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梁承志


梁承志,博士,研究员, 博士生导师
  1989年毕业于武汉大学获得遗传学学士学位,1995年于中科院遗传所获得遗传学博士学位,2001在加拿大Waterloo大学获得数学与计算机科学硕士学位。2001-2003年在加拿大Bioinformatics Solutions Inc公司任生物信息科学家。2004-2009年在美国纽约冷泉港实验室任职科技信息主管(Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, Scientific Informatics Manager I, Scientific Programmer)。2009-2012年在菲律宾国际水稻所任职作物信息系统专家(International Rice Research Institute, Scientist II, Crop Information Systems Specialist)。2012年2月回国,现任中科院遗传发育所基因组分析平台(http://seqinfo.genetics.ac.cn)首席技术专家。


主要研究领域
        1.  基因组组装和注释。我们主要结合最新的测序技术,包括PacBio实时单分子测序、大片段测序(比如fosmid或10xGenomics)、BioNano单分子图谱,遗传图谱或Hi-C,完成基因组的组装,并利用基因表达的证据进行基因注释。现在已完成的基因组有:
        a)   水稻基因组测序和组装。已组装出一个目前最高质量的植物基因组籼稻蜀恢498。
        b)   二倍体小麦测序和组装。已完成乌拉尔图(Triticum urartu)小麦的BAC测序和组装。
        c)   其它多个物种的测序和组装正在进行。
 
        2.  生物信息数据库和软件开发。主要工作是构建一个包括多个参考基因组、基因组注释和群体遗传多态信息,应用于功能基因组研究和分子育种的数据库。相关的研究内容也包括:
        a)   基因注释软件的开发。
        b)   植物基因共表达网络构建和分析,用于分析和预测基因的功能。
        c)   水稻群体的等位基因的图谱构建、地区适应性分析,及GWAS。
 
 
图1:蜀恢498和日本晴全基因的比较显示了染色体端粒的有无及二者之间的结构变异分布。

发表论文(*Corresponding author):
 
 
1. 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.
 
2. 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 near‑isogenic 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.
 
3. 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.
 
4. 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.
 
5. 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.
 
6. 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
 
7. 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.
 
8. 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.
 
9. 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.
 
10. 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.
 
11. 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
 
12. 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
 
13. Chengzhi Liang*, Long Mao, Doreen Ware, Lincoln Stein, Evidence-based gene predictions in plant genomes, Genome Research, 2009, 19(10):1912-23
 
14. 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
 
15. Bin Ma, Kaizhong Zhang, and Chengzhi Liang. An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum. Journal of Computer and System Sciences 70: 418-430. 2005
 
16. Hladish T, Gopalan V, Liang C, Qiu W, Yang P and Stoltzfus A (2007). Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics 8, 191.
 
17. Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, et al. (2006). Gramene: a bird’s eye view of cereal genomes. Nucleic Acids Res. 34, Database issue D717-D723.
 
18. Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty-Kirby A, Lajoie G (2003). PEAKS: Powerful Software for Peptide De Novo Sequencing by MS/MS. Rapid Comm. Mass Spec. 17, 2337-2342.
 
19. Williams CE, Collier CC, Nemacheck, JA, Liang C and Cambron SE (2002). A lection-like wheat gene responds systemically to attempted feeding by virulent first-instar Hessian fly larvae. J. Chem. Ecol. 28, 1411-1428.
 
20. Li XB, Liang CZ, Wu HG, Zhai WX, Huang N, Zhu LH (1996). Isolation and identification of a non-specific tandemly repeated DNA sequence in Oryza species. Theor. Appl. Genet. 92, 702-708.
 
21. Liang CZ, Gu MH, Pan XB, Liang GH, Zhu LH (1994). RFLP tagging a semi-dwarfing gene in rice. Theor. Appl. Genet. 88, 898-900.