梁承志
职称：研究员

职务：生物大数据分析平台首席科学家

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研究方向：基因组大数据分析


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。2001-2012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，中科院引进杰出技术人才（****B类），现担任中科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)
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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)
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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)
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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)
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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.
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