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14 results on '"Geng, Chunyu"'

1. A Comprehensive RNA Study to Identify circRNA and miRNA Biomarkers for Docetaxel Resistance in Breast Cancer

Author

Huang, Peide, Li, Fengyu, Mo, Zongchao, Geng, Chunyu, Wen, Fang, Zhang, Chunyan, Guo, Jia, Wu, Song, Li, Lin, Brunner, Nils, Stenvang, Jan, Huang, Peide, Li, Fengyu, Mo, Zongchao, Geng, Chunyu, Wen, Fang, Zhang, Chunyan, Guo, Jia, Wu, Song, Li, Lin, Brunner, Nils, and Stenvang, Jan

Abstract

To investigate the relationship between non-coding RNAs [especially circular RNAs (circRNAs)] and docetaxel resistance in breast cancer, and to find potential predictive biomarkers for taxane-containing therapies, we have performed transcriptome and microRNA (miRNA) sequencing for two established docetaxel-resistant breast cancer (DRBC) cell lines and their docetaxel-sensitive parental cell lines. Our analyses revealed differences between circRNA signatures in the docetaxel-resistant and -sensitive breast cancer cells, and discovered circRNAs generated by multidrug-resistance genes in taxane-resistant cancer cells. In DRBC cells, circABCB1 was identified and validated as a circRNA that is strongly up-regulated, whereas circEPHA3.1 and circEPHA3.2 are strongly down-regulated. Furthermore, we investigated the potential functions of these circRNAs by bioinformatics analysis, and miRNA analysis was performed to uncover potential interactions between circRNAs and miRNAs. Our data showed that circABCB1, circEPHA3.1 and circEPHA3.2 may sponge up eight significantly differentially expressed miRNAs that are associated with chemotherapy and contribute to docetaxel resistance via the PI3K-Akt and AGE-RAGE signaling pathways. We also integrated differential expression data of mRNA, long non-coding RNA, circRNA, and miRNA to gain a global profile of multi-level RNA changes in DRBC cells, and compared them with changes in DNA copy numbers in the same cell lines. We found that Chromosome 7 q21.12-q21.2 was a common region dominated by multi-level RNA overexpression and DNA amplification, indicating that overexpression of the RNA molecules transcribed from this region may result from DNA amplification during stepwise exposure to docetaxel. These findings may help to further our understanding of the mechanisms underlying docetaxel resistance in breast cancer.

Published
2021

2. A Comprehensive RNA Study to Identify circRNA and miRNA Biomarkers for Docetaxel Resistance in Breast Cancer

Author

Huang, Peide, Li, Fengyu, Mo, Zongchao, Geng, Chunyu, Wen, Fang, Zhang, Chunyan, Guo, Jia, Wu, Song, Li, Lin, Brunner, Nils, Stenvang, Jan, Huang, Peide, Li, Fengyu, Mo, Zongchao, Geng, Chunyu, Wen, Fang, Zhang, Chunyan, Guo, Jia, Wu, Song, Li, Lin, Brunner, Nils, and Stenvang, Jan

Abstract

To investigate the relationship between non-coding RNAs [especially circular RNAs (circRNAs)] and docetaxel resistance in breast cancer, and to find potential predictive biomarkers for taxane-containing therapies, we have performed transcriptome and microRNA (miRNA) sequencing for two established docetaxel-resistant breast cancer (DRBC) cell lines and their docetaxel-sensitive parental cell lines. Our analyses revealed differences between circRNA signatures in the docetaxel-resistant and -sensitive breast cancer cells, and discovered circRNAs generated by multidrug-resistance genes in taxane-resistant cancer cells. In DRBC cells, circABCB1 was identified and validated as a circRNA that is strongly up-regulated, whereas circEPHA3.1 and circEPHA3.2 are strongly down-regulated. Furthermore, we investigated the potential functions of these circRNAs by bioinformatics analysis, and miRNA analysis was performed to uncover potential interactions between circRNAs and miRNAs. Our data showed that circABCB1, circEPHA3.1 and circEPHA3.2 may sponge up eight significantly differentially expressed miRNAs that are associated with chemotherapy and contribute to docetaxel resistance via the PI3K-Akt and AGE-RAGE signaling pathways. We also integrated differential expression data of mRNA, long non-coding RNA, circRNA, and miRNA to gain a global profile of multi-level RNA changes in DRBC cells, and compared them with changes in DNA copy numbers in the same cell lines. We found that Chromosome 7 q21.12-q21.2 was a common region dominated by multi-level RNA overexpression and DNA amplification, indicating that overexpression of the RNA molecules transcribed from this region may result from DNA amplification during stepwise exposure to docetaxel. These findings may help to further our understanding of the mechanisms underlying docetaxel resistance in breast cancer.

Published
2021

3. Identification of balanced chromosomal rearrangements previously unknown among participants in the 1000 Genomes Project:implications for interpretation of structural variation in genomes and the future of clinical cytogenetics

Author

Dong, Zirui, Wang, Huilin, Chen, Haixiao, Jiang, Hui, Yuan, Jianying, Yang, Zhenjun, Wang, Wen-Jing, Xu, Fengping, Guo, Xiaosen, Cao, Ye, Zhu, Zhenzhen, Geng, Chunyu, Cheung, Wan Chee, Kwok, Yvonne K., Yang, Huanming, Leung, Tak Yeung, Morton, Cynthia C., Cheung, Sau Wai, Choy, Kwong Wai, Dong, Zirui, Wang, Huilin, Chen, Haixiao, Jiang, Hui, Yuan, Jianying, Yang, Zhenjun, Wang, Wen-Jing, Xu, Fengping, Guo, Xiaosen, Cao, Ye, Zhu, Zhenzhen, Geng, Chunyu, Cheung, Wan Chee, Kwok, Yvonne K., Yang, Huanming, Leung, Tak Yeung, Morton, Cynthia C., Cheung, Sau Wai, and Choy, Kwong Wai

Published
2018

4. Erratum to: Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

Author

Mak, Sarah Siu Tze, Gopalakrishnan, Shyam, Carøe, Christian, Geng, Chunyu, Liu, Shanlin, Sinding, Mikkel-Holger S., Kuderna, Lukas F. K., Zhang, Wenwei, Fu, Shujin, Vieira, Filipe G., Germonpré, Mietje, Bocherens, Hervé, Fedorov, Sergey, Petersen, Bent, Sicheritz-Pontén, Thomas, Marques-Bonet, Tomas, Zhang, Guojie, Jiang, Hui, Gilbert, M. Thomas P., Mak, Sarah Siu Tze, Gopalakrishnan, Shyam, Carøe, Christian, Geng, Chunyu, Liu, Shanlin, Sinding, Mikkel-Holger S., Kuderna, Lukas F. K., Zhang, Wenwei, Fu, Shujin, Vieira, Filipe G., Germonpré, Mietje, Bocherens, Hervé, Fedorov, Sergey, Petersen, Bent, Sicheritz-Pontén, Thomas, Marques-Bonet, Tomas, Zhang, Guojie, Jiang, Hui, and Gilbert, M. Thomas P.

Published
2018

5. Comparative performance of the BGISEQ-500 versus Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

Author

Mak, Sarah Siu Tze Mak, Gopalakrishnan, Shyam Sunder, Carøe, Christian, Geng, Chunyu, Liu, Shanlin, Sinding, Mikkel Holger Strander, Kuderna, Lukas F.K., Zhang, Wenwei, Fu, Shujin, Garrett Vieira, Filipe Jorge, Germonpré, Mietje, Bocherens, Hervé, Fedorov, Sergey, Petersen, Bent, Sicheritz-Pontén, Thomas, Marques-Bonet, Tomas, Zhang, Guojie, Jiang, Hui, Gilbert, M. Thomas P., Mak, Sarah Siu Tze Mak, Gopalakrishnan, Shyam Sunder, Carøe, Christian, Geng, Chunyu, Liu, Shanlin, Sinding, Mikkel Holger Strander, Kuderna, Lukas F.K., Zhang, Wenwei, Fu, Shujin, Garrett Vieira, Filipe Jorge, Germonpré, Mietje, Bocherens, Hervé, Fedorov, Sergey, Petersen, Bent, Sicheritz-Pontén, Thomas, Marques-Bonet, Tomas, Zhang, Guojie, Jiang, Hui, and Gilbert, M. Thomas P.

Published
2017

6. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

Author

Mak, Sarah, Gopalakrishnan, Shyam, Carøe, Christian, Geng, Chunyu, Liu, Shanlin, Sinding, Mikkel Holger Strander, Kuderna, Lukas F. K., Zhang, Wenwei, Fu, Shujin, Garrett Vieira, Filipe Jorge, Germonpré, Mietje, Bocherens, Hervé, Fedorov, Sergey, Petersen, Bent, Sicheritz-Pontén, Thomas, Marques-Bonet, Tomas, Zhang, Guojie, Jiang, Hui, Gilbert, Tom, Mak, Sarah, Gopalakrishnan, Shyam, Carøe, Christian, Geng, Chunyu, Liu, Shanlin, Sinding, Mikkel Holger Strander, Kuderna, Lukas F. K., Zhang, Wenwei, Fu, Shujin, Garrett Vieira, Filipe Jorge, Germonpré, Mietje, Bocherens, Hervé, Fedorov, Sergey, Petersen, Bent, Sicheritz-Pontén, Thomas, Marques-Bonet, Tomas, Zhang, Guojie, Jiang, Hui, and Gilbert, Tom

Published
2017

7. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

Author

Mak, Sarah, Gopalakrishnan, Shyam, Carøe, Christian, Geng, Chunyu, Liu, Shanlin, Sinding, Mikkel Holger Strander, Kuderna, Lukas F. K., Zhang, Wenwei, Fu, Shujin, Garrett Vieira, Filipe Jorge, Germonpré, Mietje, Bocherens, Hervé, Fedorov, Sergey, Petersen, Bent, Sicheritz-Pontén, Thomas, Marques-Bonet, Tomas, Zhang, Guojie, Jiang, Hui, Gilbert, Tom, Mak, Sarah, Gopalakrishnan, Shyam, Carøe, Christian, Geng, Chunyu, Liu, Shanlin, Sinding, Mikkel Holger Strander, Kuderna, Lukas F. K., Zhang, Wenwei, Fu, Shujin, Garrett Vieira, Filipe Jorge, Germonpré, Mietje, Bocherens, Hervé, Fedorov, Sergey, Petersen, Bent, Sicheritz-Pontén, Thomas, Marques-Bonet, Tomas, Zhang, Guojie, Jiang, Hui, and Gilbert, Tom

Published
2017

8. Draft genome sequence of the Tibetan antelope

Author

Ge, Ri-Li, Cai, Qingle, Shen, Yong-Yi, San, A., Ma, Lan, Zhang, Yong, Yi, Xin, Chen, Yan, Yang, Lingfeng, Huang, Ying, He, Rongjun, Hui, Yuanyuan, Hao, Meirong, Li, Yue, Wang, Bo, Ou, Xiaohua, Xu, Jiaohui, Zhang, Yongfen, Wu, Kui, Geng, Chunyu, Zhou, Weiping, Zhou, Taicheng, Irwin, David M., Yang, Yingzhong, Ying, Liu, Bao, Haihua, Kim, Jaebum, Larkin, Denis M., Ma, Jian, Lewin, Harris A., Xing, Jinchuan, Platt, Roy N., II, Ray, David A., Auvil, Loretta, Capitanu, Boris, Zhang, Xiufeng, Zhang, Guojie, Murphy, Robert W., Wang, Jun, Zhang, Ya-Ping, Wang, Jian, Ge, Ri-Li, Cai, Qingle, Shen, Yong-Yi, San, A., Ma, Lan, Zhang, Yong, Yi, Xin, Chen, Yan, Yang, Lingfeng, Huang, Ying, He, Rongjun, Hui, Yuanyuan, Hao, Meirong, Li, Yue, Wang, Bo, Ou, Xiaohua, Xu, Jiaohui, Zhang, Yongfen, Wu, Kui, Geng, Chunyu, Zhou, Weiping, Zhou, Taicheng, Irwin, David M., Yang, Yingzhong, Ying, Liu, Bao, Haihua, Kim, Jaebum, Larkin, Denis M., Ma, Jian, Lewin, Harris A., Xing, Jinchuan, Platt, Roy N., II, Ray, David A., Auvil, Loretta, Capitanu, Boris, Zhang, Xiufeng, Zhang, Guojie, Murphy, Robert W., Wang, Jun, Zhang, Ya-Ping, and Wang, Jian

Published
2013

9. Draft genome sequence of the Tibetan antelope

Author

Ge, Ri-Li, Cai, Qingle, Shen, Yong-Yi, San, A., Ma, Lan, Zhang, Yong, Yi, Xin, Chen, Yan, Yang, Lingfeng, Huang, Ying, He, Rongjun, Hui, Yuanyuan, Hao, Meirong, Li, Yue, Wang, Bo, Ou, Xiaohua, Xu, Jiaohui, Zhang, Yongfen, Wu, Kui, Geng, Chunyu, Zhou, Weiping, Zhou, Taicheng, Irwin, David M., Yang, Yingzhong, Ying, Liu, Bao, Haihua, Kim, Jaebum, Larkin, Denis M., Ma, Jian, Lewin, Harris A., Xing, Jinchuan, Platt, Roy N., II, Ray, David A., Auvil, Loretta, Capitanu, Boris, Zhang, Xiufeng, Zhang, Guojie, Murphy, Robert W., Wang, Jun, Zhang, Ya-Ping, Wang, Jian, Ge, Ri-Li, Cai, Qingle, Shen, Yong-Yi, San, A., Ma, Lan, Zhang, Yong, Yi, Xin, Chen, Yan, Yang, Lingfeng, Huang, Ying, He, Rongjun, Hui, Yuanyuan, Hao, Meirong, Li, Yue, Wang, Bo, Ou, Xiaohua, Xu, Jiaohui, Zhang, Yongfen, Wu, Kui, Geng, Chunyu, Zhou, Weiping, Zhou, Taicheng, Irwin, David M., Yang, Yingzhong, Ying, Liu, Bao, Haihua, Kim, Jaebum, Larkin, Denis M., Ma, Jian, Lewin, Harris A., Xing, Jinchuan, Platt, Roy N., II, Ray, David A., Auvil, Loretta, Capitanu, Boris, Zhang, Xiufeng, Zhang, Guojie, Murphy, Robert W., Wang, Jun, Zhang, Ya-Ping, and Wang, Jian

Published
2013

10. Draft genome sequence of the Tibetan antelope

Author

Ge, Ri-Li, Cai, Qingle, Shen, Yong-Yi, San, A., Ma, Lan, Zhang, Yong, Yi, Xin, Chen, Yan, Yang, Lingfeng, Huang, Ying, He, Rongjun, Hui, Yuanyuan, Hao, Meirong, Li, Yue, Wang, Bo, Ou, Xiaohua, Xu, Jiaohui, Zhang, Yongfen, Wu, Kui, Geng, Chunyu, Zhou, Weiping, Zhou, Taicheng, Irwin, David M., Yang, Yingzhong, Ying, Liu, Bao, Haihua, Kim, Jaebum, Larkin, Denis M., Ma, Jian, Lewin, Harris A., Xing, Jinchuan, Platt, Roy N., II, Ray, David A., Auvil, Loretta, Capitanu, Boris, Zhang, Xiufeng, Zhang, Guojie, Murphy, Robert W., Wang, Jun, Zhang, Ya-Ping, Wang, Jian, Ge, Ri-Li, Cai, Qingle, Shen, Yong-Yi, San, A., Ma, Lan, Zhang, Yong, Yi, Xin, Chen, Yan, Yang, Lingfeng, Huang, Ying, He, Rongjun, Hui, Yuanyuan, Hao, Meirong, Li, Yue, Wang, Bo, Ou, Xiaohua, Xu, Jiaohui, Zhang, Yongfen, Wu, Kui, Geng, Chunyu, Zhou, Weiping, Zhou, Taicheng, Irwin, David M., Yang, Yingzhong, Ying, Liu, Bao, Haihua, Kim, Jaebum, Larkin, Denis M., Ma, Jian, Lewin, Harris A., Xing, Jinchuan, Platt, Roy N., II, Ray, David A., Auvil, Loretta, Capitanu, Boris, Zhang, Xiufeng, Zhang, Guojie, Murphy, Robert W., Wang, Jun, Zhang, Ya-Ping, and Wang, Jian

Published
2013

11. Draft genome sequence of the Tibetan antelope

Author

Ge, Ri-Li, Cai, Qingle, Shen, Yong-Yi, San, A., Ma, Lan, Zhang, Yong, Yi, Xin, Chen, Yan, Yang, Lingfeng, Huang, Ying, He, Rongjun, Hui, Yuanyuan, Hao, Meirong, Li, Yue, Wang, Bo, Ou, Xiaohua, Xu, Jiaohui, Zhang, Yongfen, Wu, Kui, Geng, Chunyu, Zhou, Weiping, Zhou, Taicheng, Irwin, David M., Yang, Yingzhong, Ying, Liu, Bao, Haihua, Kim, Jaebum, Larkin, Denis M., Ma, Jian, Lewin, Harris A., Xing, Jinchuan, Platt, Roy N., II, Ray, David A., Auvil, Loretta, Capitanu, Boris, Zhang, Xiufeng, Zhang, Guojie, Murphy, Robert W., Wang, Jun, Zhang, Ya-Ping, Wang, Jian, Ge, Ri-Li, Cai, Qingle, Shen, Yong-Yi, San, A., Ma, Lan, Zhang, Yong, Yi, Xin, Chen, Yan, Yang, Lingfeng, Huang, Ying, He, Rongjun, Hui, Yuanyuan, Hao, Meirong, Li, Yue, Wang, Bo, Ou, Xiaohua, Xu, Jiaohui, Zhang, Yongfen, Wu, Kui, Geng, Chunyu, Zhou, Weiping, Zhou, Taicheng, Irwin, David M., Yang, Yingzhong, Ying, Liu, Bao, Haihua, Kim, Jaebum, Larkin, Denis M., Ma, Jian, Lewin, Harris A., Xing, Jinchuan, Platt, Roy N., II, Ray, David A., Auvil, Loretta, Capitanu, Boris, Zhang, Xiufeng, Zhang, Guojie, Murphy, Robert W., Wang, Jun, Zhang, Ya-Ping, and Wang, Jian

Published
2013

12. The genome of the mesopolyploid crop species Brassica rapa

Author

Wang, Xiaowu, Wang, Hanzhong, Wang, Jun, Sun, Rifei, Wu, Jian, Liu, Shengyi, Bai, Yinqi, Mun, Jeong-Hwan, Bancroft, Ian, Cheng, Feng, Huang, Sanwen, Li, Xixiang, Hua, Wei, Wang, Junyi, Wang, Xiyin, Freeling, Michael, Pires, J. Chris, Paterson, Andrew, Chalhoub, Boulos, Wang, Bo, Hayward, Alice, Sharpe, Andrew, Park, Beom-Seok, Weisshaar, Bernd, Liu, Binghang, Li, Bo, Liu, Bo, Tong, Chaobo, Song, Chi, Duran, Christopher, Peng, Chunfang, Geng, Chunyu, Koh, Chushin, Lin, Chuyu, Edwards, David, Mu, Desheng, Shen, Di, Soumpourou, Eleni, Li, Fei, Fraser, Fiona, Conant, Gavin, Lassalle, Gilles, King, Graham, Bonnema, Guusje, Tang, Haibao, Wang, Haiping, Belcram, Harry, Zhou, Heling, Hirakawa, Hideki, Abe, Hiroshi, Guo, Hui, Wang, Hui, Jin, Huizhe, Parkin, Isobel, Batley, Jacqueline, Kim, Jeong-Sun, Just, Jérémy, Li, Jianwen, Xu, Jiaohui, Deng, Jie, Kim, Jin Hyun, Li, Jingping, Yu, Jingyin, Meng, Jinling, Wang, Jinpeng, Min, Jiumeng, Poulain, Julie, Hatakeyama, Katsunori, Wu, Kui, Wang, Li, Fang, Lu, Trick, Martin, Links, Matthew, Zhao, Meixia, Jin, Mina, Ramchiary, Nirala, Drou, Nizar, Berkman, Paul, Cai, Qingle, Huang, Quanfei, Li, Ruiqiang, Tabata, Satoshi, Cheng, Shifeng, Zhang, Shu, Zhang, Shujiang, Huang, Shunmou, Sato, Shusei, Sun, Silong, Kwon, Soo-Jin, Choi, Su-Ryun, Lee, Tae-Ho, Fan, Wei, Zhao, Xiang, Tan, Xu, Xu, Xun, Wang, Yan, Qiu, Yang, Yin, Ye, Li, Yingrui, Wang, Xiaowu, Wang, Hanzhong, Wang, Jun, Sun, Rifei, Wu, Jian, Liu, Shengyi, Bai, Yinqi, Mun, Jeong-Hwan, Bancroft, Ian, Cheng, Feng, Huang, Sanwen, Li, Xixiang, Hua, Wei, Wang, Junyi, Wang, Xiyin, Freeling, Michael, Pires, J. Chris, Paterson, Andrew, Chalhoub, Boulos, Wang, Bo, Hayward, Alice, Sharpe, Andrew, Park, Beom-Seok, Weisshaar, Bernd, Liu, Binghang, Li, Bo, Liu, Bo, Tong, Chaobo, Song, Chi, Duran, Christopher, Peng, Chunfang, Geng, Chunyu, Koh, Chushin, Lin, Chuyu, Edwards, David, Mu, Desheng, Shen, Di, Soumpourou, Eleni, Li, Fei, Fraser, Fiona, Conant, Gavin, Lassalle, Gilles, King, Graham, Bonnema, Guusje, Tang, Haibao, Wang, Haiping, Belcram, Harry, Zhou, Heling, Hirakawa, Hideki, Abe, Hiroshi, Guo, Hui, Wang, Hui, Jin, Huizhe, Parkin, Isobel, Batley, Jacqueline, Kim, Jeong-Sun, Just, Jérémy, Li, Jianwen, Xu, Jiaohui, Deng, Jie, Kim, Jin Hyun, Li, Jingping, Yu, Jingyin, Meng, Jinling, Wang, Jinpeng, Min, Jiumeng, Poulain, Julie, Hatakeyama, Katsunori, Wu, Kui, Wang, Li, Fang, Lu, Trick, Martin, Links, Matthew, Zhao, Meixia, Jin, Mina, Ramchiary, Nirala, Drou, Nizar, Berkman, Paul, Cai, Qingle, Huang, Quanfei, Li, Ruiqiang, Tabata, Satoshi, Cheng, Shifeng, Zhang, Shu, Zhang, Shujiang, Huang, Shunmou, Sato, Shusei, Sun, Silong, Kwon, Soo-Jin, Choi, Su-Ryun, Lee, Tae-Ho, Fan, Wei, Zhao, Xiang, Tan, Xu, Xu, Xun, Wang, Yan, Qiu, Yang, Yin, Ye, and Li, Yingrui

Abstract

We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

Published
2011

13. The genome of the mesopolyploid crop species Brassica rapa

Author

Wang, Xiaowu, Wang, Hanzhong, Wang, Jun, Sun, Rifei, Wu, Jian, Liu, Shengyi, Bai, Yinqi, Mun, Jeong-Hwan, Bancroft, Ian, Cheng, Feng, Huang, Sanwen, Li, Xixiang, Hua, Wei, Wang, Junyi, Wang, Xiyin, Freeling, Michael, Pires, J. Chris, Paterson, Andrew, Chalhoub, Boulos, Wang, Bo, Hayward, Alice, Sharpe, Andrew, Park, Beom-Seok, Weisshaar, Bernd, Liu, Binghang, Li, Bo, Liu, Bo, Tong, Chaobo, Song, Chi, Duran, Christopher, Peng, Chunfang, Geng, Chunyu, Koh, Chushin, Lin, Chuyu, Edwards, David, Mu, Desheng, Shen, Di, Soumpourou, Eleni, Li, Fei, Fraser, Fiona, Conant, Gavin, Lassalle, Gilles, King, Graham, Bonnema, Guusje, Tang, Haibao, Wang, Haiping, Belcram, Harry, Zhou, Heling, Hirakawa, Hideki, Abe, Hiroshi, Guo, Hui, Wang, Hui, Jin, Huizhe, Parkin, Isobel, Batley, Jacqueline, Kim, Jeong-Sun, Just, Jérémy, Li, Jianwen, Xu, Jiaohui, Deng, Jie, Kim, Jin Hyun, Li, Jingping, Yu, Jingyin, Meng, Jinling, Wang, Jinpeng, Min, Jiumeng, Poulain, Julie, Hatakeyama, Katsunori, Wu, Kui, Wang, Li, Fang, Lu, Trick, Martin, Links, Matthew, Zhao, Meixia, Jin, Mina, Ramchiary, Nirala, Drou, Nizar, Berkman, Paul, Cai, Qingle, Huang, Quanfei, Li, Ruiqiang, Tabata, Satoshi, Cheng, Shifeng, Zhang, Shu, Zhang, Shujiang, Huang, Shunmou, Sato, Shusei, Sun, Silong, Kwon, Soo-Jin, Choi, Su-Ryun, Lee, Tae-Ho, Fan, Wei, Zhao, Xiang, Tan, Xu, Xu, Xun, Wang, Yan, Qiu, Yang, Yin, Ye, Li, Yingrui, Wang, Xiaowu, Wang, Hanzhong, Wang, Jun, Sun, Rifei, Wu, Jian, Liu, Shengyi, Bai, Yinqi, Mun, Jeong-Hwan, Bancroft, Ian, Cheng, Feng, Huang, Sanwen, Li, Xixiang, Hua, Wei, Wang, Junyi, Wang, Xiyin, Freeling, Michael, Pires, J. Chris, Paterson, Andrew, Chalhoub, Boulos, Wang, Bo, Hayward, Alice, Sharpe, Andrew, Park, Beom-Seok, Weisshaar, Bernd, Liu, Binghang, Li, Bo, Liu, Bo, Tong, Chaobo, Song, Chi, Duran, Christopher, Peng, Chunfang, Geng, Chunyu, Koh, Chushin, Lin, Chuyu, Edwards, David, Mu, Desheng, Shen, Di, Soumpourou, Eleni, Li, Fei, Fraser, Fiona, Conant, Gavin, Lassalle, Gilles, King, Graham, Bonnema, Guusje, Tang, Haibao, Wang, Haiping, Belcram, Harry, Zhou, Heling, Hirakawa, Hideki, Abe, Hiroshi, Guo, Hui, Wang, Hui, Jin, Huizhe, Parkin, Isobel, Batley, Jacqueline, Kim, Jeong-Sun, Just, Jérémy, Li, Jianwen, Xu, Jiaohui, Deng, Jie, Kim, Jin Hyun, Li, Jingping, Yu, Jingyin, Meng, Jinling, Wang, Jinpeng, Min, Jiumeng, Poulain, Julie, Hatakeyama, Katsunori, Wu, Kui, Wang, Li, Fang, Lu, Trick, Martin, Links, Matthew, Zhao, Meixia, Jin, Mina, Ramchiary, Nirala, Drou, Nizar, Berkman, Paul, Cai, Qingle, Huang, Quanfei, Li, Ruiqiang, Tabata, Satoshi, Cheng, Shifeng, Zhang, Shu, Zhang, Shujiang, Huang, Shunmou, Sato, Shusei, Sun, Silong, Kwon, Soo-Jin, Choi, Su-Ryun, Lee, Tae-Ho, Fan, Wei, Zhao, Xiang, Tan, Xu, Xu, Xun, Wang, Yan, Qiu, Yang, Yin, Ye, and Li, Yingrui

Abstract

We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

Published
2011

14. The genome of the mesopolyploid crop species Brassica rapa

Author

Wang, Xiaowu, Wang, Hanzhong, Wang, Jun, Sun, Rifei, Wu, Jian, Liu, Shengyi, Bai, Yinqi, Mun, Jeong-Hwan, Bancroft, Ian, Cheng, Feng, Huang, Sanwen, Li, Xixiang, Hua, Wei, Wang, Junyi, Wang, Xiyin, Freeling, Michael, Pires, J. Chris, Paterson, Andrew, Chalhoub, Boulos, Wang, Bo, Hayward, Alice, Sharpe, Andrew, Park, Beom-Seok, Weisshaar, Bernd, Liu, Binghang, Li, Bo, Liu, Bo, Tong, Chaobo, Song, Chi, Duran, Christopher, Peng, Chunfang, Geng, Chunyu, Koh, Chushin, Lin, Chuyu, Edwards, David, Mu, Desheng, Shen, Di, Soumpourou, Eleni, Li, Fei, Fraser, Fiona, Conant, Gavin, Lassalle, Gilles, King, Graham, Bonnema, Guusje, Tang, Haibao, Wang, Haiping, Belcram, Harry, Zhou, Heling, Hirakawa, Hideki, Abe, Hiroshi, Guo, Hui, Wang, Hui, Jin, Huizhe, Parkin, Isobel, Batley, Jacqueline, Kim, Jeong-Sun, Just, Jérémy, Li, Jianwen, Xu, Jiaohui, Deng, Jie, Kim, Jin Hyun, Li, Jingping, Yu, Jingyin, Meng, Jinling, Wang, Jinpeng, Min, Jiumeng, Poulain, Julie, Hatakeyama, Katsunori, Wu, Kui, Wang, Li, Fang, Lu, Trick, Martin, Links, Matthew, Zhao, Meixia, Jin, Mina, Ramchiary, Nirala, Drou, Nizar, Berkman, Paul, Cai, Qingle, Huang, Quanfei, Li, Ruiqiang, Tabata, Satoshi, Cheng, Shifeng, Zhang, Shu, Zhang, Shujiang, Huang, Shunmou, Sato, Shusei, Sun, Silong, Kwon, Soo-Jin, Choi, Su-Ryun, Lee, Tae-Ho, Fan, Wei, Zhao, Xiang, Tan, Xu, Xu, Xun, Wang, Yan, Qiu, Yang, Yin, Ye, Li, Yingrui, Wang, Xiaowu, Wang, Hanzhong, Wang, Jun, Sun, Rifei, Wu, Jian, Liu, Shengyi, Bai, Yinqi, Mun, Jeong-Hwan, Bancroft, Ian, Cheng, Feng, Huang, Sanwen, Li, Xixiang, Hua, Wei, Wang, Junyi, Wang, Xiyin, Freeling, Michael, Pires, J. Chris, Paterson, Andrew, Chalhoub, Boulos, Wang, Bo, Hayward, Alice, Sharpe, Andrew, Park, Beom-Seok, Weisshaar, Bernd, Liu, Binghang, Li, Bo, Liu, Bo, Tong, Chaobo, Song, Chi, Duran, Christopher, Peng, Chunfang, Geng, Chunyu, Koh, Chushin, Lin, Chuyu, Edwards, David, Mu, Desheng, Shen, Di, Soumpourou, Eleni, Li, Fei, Fraser, Fiona, Conant, Gavin, Lassalle, Gilles, King, Graham, Bonnema, Guusje, Tang, Haibao, Wang, Haiping, Belcram, Harry, Zhou, Heling, Hirakawa, Hideki, Abe, Hiroshi, Guo, Hui, Wang, Hui, Jin, Huizhe, Parkin, Isobel, Batley, Jacqueline, Kim, Jeong-Sun, Just, Jérémy, Li, Jianwen, Xu, Jiaohui, Deng, Jie, Kim, Jin Hyun, Li, Jingping, Yu, Jingyin, Meng, Jinling, Wang, Jinpeng, Min, Jiumeng, Poulain, Julie, Hatakeyama, Katsunori, Wu, Kui, Wang, Li, Fang, Lu, Trick, Martin, Links, Matthew, Zhao, Meixia, Jin, Mina, Ramchiary, Nirala, Drou, Nizar, Berkman, Paul, Cai, Qingle, Huang, Quanfei, Li, Ruiqiang, Tabata, Satoshi, Cheng, Shifeng, Zhang, Shu, Zhang, Shujiang, Huang, Shunmou, Sato, Shusei, Sun, Silong, Kwon, Soo-Jin, Choi, Su-Ryun, Lee, Tae-Ho, Fan, Wei, Zhao, Xiang, Tan, Xu, Xu, Xun, Wang, Yan, Qiu, Yang, Yin, Ye, and Li, Yingrui

Abstract

We report the annotation and analysis of the draft genome sequence of Brassica rapa accession Chiifu-401-42, a Chinese cabbage. We modeled 41,174 protein coding genes in the B. rapa genome, which has undergone genome triplication. We used Arabidopsis thaliana as an outgroup for investigating the consequences of genome triplication, such as structural and functional evolution. The extent of gene loss (fractionation) among triplicated genome segments varies, with one of the three copies consistently retaining a disproportionately large fraction of the genes expected to have been present in its ancestor. Variation in the number of members of gene families present in the genome may contribute to the remarkable morphological plasticity of Brassica species. The B. rapa genome sequence provides an important resource for studying the evolution of polyploid genomes and underpins the genetic improvement of Brassica oil and vegetable crops.

Published
2011

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