梁承志

中国科学院遗传与发育生物学研究所

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  • 梁承志
  • 生物大数据分析平台首席科学家
  • 研究员

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年于中国科学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。2001-2012年先后在加拿大Bioinformatics Solutions Inc公司、美国纽约冷泉港实验室、菲律宾国际水稻所从事生物信息研发工作。2012年2月回国,中国科学院引进杰出技术人才(百人计划B类),现担任中国科学院遗传发育所生物大数据分析平台首席科学家。主要研究领域 1. 基因组组装和注释。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10x Genomics)、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:(1)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;(2)小麦测序和组装。已完成二倍体乌拉尔图(Triticum urartu)小麦的BAC测序和组装;(3)苦荞、金鱼草等。其它多个物种的组装分析正在进行。 2. 比较基因组和群体基因组分析。我们对水稻、小麦、苦荞、金鱼草等多个物种进行了比较基因组分析,发现了导致各个物种各自在进化上的一些关键特征的相关遗传基础,比如小麦基因组的快速变异导致的基因丢失、苦荞和金鱼草的全基因组复制后产生的对环境适应能力的增强或关键性状的演化。我们通过对中国主栽水稻品种的大规模群体基因组分析和GWAS,发现一些当前水稻育种中有利等位基因利用的特点及在不同亚群中性状改良侧重点的不同。后续工作将结合组学大数据的整合对多种作物的群体基因组和表型组进行进一步的分析。 3. 生物信息软件和数据库开发。在基因组组装方面,开发了一个基于单分子长片段测序的组装基因组复杂区域的软件HERA,在现有软件的基础上大大提高了基因组的组装质量,也提高了分离高杂合二倍体基因组的能力。这个软件已经应用到多个水稻、小麦、玉米、大豆等基因组的组装。在基因注释方面对Gramene-pipeline进行了改进。在数据库建设方面,构建了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知识库MBKbase(www.mbkbase.org)。对于每个物种,泛基因组将是这个数据库的一个重要组成部分。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.Du H and Liang C*, Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads'. Nature Comm. (Accepted)2.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 Res. doi: 10.1093/nar/gkz921. (2019)3.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. doi: 10.1126/science.aaw7166 (2019)4.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. Nat Plants 5:174–183. doi: 10.1038/s41477-018-0349-9 (2019)5.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. doi: 10.1093/bioinformatics/bty642 (2019)6.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 wheat A subgenome Triticum urartu. Nature 557:424–428. doi: 10.1038/s41586-018-0108-0 (2018)7.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 noncoding RNA landscape of sperm cell lineage development. Plant J doi: 10.1111/tpj.14041 (2018)8.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. Nat Genet 50:1289–1295. doi: 10.1038/s41588-018-0182-0 (2018)9.Wu Z, Fang D, Yang R, Gao F, An X, Zhuo X, Li Y, Yi C, Zhang T, Liang C, Cui P, Cheng Z, Luo Q, De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. Commun Biol 1:84. doi: 10.1038/s42003-018-0089-4 (2018)10. 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. Theor Appl Genet 131:1391–1403. doi: 10.1007/s00122-018-3085-7 (2018)11. 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 Physiol 177:1108–1123. doi: 10.1104/pp.18.00209 (2018)12. Xiao N, Wu Y, Pan C, Yu L, Chen Y, Liu G, Li Y, Zhang X, Wang Z, Dai Z, Liang C*, Li A*, Improving of Rice Blast Resistances in Japonica by Pyramiding Major R Genes. Front Plant Sci 7:1918. doi: 10.3389/fpls.2016.01918 (2017)13. 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)14. Du H#, Yu Y#, Ma Y#, Gao Q#, Cao Y#, Chen Z, Ma B, Qi M, Li Y, Zhao X, Wang J, Liu K, Qin P, Yang X, Zhu L, Li S*, Liang C*. Sequencing and de novo assembly of a near complete indica rice genome. Nature Communications 8:15324 (2017)15. Wu Y, Chen Y, Pan C, Xiao N, Yu L, Li Y, Zhang X, Pan X, Chen X, Liang C, Dai Z, Li A, Development and evaluation of near-isogenic lines with different blast resistance alleles at the Piz Locus in Japonica rice from the lower region of the Yangtze River, China. Plant Dis 101:1283–1291. doi: 10.1094/PDIS-12-16-1855-RE (2017)16. Wu Y, Yu L, Pan C, Dai Z, Li Y, Xiao N, Zhang X, Ji H, Huang N, Zhao B, Zhou C, Liu G, Liu X, Pan X, Liang C, Li A, Development of near-isogenic lines with different alleles of Piz locus and analysis of their breeding effect under Yangdao 6 background. Mol Breed 36:12. doi: 10.1007/s11032-016-0433-7 (2016)17. 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: 134.18. Li D, Huang Z, Song S, Xin Y, Mao D, Lv Q, Zhou M, Tian D, Tang M, Wu Q, Liu X, Chen T, Song X, Fu X, Zhao B, Liang C, Li A, Liu G, Li S, Hu S, Cao X, Yu J, Yuan L, Chen C, Zhu L, Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase. Proc Natl Acad Sci 113:201610115. doi: 10.1073/pnas.1610115113 (2016)19. Li D#, Zeng R#, Li Y#, Zhao M, Chao J, Li Y, Wang K, Zhu L*, Tian W-M*, Liang C*. Gene expression analysis and SNP/InDel discovery to investigate yield heterosis of two rubber tree F1 hybrids. Scientific Reports 6: 24984 (2016)20. Chen J, Huang Q, Gao D, Wang J, Lang Y, Liu T, Li B, Bai Z, Goicoechea LJ, Liang C, Chen C, Zhang W, Sun S, Liao Y, Zhang X, Yang L, Song C, Wang M, Shi J, Liu G, Liu J, Zhou H, Zhou W, Yu Q, An N, Chen Y, Cai Q, Wang B, Liu B, Min J, Huang Y, Wu H, Li Z, Zhang Y, Yin Y, Song W, Jiang J, Jackson SA, Wing RA*, Wang Jun*, Chen M*. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Communications 4:1595 (2013)21. Xie W, Liang C, Birchler JA, Inhibition of RNA interference and modulation of transposable element expression by cell death in Drosophila. Genetics 188, 823-34 (2011)22. Wei F, Stein JC, Liang C, Zhang J, Fulton RS, Baucom RS, De Paoli E, Zhou S, Yang L, Han Y, et al. Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome. PLoS Genet 5(11): e1000728 (2009)23. Liang C*, Mao L, Ware D, Stein L, Evidence-based gene predictions in plant genomes. Genome Res 19, 1912-23 (2009)24. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, …, McCombie WR, Wing RA, Wilson RK, The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–5. doi: 10.1126/science.1178534 (2009)25. Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung C-W, Wei X, Yap I, Youens-Clark K, Ware D, Stein L*; Gramene: a growing plant comparative genomics resource, Nucleic Acids Research 36: D947-D953 (2008)26. Hladish T, Gopalan V, Liang C, Qiu W, Yang P and Stoltzfus A, Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics 8, 191 (2007)27. Jaiswal P, Ni J, Yap I, Ware D, Spooner W, Youens-Clark K, Ren L, Liang C, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S, Gramene: a bird’s eye view of cereal genomes. Nucleic Acids Res 34:D717-23. doi: 10.1093/nar/gkj154 (2006)28. Ma B, Zhang K, and Liang C, An Effective Algorithm for the Peptide De Novo Sequencing from MS/MS Spectrum. J Computer and System Sciences 70, 418-430 (2005)29. Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty-Kirby A, Lajoie G, PEAKS: Powerful Software for Peptide De Novo Sequencing by MS/MS. Rapid Comm Mass Spec 17, 2337-2342 (2003)30. Williams CE, Collier CC, Nemacheck, JA, Liang C and Cambron SE, A lection-like wheat gene responds systemically to attempted feeding by virulent first-instar Hessian fly larvae. J Chem Ecol 28, 1411-1428 (2002)31. Li XB, Liang CZ, Wu HG, Zhai WX, Huang N, Zhu LH, Isolation and identification of a non-specific tandemly repeated DNA sequence in Oryza species. Theor Appl Genet 92, 702-708 (1996)32. Liang CZ, Gu MH, Pan XB, Liang GH, Zhu LH, RFLP tagging a semi-dwarfing gene in rice. Theor Appl Genet 88, 898-900 (1994)