--中国科学院遗传与发育生物学研究所

姓　　名：	梁承志
职　　称：	研究员
职　　务：	科学数据中心主任
电话/传真：	010-64801262
电子邮件：	cliang@genetics.ac.cn
实验室主页：
研究方向：	基因组大数据分析

简历介绍：

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月起，任中科院遗传发育所研究员，入选中科院“引进杰出技术人才”计划，现担任研究所科学数据中心主任。

研究领域：

主要研究领域

1. 基因组组装和泛基因组构建。结合最新的单分子测序技术、BioNano单分子图谱、Hi-C测序等，完成高质量基因组的组装，或进一步构建泛基因组。已完成水稻（表1）、小麦、大豆、苦荞、金鱼草、高粱、番茄等大量基因组组装，并构建了大豆和水稻两个物种的高质量泛基因组。

2. 比较基因组和群体基因组分析。对水稻（图1、图2）、小麦、苦荞、金鱼草等多个物种进行了比较基因组分析，发现了各个物种在进化上的一些关键特征的相关基因组基础，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。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在不同群体间的渗入和利用特点（图3）。

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，在已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。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）（图4）。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二者之间的结构变异分布。其中6号染色体上的大倒位（~5Mb）仅发生在少数粳稻（包括日本晴）中。

图2：对33个水稻基因组比较分析显示了大量结构变异，部分可被溯源。

图3：中国水稻群体分化区域包含大量重要农艺性状基因。

图4：水稻分子育种知识库。

社会任职：

获奖及荣誉：

承担科研项目情况：

代表论著：

部分发表论文（*通讯作者）：

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, DuH, 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.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)

12.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)

13.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)

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. doi: 10.1126/science.aaw7166 (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. Nat Plants 5:174–183. doi: 10.1038/s41477-018-0349-9 (2019)

17.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)

18.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)

19.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 96:421-437. doi: 10.1111/tpj.14041 (2018)

20.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)

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. Theor Appl Genet 131:1391–1403. doi: 10.1007/s00122-018-3085-7 (2018)

22.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)

23.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)

24.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)

25.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)

26.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)

27.Liang C*, Mao L, Ware D, Stein L, Evidence-based gene predictions in plant genomes. Genome Res 19, 1912-23 (2009)

28.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)

29.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)

30.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)

31.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)