General

梁承志 男 汉族 博导 遗传与发育生物学研究所
Email: cliang@genetics.ac.cn
Telephone: 010-64801262
Address: 北京市朝阳区北辰西路1号院2号
Postcode: 100101

Research Areas

Comprative Genomics, Genomic big data analysis, Bioinformatics method development

Publications

发表论文(*Corresponding author):

  1.  Xu P, Wang Y, Sun F, Wu R, Du H, Wang Y, Jiang L, Wu X, Wu X, Yang L, Xing N, Hu Y, Wang B, Huang Y, Tao Y, Gao Q, Liang C, Li Y, Lu Z, Li G. Long-read genome assembly and genetic architecture of fruit shape in the bottle gourd. Plant J tpj.15358. https://doi.org/10.1111/tpj.15358. (2021)
  2. Qiu L, Wu Q, Wang X, Han J, Zhuang G, Wang H, Shang Z, Tian W, Chen Z, Lin Z, He H, Hu J, Lv Q, Ren J, Xu J, Li C, Wang X, Li Y, Li S, Huang R, Chen X, Zhang C, Lu M, Liang C, Qin P, Huang X, Li S, Ouyang X. Forecasting rice latitude adaptation through a daylength-sensing-based environment adaptation simulator. Nat Food 2:348–362. https://doi.org/10.1038/s43016-021-00280-2. (2021)
  3.  Chen J, Zhang H, Dai D, Li X, Ma L, Liang C, Zhang R, Liang C, Du H, Chen Z, Zhao Y, Deng S. A backbone parent contributes key genomic architecture to pedigree breeding of early-season indica rice. J Genet Genomics. https://doi.org/10.1016/j.jgg.2021.07.011. (2021)
  4.  Huang C, Chen Z, Liang C*. Oryza pan-genomics: A new foundation for future rice research and improvement. Crop J. 9:622–632. (2021)
  5.  Qin P*#, Lu H#, Du H#, Wang H#, Chen W#, Chen Z#, He Q, Ou S, Zhang H, Li X, Li X, Li Y, Liao Y, Gao Q, Tu B, Yuan H, Ma B, Wang Y, Qian Y, Fan S, Li W, Wang J, He M, Yin J, Li T, Jiang N, Chen X, Liang C*, Li S*. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell 184:3542-3558.e16. https://doi.org/10.1016/j.cell.2021.04.046. (2021)
  6.  Yu H#*, Lin T#, Meng X#, Du H#, Zhang J#, Liu G, Chen M, Jing Y, Kou L, Li X, Gao Q, Liang Y, Liu X, Fan Z, Liang Y, Cheng Z, Chen M, Tian Z, Wang Y, Chu C, Zuo J, Wan J, Qian Q, Han B, Zuccolo A, Wing RA, Gao C*, Liang C*, Li J*. A route to de novo domestication of wild allotetraploid rice. Cell 184:1156-1170.e14. (2021)
  7.  Chen Z, Li X, Lu H, Gao G, Du H, Peng H, Qin P and Liang C*. Genomic atlases of introgression and differentiation reveal breeding footprints in Chinese cultivated rice. Journal of Genetics and Genomics 47:637-649. (2020)
  8.  Shen C#, Du H#, Chen Z#, Lu H#, Zhu F, Chen H, Meng X, Liu Q, Liu P, Zheng L, Li X, Dong J*, Liang C*, Wang T*. The chromosome-level genome sequence of the autotetraploid alfalfa and resequencing of core germplasms provide genomic resources for alfalfa research. Molecular Plant 13:1250-1261. (2020)
  9.  Xie X#, Du H#, Tang H, Tang J, Tan X, Liu W, Li T, Lin Z, Liang C*, Liu Y-G*. A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice. Science China Life Sciences 1–12. https://doi.org/10.1007/s11427-020-1738-x. (2020)
  10.  Liu Y#, Du H#, Li P, Shen Y, Peng H, Liu S, Zhou GA, Zhang H, Liu Z, Shi M, Huang X, Li Y, Zhang M, Wang Z, Zhu B, Han B, Liang C*, Tian Z*. Pan-Genome of Wild and Cultivated Soybeans. Cell 182:162-176. (2020)
  11. Peng H, Wang K, Chen Z, Cao Y, Gao Q, Li Y, Li X, Lu H, Du H, Lu M, Yang X, Liang C*. MBKbase for rice: An integrated omics knowledgebase for molecular breeding in rice. Nucleic acids research 48:D1085–D1092. (2020)
  12. Li X#, Chen Z#, Zhang G#, Lu H#, Qin P, Qi M, Yu Y, Jiao B, Zhao X, Gao Q, Wang H, Wu Y, Ma J, Zhang L, Wang Y, Deng L, Yao S, Cheng Z, Yu D, Zhu L, Xue Y, Chu C, Li A*, Li S*, Liang C*. Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions. Science China Life Sciences 41:1518. (2020)
  13. Liu H, Shi J, Cai Z, Huang Y, Lv M, Du H, Gao Q, Zuo Y, Dong Z, Huang W, Qin R, Liang C, Lai J, Jin W. Evolution and Domestication Footprints Uncovered from the Genomes of Coix. Molecular Plant 13:295–308. (2020)
  14. Du H, Liang C*. Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads. Nature Communications 10:5360. (2019)
  15. Jin S#, Zong Y#, Gao Q#, Zhu Z, Wang Y, Qin P, Liang C, Wang D, Qiu JL, Zhang F, Gao C. Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice. Science 364:292–295. (2019)
  16. Li M#, Zhang D#, Gao Q#, Luo Y#, Zhang H#, Ma B#, Chen C, Whibley A, Zhang Y, Cao Y, Li Q, Guo H, Li J, Song Y, Zhang Y, Copsey L, Li Y, Li X, Qi M, Wang J, Chen Y, Wang D, Zhao J, Liu G, Wu B, Yu L, Xu C, Li J, Zhao S, Zhang Y, Hu S, Liang C*, Yin Y*, Coen E*, Xue Y*. Genome structure and evolution of Antirrhinum majus L. Nature Plants 5:174–183. (2019)
  17. Shen Y, Du H, Liu Y, Ni L, Wang Z, Liang C*, Tian Z*. Update soybean Zhonghuang 13 genome to a golden reference. Science China Life Sciences 62:1257–1260. (2019)
  18. Yu H*, Lu L, Jiao B, Liang C*. Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples. Bioinformatics 35:361–364. (2019)
  19. Ling H-Q#*, Ma B#, Shi X#, Liu H#, Dong L#, Sun H#, Cao Y, Gao Q, Zheng S, Li Y, Yu Y, Du H, Qi M, Li Y, Lu H, Yu H, Cui Y, Wang N, Chen C, Wu H, Zhao Y, Zhang J, Li Y, Zhou W, Zhang B, Hu W, van Eijk MJT, Tang J, Witsenboer HMA, Zhao S, Li Z, Zhang A*, Wang D*, Liang C*. Genome sequence of the progenitor of the wheat A subgenome Triticum Urartu. Nature 557:424–428. (2018)
  20. Liu L#, Lu Y#, Wei L#, Yu H#, Cao Y, Li Y, Yang N, Song Y, Liang C*, Wang T*. Transcriptomics analyses reveal the molecular roadmap and long non-coding RNA landscape of sperm cell lineage development. Plant Journal 96:421–437. (2018)
  21. Wang S, Ma B, Gao Q, Jiang G, Zhou L, Tu B, Qin P, Tan X, Liu P, Kang Y, Wang Y, Chen W, Liang C*, Li S*, Dissecting the genetic basis of heavy panicle hybrid rice uncovered Gn1a and GS3 as key genes. Theoretical and Applied Genetics 131:1391–1403. (2018)
  22. Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, Song W, Zhang M, Cui Y, Dong X, Liu H, Ma X, Jiao Y, Wang B, Wei X, Stein JC, Glaubitz JC, Lu F, Yu G, Liang C, Fengler K, Li B, Rafalski A, Schnable PS, Ware DH, Buckler ES, Lai J. Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nature Genetics 50:1289–1295. (2018)
  23. Xiao N, Gao Y, Qian H, Gao Q, Wu Y, Zhang D, Zhang X, Yu L, Li Y, Pan C, Liu G, Zhou C, Jiang M, Huang N, Dai Z, Liang C, Chen Z, Chen J, Li A. Identification of genes related to cold tolerance and a functional allele that confers cold tolerance. Plant Physiology 177:1108–1123. (2018)
  24. Zhang L#, Li X#, Ma B#, Gao Q#, Du H#, Han Y, Li Y, Cao Y, Qi M, Zhu Y, Lu H, Ma M, Liu L, Zhou J, Nan C, Qin Yn, Wang J*, Cui L*, Liu H*, Liang C*, Qiao Z*. The Tartary buckwheat genome provides insights into rutin biosynthesis and abiotic stress tolerance. Molecular Plant 10(9): 1224-1237. (2017)
  25. Huilong Du, Ying Yu, Yanfei Ma, Qiang Gao, Yinghao Cao, Zhuo Chen, Bin Ma, Ming Qi, Yan Li, Xianfeng Zhao, Jing Wang, Kunfan Liu, Peng Qin, Xin Yang, Lihuang Zhu, Shigui Li* and Chengzhi Liang*, (2017) Sequencing and de novo assembly of a near complete indica rice genome. Nature Communications 8:15324 | DOI: 10.1038/ncomms15324.
  26. Yunyu Wu, Yu Chen, Cunhong Pan, Ning Xiao, Ling Yu, Yuhong Li, Xiaoxiang Zhang, Xuebiao Pan, Xijun Chen, Chengzhi Liang, Zhengyuan Dai, and Aihong Li, (2017) Development and evaluation of nearisogenic lines with different blast resistance alleles at Piz locus in japonica rice from the lower region of Yangtze River, China. Plant Disease doi:http://dx.doi.org/10.1094/PDIS-12-16-1855-RE.
  27. Chengzhen Liang, Aifu Li, Hua Yu, Wenzhen Li, Chengzhi Liang, Sandui Guo, Rui Zhang, and Chengcai Chu, (2017) Melatonin regulates root architecture by modulating auxin response in rice. Frontiers in Plant Science 8: 134.
  28. Xiao Ning, Wu Yunyu, Pan Cunhong, Yu Ling, Chen Yu, Liu Guangqing, Li Yuhong, Zhang Xiaoxiang, Wang Zhiping, Dai Zhengyuan, Liang Chengzhi, Li Aihong, Improving of Rice Blast Resistances in Japonica by Pyramiding Major R Genes. Frontiers in Plant Science (2017) 7:1918.
  29. Dayong Li, Zhiyuan Huang, Shuhui Song, …, Chengzhi Liang, Aihong Li, Guozhen Liu, Shigui Li, Songnian Hu, Xiaofeng Cao, Jun Yu, Longping Yuan, Caiyan Chen, and Lihuang Zhu, Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase. PNAS, 2016, vol. 113 no. 41, E6026-E6035.
  30. Dejun Li, Rizhong Zeng, Yan Li, Manman Zhao, Jinquan Chao, Yu Li, Kai Wang, Lihuang Zhu*, Wei-Min Tian* & Chengzhi Liang*, Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids. Scientific Reports 6, Article number: 24984 (2016), doi:10.1038/srep24984
  31. Shaofeng Li,# Chengming Fan,# Yan Li,# Jianhui Zhang, Jingshuang Sun, Yuhong Chen, Changyan Tian, Xiaohua Su, Mengzhu Lu, Chengzhi Liang, and Zanmin Hu*, Effects of drought and salt-stresses on gene expression in Caragana korshinskii seedlings revealed by RNA-seq. BMC Genomics. 2016; 17: 200.
  32. Yunyu Wu, Ling Yu, Cunhong Pan, Zhengyuan Dai, Yuhong Li, Ning Xiao, Xiaoxiang Zhang, Hongjuan Ji, Niansheng Huang, Buhong Zhao, Changhai Zhou, Guangqing Liu, Xiaojing Liu, Xuebiao Pan, Chengzhi Liang, Aihong Li, Development of near-isogenic lines with different alleles of Piz locus and analysis of their breeding effect under Yangdao 6 background. Mol Breeding (2016) 36: 12.
  33. Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Luis Goicoechea J, Liang C, et al. (2013). Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Comm. 4:1595, doi:10.1038/ncomms2596.
  34. Xie W, Liang C, Birchler JA (2011). Inhibition of RNA interference and modulation of transposable element expression by cell death in Drosophila. Genetics 188, 823-34.
  35. Patrick S. Schnable, Doreen Ware, Robert Fulton, Joshua Stein, Fusheng Wei, Shiran Pasternak, Chengzhi Liang, Jianwei Zhang, et al, The B73 maize genome: complexity, diversity and dynamics, 2009, Science, Vol. 326. no. 5956, pp. 1112 – 1115, DOI: 10.1126/science.1178534
  36. Fusheng Wei, Joshua C. Stein, Chengzhi Liang, Jianwei Zhang, Robert S. Fulton, Regina S. Baucom, Emanuele De Paoli, Shiguo Zhou, Lixing Yang, Yujun Han, et al., Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome, PLoS Genet. 2009 November; 5(11): e1000728
  37. Chengzhi Liang*, Long Mao, Doreen Ware, Lincoln Stein, Evidence-based gene predictions in plant genomes, Genome Research, 2009, 19(10):1912-23
  38. Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard, Shuly Avraham, Edward S. Buckler, Terry Casstevens et al., Gramene: a growing plant comparative genomics resource, Nucleic Acid Res, 2008 Vol. 36, Database issue D947-D953 


Students

已指导学生

余华  博士研究生  0710J3-生物信息学  

杜会龙  博士研究生  0710J3-生物信息学  

鲁宏伟  博士研究生  0710J3-生物信息学  

李秀秀  博士研究生  0710J3-生物信息学  

焦丙可  硕士研究生  071021-生物信息学  

陈倬  博士研究生  0710J3-生物信息学  

彭骅  博士研究生  0710J3-生物信息学  

陆敏  硕士研究生  0710J3-生物信息学  

现指导学生

陈永顺  硕士研究生  086000-生物与医药  

潘颖  硕士研究生  086000-生物与医药  

杨凯欣  硕士研究生  086000-生物与医药  

黄超  博士研究生  0710J3-生物信息学  

田骄阳  博士研究生  0710J3-生物信息学  

周健  硕士研究生  086000-生物与医药  

姬玉  硕士研究生  086000-生物与医药