Oil Crops Genomics Database System
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yujy Jingyin Yu (于景印), Ph D, Assistant Research Fellow.

Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture; Oil Crops Research Institute, the Chinese Academy of Agricultural Sciences, Wuhan 430062, China


Phone: 86-027-86711856
Email:yujingyin@caas.cn

Academic Positions:

2009 – Present

Assistant Research Fellow, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China.

Education:

2014 -2017

Ph.D. in Crop Genetics and Breeding, Graduate School of Chinese Academy of Agricultural Sciences, Beijing, China;
Advisor: Prof. Boshou Liao

 

2006 -2009

M.S. in Bioinformatics, College of Biological Sciences, China Agricultural University, Beijing, China;
Advisor: Dr. Zhen Su

 

2001 -2004

B.S. in Computer Science and Technology, School of Infomation Engineering, China University of Geosciences, Beijing, China

 

Publication:

I. First or Co-first authored:

1. Jingyin Yu, Fan Hu, Komovi Dossa, Zhaokai Wang*, Tao Ke*. Genome-wide analysis 1 of UDP-glycosyltransferase super family in Brassica rapa and Brassica oleracea reveals its evolutionary history and functional characterization. BMC Genomics 2017, 18(1):474, doi: 10.1186/s12864-017-3844-x. (equal contribution)

2. Jingyin Yu, Linhai Wang, Hui Guo, Boshou Liao, Graham King*, Xiurong Zhang*. Genome evolutionary dynamics followed by diversifying selection explains the complexity of the Sesamum indicum genome. BMC Genomics 2017, 18:257, doi:10.1186/s12864-017-3599-4.

3. Jingyin Yu, Komivi Dossa, Linhai Wang, Yanxin Zhang, Xin Wei, Boshou Liao, Xiurong Zhang*. PMDBase: a database for studying microsatellite DNA and marker development in plants. Nucleic Acids Research 2017, doi: 10.1093/nar/gkw906.

4. Jingyin Yu, Tao Ke, Sadia Tehrim, Fengming Sun, Boshou Liao*, Wei Hua*. PTGBase: an integrated database to study tandem duplicated genes in plants. Database (Oxford) 2015, doi: 10.1093/database/bav017. (equal contribution)

5. Tao Ke, Jingyin Yu, Caihua Dong, Han Mao, Wei Hua and Shengyi Liu*. ocsESTdb: a database of oil crop seed EST sequences for comparative analysis and investigation of a global metabolic network and oil accumulation metabolism. BMC Plant Biology 2015, 15:19, doi:10.1186/s12870-014-0399-8. (equal contribution)

6. Linhai Wang; Jingyin Yu; Donghua Li; Xiurong Zhang*. Sinbase: An Integrated Database to Study Genomics, Genetics, and Comparative Genomics in Sesamum indicum. Plant and Cell Physiology 2014, doi: 10.1093/pcp/pcu175. (equal contribution)

7. Jingyin Yu, Sadia Tehrim, Fengqi Zhang, Chaobo Tong, Junyan Huang, Xiaohui Cheng, Caihua Dong, Yanqiu Zhou, Rui Qin, Wei Hua, Shengyi Liu*. Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana. BMC Genomics 2014, 15:3. doi:10.1186/1471-2164-15-3. (equal contribution)

8. Jingyin Yu, Meixia Zhao, Xiaowu Wang, Chaobo Tong, Shunmou Huang, Sadia Tehrim, Yumei Liu, Wei Hua* and Shengyi Liu*. Bolbase: a comprehensive genomics database for Brassica oleracea. BMC Genomics 2013, 14:664 doi:10.1186/1471-2164-14-664. (equal contribution)

9. Xiaohong Yan, Caihua Dong, Jingyin Yu, Wanghui Liu, Chenghong Jiang, Jia Liu, Qiong Hu, Xiaoping Fang and Wenhui Wei*. Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus. BMC Genomics 2013, 14:26, 1471-2164. (equal contribution)

II. Co-authored publications:

10. Xin Wei, Hao Gong, Jingyin Yu, Pan Liu, Linhai Wang, Yanxin Zhang & Xiurong Zhang. SesameFG: an integrated database for the functional genomics of sesame. Scientific Reports 2017, May 24;7(1):2342. doi: 10.1038/s41598-017-02586-3.

11. Huaiyong Luo, Zhijun Xu, Zhendong Li, Xinping Li, Jianwei Lv, Xiaoping Ren, Li Huang, Xiaojing Zhou, Yuning Chen, Jingyin Yu, Weigang Chen, Yong Lei, Boshou Liao, Huifang Jiang. Development of SSR markers and identification of major quantitative trait loci controlling shelling percentage in cultivated peanut (Arachis hypogaea L.). Theor Appl Genet, 2017:1-14, doi:10.1007/s00122-017-2915-3.

13. Linhai Wang, Qiuju Xia, Yanxin Zhang, Xiaodong Zhu, Xiaofeng Zhu, Donghua Li, Xuemei Ni, Yuan Gao, Haitao Xiang, Xin Wei, Jingyin Yu, Zhiwu Quan and Xiurong Zhang. Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map. BMC Genomics 2016, 17:31, doi: 10.1186/s12864-015-2316-4.

14. Jiaqin Mei, Yijuan Ding, Yuehua Li, Chaobo Tong, Hai Du, Yang Yu, Huafang Wan, Qing Xiong, Jingyin Yu, Shengyi Liu, Jiana Li & Wei Qian. Transcriptomic comparison between Brassica oleracea and rice (Oryza sativa) reveals diverse modulations on cell death in response to Sclerotinia sclerotiorum. Scientific Reports 2016, 6:33706, doi: 10.1038/srep33706.

15. Linhai Wang, Donghua Li, Yanxin Zhang, Yuan Gao, Jingyin Yu, Xin Wei, Xiurong Zhang*. Tolerant and Susceptible Sesame Genotypes Reveal Waterlogging Stress Response Patterns. PLoS ONE 2016, 11(3): e0149912. doi:10.1371/journal.pone.0149912.

16. Komivi Dossa, Xin Wei, Donghua Li, Daniel Fonceka, Yanxin Zhang, Linhai Wang, Jingyin Yu, Liao Boshou, Diaga Diouf, Ndiaga Cisséand Xiurong Zhang*. Insight into the AP2/ERF transcription factor superfamily in sesame and expression profiling of DREB subfamily under drought stress. BMC Plant Biology 2016, 16:171, doi: 10.1186/s12870-016-0859-4.

17. Xin Wei, Xiaodong Zhu, Jingyin Yu, Linhai Wang, Yanxin Zhang, Donghua Li, Rong Zhou, Xiurong Zhang*. Identification of Sesame Genomic Variations from Genome Comparison of Landrace and Variety. Front. Plant Sci. 2016, 7:1169. doi: 10.3389/fpls.2016.01169.

18. Huihui Cao, Tao Ke, Renhu Liu, Jingyin Yu, Caihua Dong, Mingxing Cheng, Junyan Huang*, Shengyi Liu. Identification of a Novel Proline-Rich Antimicrobial Peptide from Brassica napus. PLoS ONE 2015, 10(9): e0137414. doi:10.1371/journal. pone.0137414.

19. XinWei, Linhai Wang, Jingyin Yu, Yanxin Zhang, Donghua Li, Xiurong Zhang. Genome-wide identification and analysis of the MADS-box gene family in sesame. Gene 2015, 569:66–76.

20. Tao Ke, Huihui Cao, Junyan Huang, Fan Hu, Jin Huang, Caihua Dong, Xiangdong Ma, Jingyin Yu, Han Mao, Xi Wang, Qiuhong Niu, Fengli Hui and Shengyi Liu*. EST-based in silico identification and in vitro test of antimicrobial peptides in Brassica napus. BMC Genomics 2015, 16:653, doi: 10.1186/s12864-015-1849-x.

21. Yi Huang, Zhangsheng Tao, Qiong Liu, Xinfa Wang, Jingyin Yu, Guihua Liu, Hanzhong Wang. BnEPFL6, an EPIDERMAL PATTERNING FACTOR‑LIKE (EPFL) secreted peptide gene, is required for filament elongation in Brassica napus. Plant Mol Biol 2014, 85:505–517, doi 10.1007/s11103-014-0200-2.

22. Yongxue Yang, Caihua Dong, Jingyin Yu, Lei Shi, Chaobo Tong,Zhen bo Li, Junyan Huang, Shengyi Liu. Cysteine Protease 51 (CP51), an anther-specific cysteine protease gene, is essential for pollen exine formation in Arabidopsis. Plant Cell Tiss Organ Cult 2014, doi: 10.1007/s11240-014-0542-0.

23. 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 Tu1, Mei Guan, Cunkou Qi, Dezhi Du, Jiana Li, Liangcai Jiang, Jacqueline Batley, Andrew G. Sharpe, Beom-Seok Park, Pradeep Ruperao, Feng Cheng, Nomar Espinosa Wamina, 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, Andrew H Paterson. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications 2014, 5:3930. doi: 10.1038/ncomms4930.

24. Linhai Wang, Sheng Yu, Chaobo Tong, Yingzhong Zhao, Yan Liu, Chi Song, Yanxin Zhang, Xudong Zhang, Ying Wang, Wei Hua, Donghua Li, Dan Li, Fang Li, Jingyin Yu, Chunyan Xu, Xuelian Han, Shunmou Huang, Shuaishuai Tai, Junyi Wang, Xun Xu, Yingrui Li, Shengyi Liu*, Rajeev K Varshney, Jun Wang and Xiurong Zhang. Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis. Genome Biology 2014, 15:R39, doi:10.1186/gb-2014-15-2-r39.

25. Shi, Jiaqin; Huang, Shunmou; Zhan, Jiepeng; Yu, Jingyin; *Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong. Genome-Wide Microsatellite Characterization and Marker Development in the Sequenced Brassica Crop Species. DNA Research, 21(1), pp 53-68, 2014/2.

26. Chaobo Tong, Xiaowu Wang, Jingyin Yu, Jian Wu, Wanshun Li, Junyan Huang, Caihua Dong, Wei Hua and Shengyi Liu*. Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa. BMC Genomics 2013, 14:689 doi:10.1186/1471-2164-14-689.

27. Meixia Zhao, Jianchang Du, Feng Lin, Chaobo Tong, Jingyin Yu, Shunmou Huang, Xiaowu Wang, Shengyi Liu*, Jianxin Ma*. Shifts in evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous transposons and relics of a whole genome triplication. Plant Journal 2013, doi: 10.1111/tpj.12291.

28. Jiaqin Shi, Shunmou Huang, Donghui Fu, Jinyin Yu, Xinfa Wang, Wei Hua, Shengyi Liu,Guihua Liu, Hanzhong Wang*. Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica, Arabidopsis and Other Angiosperm Species. PLoS ONE 2013, 8(3): e59988. doi:10.1371/journal.pone.0059988.

29. Xiaohong Yan, Lei Zhang, Bo Chen, Zhiyong Xiong, Chunli Chen, Lijun Wang, Jingyin Yu, Changming Lu* & Wenhui Wei*. Functional Identification and Characterization of the Brassica napus Transcription Factor Gene BnAP2, the Ortholog of Arabidopsis thaliana APETALA2. PLoS ONE 2012, 7(3): e33890. doi:10.1371/journal.pone.0033890.

30. Xiaowu Wang, Jian Wu, Shengyi Liu, Yinqi Bai, Jeong-Hwan Mun, Ian Bancroft6, Feng Cheng1, Sanwen Huang, Xixiang Li, Wei Hua, Junyi Wang, Xiyin Wang, Michael Freeling, J Chris Pires, Andrew H Paterson, Boulos Chalhoub, Bo Wang, Alice Hayward1, 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 & Zhonghua Zhang, Hanzhong Wang*, Jun Wang* & Rifei Sun*. The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 2011, 43(10):1035-1039.

31. Zhenhai Zhang, Jingyin Yu, Daofeng Li, Zuyong Zhang, Fengxia Liu, Xin Zhou, Tao Wang, Yi Ling and Zhen Su*. PMRD: plant microRNA database. Nucleic Acids Research 2010, Vol. 38, (Database issue) doi:10.1093 /nar/ gkp818.

 

 


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