Shen, Jianghong, additional, Long, Anxing, additional, Zhan, Chengyu, additional, Ding, Xin, additional, Gao, Qiang, additional, Zhang, Bili, additional, Tan, Duan, additional, Yuan, Yajie, additional, Guo, Nangkuo, additional, Li, Yanhong, additional, Wu, Zhangyan, additional, Liu, Lulu, additional, Li, Chunlin, additional, Lu, Yaru, additional, Gai, Tingting, additional, Zhang, Yahui, additional, Yang, Renkui, additional, Qian, Heying, additional, Liu, Yanqun, additional, Luo, Jiangwen, additional, Zheng, Lu, additional, Lou, Jinghou, additional, Peng, Yunwu, additional, Zuo, Weidong, additional, Song, Jiangbo, additional, He, Songzhen, additional, Wu, Songyuan, additional, Zou, Yunlong, additional, Zhou, Lei, additional, Zhou, Linli, additional, Cheng, Lan, additional, Tang, Yuxia, additional, Cheng, Guotao, additional, Yuan, Lianwei, additional, He, Weiming, additional, Xu, Jiabao, additional, Fu, Tao, additional, Xiao, Yang, additional, Lei, Ting, additional, Xu, Anying, additional, Yin, Ye, additional, Wang, Jian, additional, Monteiro, Antónia, additional, Westhof, Eric, additional, Lu, Cheng, additional, Tian, Zhixi, additional, Wang, Wen, additional, Xiang, Zhonghuai, additional, and Dai, Fangyin, additional more...
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- 2021
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11. Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway
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Li, Hong-Lei, primary, Wu, Lin, additional, Dong, Zhaoming, additional, Jiang, Yusong, additional, Jiang, Sanjie, additional, Xing, Haitao, additional, Li, Qiang, additional, Liu, Guocheng, additional, Tian, Shuming, additional, Wu, Zhangyan, additional, Wu, Bin, additional, Li, Zhexin, additional, Zhao, Ping, additional, Zhang, Yan, additional, Tang, Jianmin, additional, Xu, Jiabao, additional, Huang, Ke, additional, Liu, Xia, additional, Zhang, Wenlin, additional, Liao, Qinhong, additional, Ren, Yun, additional, Huang, Xinzheng, additional, Li, Qingzhi, additional, Li, Chengyong, additional, Wang, Yi, additional, Xavier-Ravi, Baskaran, additional, Li, Honghai, additional, Liu, Yang, additional, Wan, Tao, additional, Liu, Qinhu, additional, Zou, Yong, additional, Jian, Jianbo, additional, Xia, Qingyou, additional, and Liu, Yiqing, additional more...
- Published
- 2021
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12. Chromosome‐scale genome assembly of areca palm ( Areca catechu )
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Yang, Yaodong, primary, Huang, Liyun, additional, Xu, Chunyan, additional, Qi, Lan, additional, Wu, Zhangyan, additional, Li, Jia, additional, Chen, Haixin, additional, Wu, Yi, additional, Fu, Tao, additional, Zhu, Hui, additional, Saand, Mumtaz Ali, additional, Li, Jing, additional, Liu, Liyun, additional, Fan, Haikou, additional, Zhou, Huanqi, additional, and Qin, Weiquan, additional more...
- Published
- 2021
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13. Genome of wild olive and the evolution of oil biosynthesis
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Ministry of Food, Agriculture and Livestock (Turkey), Junta de Andalucía, Universidad de Córdoba (España), Ghent University, European Commission, Ankara University, Turkish Academy of Sciences, Çankırı Karatekin University, Hatay Mustafa Kemal University, Tokat Gaziosmanpaşa University, Unver, Turgay, Wu, Zhangyan, Sterck, Lieven, Turktas, Mine, Lohaus, Rolf, Li, Zhen, Yang, Ming, He, Lijuan, Deng, Tianquan, Escalante, Francisco Javier, Llorens, Carlos, Roig, Francisco J., Parmaksiz, Iskender, Dundar, Ekrem, Xie, Fuliang, Zhang, Baohong, Ipek, Arif, Uranbey, Serkan, Erayman, Mustafa, Ilhan, Ekrem, Badad, Oussama, Ghazal, Hassan, Lightfoot, David A., Kasarla, Pavan, Colantonio, Vincent, Tombuloglu, Huyesin, Hernández Molina, Pilar, Mete, Nurengin, Cetin, Oznur, Van Montagu, Marc, Yang, Huanming, Gao, Qiang, Dorado, Gabriel, Van de Peer, Yves, Ministry of Food, Agriculture and Livestock (Turkey), Junta de Andalucía, Universidad de Córdoba (España), Ghent University, European Commission, Ankara University, Turkish Academy of Sciences, Çankırı Karatekin University, Hatay Mustafa Kemal University, Tokat Gaziosmanpaşa University, Unver, Turgay, Wu, Zhangyan, Sterck, Lieven, Turktas, Mine, Lohaus, Rolf, Li, Zhen, Yang, Ming, He, Lijuan, Deng, Tianquan, Escalante, Francisco Javier, Llorens, Carlos, Roig, Francisco J., Parmaksiz, Iskender, Dundar, Ekrem, Xie, Fuliang, Zhang, Baohong, Ipek, Arif, Uranbey, Serkan, Erayman, Mustafa, Ilhan, Ekrem, Badad, Oussama, Ghazal, Hassan, Lightfoot, David A., Kasarla, Pavan, Colantonio, Vincent, Tombuloglu, Huyesin, Hernández Molina, Pilar, Mete, Nurengin, Cetin, Oznur, Van Montagu, Marc, Yang, Huanming, Gao, Qiang, Dorado, Gabriel, and Van de Peer, Yves more...
- Abstract
Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at ∼28 and ∼59 Mya. These events contributed to the expansion and neofunctionalization of genes and gene families that play important roles in oil biosynthesis. The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR, and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an siRNA derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression. Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2, 3, 5, and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics. more...
- Published
- 2017
14. Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics
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Lin, Yuling, primary, Min, Jiumeng, additional, Lai, Ruilian, additional, Wu, Zhangyan, additional, Chen, Yukun, additional, Yu, Lili, additional, Cheng, Chunzhen, additional, Jin, Yuanchun, additional, Tian, Qilin, additional, Liu, Qingfeng, additional, Liu, Weihua, additional, Zhang, Chengguang, additional, Lin, Lixia, additional, Hu, Yan, additional, Zhang, Dongmin, additional, Thu, Minkyaw, additional, Zhang, Zihao, additional, Liu, Shengcai, additional, Zhong, Chunshui, additional, Fang, Xiaodong, additional, Wang, Jian, additional, Yang, Huanming, additional, Varshney, Rajeev K., additional, Yin, Ye, additional, and Lai, Zhongxiong, additional more...
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- 2017
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15. Musa balbisianagenome reveals subgenome evolution and functional divergence
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Wang, Zhuo, Miao, Hongxia, Liu, Juhua, Xu, Biyu, Yao, Xiaoming, Xu, Chunyan, Zhao, Shancen, Fang, Xiaodong, Jia, Caihong, Wang, Jingyi, Zhang, Jianbin, Li, Jingyang, Xu, Yi, Wang, Jiashui, Ma, Weihong, Wu, Zhangyan, Yu, Lili, Yang, Yulan, Liu, Chun, Guo, Yu, Sun, Silong, Baurens, Franc-Christophe, Martin, Guillaume, Salmon, Frederic, Garsmeur, Olivier, Yahiaoui, Nabila, Hervouet, Catherine, Rouard, Mathieu, Laboureau, Nathalie, Habas, Remy, Ricci, Sebastien, Peng, Ming, Guo, Anping, Xie, Jianghui, Li, Yin, Ding, Zehong, Yan, Yan, Tie, Weiwei, D’Hont, Angélique, Hu, Wei, and Jin, Zhiqiang more...
- Abstract
Banana cultivars (Musassp.) are diploid, triploid and tetraploid hybrids derived from Musa acuminataand Musa balbisiana. We presented a high-quality draft genome assembly of M. balbisianawith 430 Mb (87%) assembled into 11 chromosomes. We identified that the recent divergence of M. acuminata(A-genome) and M. balbisiana(B-genome) occurred after lineage-specific whole-genome duplication, and that the B-genome may be more sensitive to the fractionation process compared to the A-genome. Homoeologous exchanges occurred frequently between A- and B-subgenomes in allopolyploids. Genomic variation within progenitors resulted in functional divergence of subgenomes. Global homoeologue expression dominance occurred between subgenomes of the allotriploid. Gene families related to ethylene biosynthesis and starch metabolism exhibited significant expansion at the pathway level and wide homoeologue expression dominance in the B-subgenome of the allotriploid. The independent origin of 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) homoeologue gene pairs and tandem duplication-driven expansion of ACOgenes in the B-subgenome contributed to rapid and major ethylene production post-harvest in allotriploid banana fruits. The findings of this study provide greater context for understanding fruit biology, and aid the development of tools for breeding optimal banana cultivars. more...
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- 2019
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16. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes
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Liu, Shengyi, Liu, Yumei, Yang, Xinhua, Tong, Chaobo, Edwards, David, Parkin, Isobel A.P., Zhao, Meixia, Ma, Jianxin, Yu, Jingyin, Huang, Shunmou, Wang, Xiyin, Wang, Junyi, Lu, Kun, Fang, Zhiyuan, Bancroft, Ian, Yang, Tae-Jin, Hu, Qiong, Wang, Xinfa, Yue, Zhen, Li, Haojie, Yang, Linfeng, Wu, Jian, Zhou, Qing, Wang, Wanxin, King, Graham J., Pires, J. Chris, Lu, Changxin, Wu, Zhangyan, Sampath, Perumal, Wang, Zhuo, Guo, Hui, Pan, Shengkai, Yang, Limei, Min, Jiumeng, Zhang, Dong, Jin, Dianchuan, Li, Wanshun, Belcram, Harry, Tu, Jinxing, Guan, Mei, Qi, Cunkou, Du, Dezhi, Li, Jiana, Jiang, Liangcai, Batley, Jacqueline, Sharpe, Andrew G., Park, Beom-Seok, Ruperao, Pradeep, Cheng, Feng, Waminal, Nomar Espinosa, Huang, Yin, Dong, Caihua, Wang, Li, Li, Jingping, Hu, Zhiyong, Zhuang, Mu, Huang, Yi, Huang, Junyan, Shi, Jiaqin, Mei, Desheng, Liu, Jing, Lee, Tae-Ho, Wang, Jinpeng, Jin, Huizhe, Li, Zaiyun, Li, Xun, Zhang, Jiefu, Xiao, Lu, Zhou, Yongming, Liu, Zhongsong, Liu, Xuequn, Qin, Rui, Tang, Xu, Liu, Wenbin, Wang, Yupeng, Zhang, Yangyong, Lee, Jonghoon, Kim, Hyun Hee, Denoeud, France, Xu, Xun, Liang, Xinming, Hua, Wei, Wang, Xiaowu, Wang, Jun, Chalhoub, Boulos, Paterson, Andrew H., Liu, Shengyi, Liu, Yumei, Yang, Xinhua, Tong, Chaobo, Edwards, David, Parkin, Isobel A.P., Zhao, Meixia, Ma, Jianxin, Yu, Jingyin, Huang, Shunmou, Wang, Xiyin, Wang, Junyi, Lu, Kun, Fang, Zhiyuan, Bancroft, Ian, Yang, Tae-Jin, Hu, Qiong, Wang, Xinfa, Yue, Zhen, Li, Haojie, Yang, Linfeng, Wu, Jian, Zhou, Qing, Wang, Wanxin, King, Graham J., Pires, J. Chris, Lu, Changxin, Wu, Zhangyan, Sampath, Perumal, Wang, Zhuo, Guo, Hui, Pan, Shengkai, Yang, Limei, Min, Jiumeng, Zhang, Dong, Jin, Dianchuan, Li, Wanshun, Belcram, Harry, Tu, Jinxing, Guan, Mei, Qi, Cunkou, Du, Dezhi, Li, Jiana, Jiang, Liangcai, Batley, Jacqueline, Sharpe, Andrew G., Park, Beom-Seok, Ruperao, Pradeep, Cheng, Feng, Waminal, Nomar Espinosa, Huang, Yin, Dong, Caihua, Wang, Li, Li, Jingping, Hu, Zhiyong, Zhuang, Mu, Huang, Yi, Huang, Junyan, Shi, Jiaqin, Mei, Desheng, Liu, Jing, Lee, Tae-Ho, Wang, Jinpeng, Jin, Huizhe, Li, Zaiyun, Li, Xun, Zhang, Jiefu, Xiao, Lu, Zhou, Yongming, Liu, Zhongsong, Liu, Xuequn, Qin, Rui, Tang, Xu, Liu, Wenbin, Wang, Yupeng, Zhang, Yangyong, Lee, Jonghoon, Kim, Hyun Hee, Denoeud, France, Xu, Xun, Liang, Xinming, Hua, Wei, Wang, Xiaowu, Wang, Jun, Chalhoub, Boulos, and Paterson, Andrew H. more...
- Published
- 2014
17. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes
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Liu, Shengyi, primary, Liu, Yumei, additional, Yang, Xinhua, additional, Tong, Chaobo, additional, Edwards, David, additional, Parkin, Isobel A. P., additional, Zhao, Meixia, additional, Ma, Jianxin, additional, Yu, Jingyin, additional, Huang, Shunmou, additional, Wang, Xiyin, additional, Wang, Junyi, additional, Lu, Kun, additional, Fang, Zhiyuan, additional, Bancroft, Ian, additional, Yang, Tae-Jin, additional, Hu, Qiong, additional, Wang, Xinfa, additional, Yue, Zhen, additional, Li, Haojie, additional, Yang, Linfeng, additional, Wu, Jian, additional, Zhou, Qing, additional, Wang, Wanxin, additional, King, Graham J, additional, Pires, J. Chris, additional, Lu, Changxin, additional, Wu, Zhangyan, additional, Sampath, Perumal, additional, Wang, Zhuo, additional, Guo, Hui, additional, Pan, Shengkai, additional, Yang, Limei, additional, Min, Jiumeng, additional, Zhang, Dong, additional, Jin, Dianchuan, additional, Li, Wanshun, additional, Belcram, Harry, additional, Tu, Jinxing, additional, Guan, Mei, additional, Qi, Cunkou, additional, Du, Dezhi, additional, Li, Jiana, additional, Jiang, Liangcai, additional, Batley, Jacqueline, additional, Sharpe, Andrew G, additional, Park, Beom-Seok, additional, Ruperao, Pradeep, additional, Cheng, Feng, additional, Waminal, Nomar Espinosa, additional, Huang, Yin, additional, Dong, Caihua, additional, Wang, Li, additional, Li, Jingping, additional, Hu, Zhiyong, additional, Zhuang, Mu, additional, Huang, Yi, additional, Huang, Junyan, additional, Shi, Jiaqin, additional, Mei, Desheng, additional, Liu, Jing, additional, Lee, Tae-Ho, additional, Wang, Jinpeng, additional, Jin, Huizhe, additional, Li, Zaiyun, additional, Li, Xun, additional, Zhang, Jiefu, additional, Xiao, Lu, additional, Zhou, Yongming, additional, Liu, Zhongsong, additional, Liu, Xuequn, additional, Qin, Rui, additional, Tang, Xu, additional, Liu, Wenbin, additional, Wang, Yupeng, additional, Zhang, Yangyong, additional, Lee, Jonghoon, additional, Kim, Hyun Hee, additional, Denoeud, France, additional, Xu, Xun, additional, Liang, Xinming, additional, Hua, Wei, additional, Wang, Xiaowu, additional, Wang, Jun, additional, Chalhoub, Boulos, additional, and Paterson, Andrew H, additional more...
- Published
- 2014
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18. A heterozygous moth genome provides insights into herbivory and detoxification
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You, Minsheng, Yue, Zhen, He, Weiyi, Yang, Xinhua, Yang, Guang, Xie, Miao, Zhan, Dongliang, Baxter, Simon W., Vasseur, Liette, Gurr, Geoff M., Douglas, Carl J., Bai, Jianlin, Wang, Ping, Cui, Kai, Huang, Shiguo, Li, Xianchun, Zhou, Qing, Wu, Zhangyan, Chen, Qilin, Liu, Chunhui, Wang, Bo, Li, Xiaojing, Xu, Xiufeng, Lu, Changxin, Hu, Min, Davey, John W., Smith, Sandy M., Chen, Mingshun, Xia, Xiaofeng, Tang, Weiqi, Ke, Fushi, Zheng, Dandan, Hu, Yulan, Song, Fengqin, You, Yanchun, Ma, Xiaoli, Peng, Lu, Zheng, Yunkai, Liang, Yong, Chen, Yaqiong, Yu, Liying, Zhang, Younan, Liu, Yuanyuan, Li, Guoqing, Fang, Lin, Li, Jingxiang, Zhou, Xin, Luo, Yadan, Gou, Caiyun, Wang, Junyi, Wang, Jian, Yang, Huanming, Wang, Jun, You, Minsheng, Yue, Zhen, He, Weiyi, Yang, Xinhua, Yang, Guang, Xie, Miao, Zhan, Dongliang, Baxter, Simon W., Vasseur, Liette, Gurr, Geoff M., Douglas, Carl J., Bai, Jianlin, Wang, Ping, Cui, Kai, Huang, Shiguo, Li, Xianchun, Zhou, Qing, Wu, Zhangyan, Chen, Qilin, Liu, Chunhui, Wang, Bo, Li, Xiaojing, Xu, Xiufeng, Lu, Changxin, Hu, Min, Davey, John W., Smith, Sandy M., Chen, Mingshun, Xia, Xiaofeng, Tang, Weiqi, Ke, Fushi, Zheng, Dandan, Hu, Yulan, Song, Fengqin, You, Yanchun, Ma, Xiaoli, Peng, Lu, Zheng, Yunkai, Liang, Yong, Chen, Yaqiong, Yu, Liying, Zhang, Younan, Liu, Yuanyuan, Li, Guoqing, Fang, Lin, Li, Jingxiang, Zhou, Xin, Luo, Yadan, Gou, Caiyun, Wang, Junyi, Wang, Jian, Yang, Huanming, and Wang, Jun more...
- Published
- 2013
19. A heterozygous moth genome provides insights into herbivory and detoxification
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You, Minsheng, primary, Yue, Zhen, additional, He, Weiyi, additional, Yang, Xinhua, additional, Yang, Guang, additional, Xie, Miao, additional, Zhan, Dongliang, additional, Baxter, Simon W, additional, Vasseur, Liette, additional, Gurr, Geoff M, additional, Douglas, Carl J, additional, Bai, Jianlin, additional, Wang, Ping, additional, Cui, Kai, additional, Huang, Shiguo, additional, Li, Xianchun, additional, Zhou, Qing, additional, Wu, Zhangyan, additional, Chen, Qilin, additional, Liu, Chunhui, additional, Wang, Bo, additional, Li, Xiaojing, additional, Xu, Xiufeng, additional, Lu, Changxin, additional, Hu, Min, additional, Davey, John W, additional, Smith, Sandy M, additional, Chen, Mingshun, additional, Xia, Xiaofeng, additional, Tang, Weiqi, additional, Ke, Fushi, additional, Zheng, Dandan, additional, Hu, Yulan, additional, Song, Fengqin, additional, You, Yanchun, additional, Ma, Xiaoli, additional, Peng, Lu, additional, Zheng, Yunkai, additional, Liang, Yong, additional, Chen, Yaqiong, additional, Yu, Liying, additional, Zhang, Younan, additional, Liu, Yuanyuan, additional, Li, Guoqing, additional, Fang, Lin, additional, Li, Jingxiang, additional, Zhou, Xin, additional, Luo, Yadan, additional, Gou, Caiyun, additional, Wang, Junyi, additional, Wang, Jian, additional, Yang, Huanming, additional, and Wang, Jun, additional more...
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- 2013
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20. Correction: Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway.
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Li, Hong-Lei, Wu, Lin, Dong, Zhaoming, Jiang, Yusong, Jiang, Sanjie, Xing, Haitao, Li, Qiang, Liu, Guocheng, Tian, Shuming, Wu, Zhangyan, Bin Wu, Li, Zhexin, Zhao, Ping, Zhang, Yan, Tang, Jianmin, Xu, Jiabao, Huang, Ke, Liu, Xia, Zhang, Wenlin, and Liao, Qinhong more...
- Subjects
HAPLOTYPES ,GENOMES ,GINGER ,LANDSCAPE architecture ,ELECTRONIC publications - Abstract
Res i . https://doi.org/10.1038/s41438-021-00627-7 published online 5 August 2021 After online publication of the article[1], the authors noticed the affiliation "College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China" for author Yiqing Liu was missing. These authors contributed equally: Hong-Lei Li, Lin Wu, Zhaoming Dong, Yusong Jiang, Sanjie Jiang Correction to: I Hortic. The original article has been corrected Reference 1 Li HL, Wu L, Dong Z. Haplotype-resolved genome of diploid ginger (Zingiber officinale) and its unique gingerol biosynthetic pathway. [Extracted from the article] more...
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- 2021
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21. A de novo Genome of a Chinese Radish Cultivar
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Zhang Xiaohui, Yue Zhen, Mei Shiyong, Qiu Yang, Yang Xinhua, Chen Xiaohua, Cheng Feng, Wu Zhangyan, Sun Yuyan, Jing Yi, Liu Bo, Shen Di, Wang Haiping, Cui Na, Duan Yundan, Wu Jian, Wang Jinglei, Gan Caixia, Wang Jun, Wang Xiaowu, and Li Xixiang more...
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food and beverages ,Raphanus sativus ,lcsh:SB1-1110 ,sequencing ,lcsh:Plant culture ,genome - Abstract
Here, we report a high-quality draft genome of a Chinese radish (Raphanus sativus) cultivar. This draft contains 387.73Mb of assembled scaffolds, 83.93% of the scaffolds were anchored onto nine pseudochromosomes and 95.09% of 43 240 protein-coding genes were functionally annotated. 184.75Mb (47.65%) of repeat sequences was identified in the assembled genome. By comparative analyses of the radish genome against 10 other plant genomes, 2 275 genes in 780 gene families were found unique to R. sativus. This genome is a good reference for genomic study and of great value for genetic improvement of radish. more...
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22. Long-read genome sequencing provides novel insights into the harmful algal bloom species Prymnesium parvum.
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Jian J, Wu Z, Silva-Núñez A, Li X, Zheng X, Luo B, Liu Y, Fang X, Workman CT, Larsen TO, Hansen PJ, and Sonnenschein EC
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- Animals, Fishes, Harmful Algal Bloom, Haptophyta genetics, Haptophyta metabolism
- Abstract
Prymnesium parvum is a toxin-producing haptophyte that causes harmful algal blooms worldwide, which are often associated with massive fish-kills and subsequent economic losses. In here, we present nuclear and plastid genome assemblies using PacBio HiFi long reads and DNBseq short reads for the two P. parvum strains UTEX 2797 and CCMP 3037, representing producers of type A prymnesins. Our results show that the P. parvum strains have a moderate haptophyte genome size of 97.56 and 107.32 Mb. The genome assemblies present one of highest contiguous assembled contig sequences to date consisting of 463 and 362 contigs with a contig N50 of 596.99 kb and 968.39 kb for strain UTEX 2797 and CCMP 3037, respectively. The assembled contigs of UTEX 2797 and CCMP 3037 were anchored to 34 scaffolds, with a scaffold N50 of 5.35 Mb and 3.61 Mb, respectively, accounting for 93.2 % and 97.9 % of the total length. Each plastid genome comprises a circular contig. A total of 20,578 and 19,426 protein-coding genes were annotated for UTEX 2797 and CCMP 3037. The expanded gene family analysis showed that starch and sucrose metabolism, sulfur metabolism, energy metabolism and ABC transporters are involved in the evolution of P. parvum. Polyketide synthase (PKS) genes responsible for the production of secondary metabolites such as prymnesins displayed different expression patterns under nutrient limitation. Overlap with repeats and horizontal gene transfer may be two contributing factors to the high number of PKS genes found in this species. The two high quality P. parvum genomes will serve as valuable resources for ecological, genetic, and toxicological studies of haptophytes that can be used to monitor and potentially manage harmful blooms of ichthyotoxic P. parvum in the future., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.) more...
- Published
- 2024
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