工作概述 面对海量、复杂的各种基因组信息，组装高质量基因组、从中挖掘重要功能基因信息是生物信息学面临的一个巨大的挑战。本人的工作主要是基于各类测序数据的基因组组装流程开发、复杂植物高质量基因组的构建、比较基因组分析、功能基因组分析、泛基因组分析以及图形基因组构建及应用等工作，开展了深入的研究，极大地推进了本领域的研究进展，取得了以下研究成果：1. 利用自主开发的组装流程成功地构建了一个几乎完整的籼稻R498参考基因组；通过与17个水稻基因组进行比较分析，构建了籼粳稻基因组之间较为全面的基因以及结构变异图谱，为籼稻和粳稻驯化育种等研究提供了基础(Du et al., Nature Communications, 2017); 2. 开发了一套基于单分子测序长片段对基因组复杂区域进行组装的软件HERA；成功构建了水稻、苦荞麦、玉米和中国人的基因组，并显著提高了基因组的完整度和连续性(Du and Liang, Nature Communications, 2019); 3. 构建了26个高质量的大豆基因组并结合2898份大豆种质材料的重测序数据的分析结果首次在大豆中实现了基于图形结构的泛基因组分析，突破了传统线性基因组的存储形式，为大豆重要农艺性状的挖掘和利用提供了宝贵的资源(Liu et al., Cell, 2020); 4. 完成了33个水稻高质量基因组的构建及比较分析，鉴定到了大量先前尚未发现的结构性变异(Structural variations，SVs)和基因拷贝数目变异(gene copy number variations, gCNVs)，探究了SV在亚洲栽培稻群体中的分布规律和形成机制，揭示了大量SVs和gCNVs与基因表达量变化显著相关，发现了多个与重要农艺性状相关的复杂优异等位变异(Qin et al., Cell, 2021)；5. 完成了四倍体水稻(Yu et al., Cell, 2021)和苜蓿(Shen et al., Molecular Plant, 2020)等多个复杂植物高质量基因组的构建，挖掘到多个与重要农艺性状相关的区域和基因，并分析了不同材料或不同物种基因组之间存在的结构变异及进化关系。在Nature、Cell、Nature Communications、Molecular Plant、Nucleic Acids Research和SCIENCE CHINA Life Sciences等SCI期刊上共发表16篇学术论文，获得国家专利两项。以第一作者或通讯作者（含共同）在Cell（2020，2021，2021）、Nature Communications（2017，2019）、Molecular Plant（2017，2020）、Journal of Integrative Plant Biology（2023）、SCIENCE CHINA Life Sciences（2019，2020，2021）和Journal of Genetics and Genomics（2022）等SCI刊物发表多篇论文，SCI他引1395次。曾获得中国科学院院长特别奖、中国科学院大学优秀毕业生、中国科学院大学优秀博士学位论文、北京市优秀毕业生、朱李月华优秀博士奖学金、益海嘉里优秀博士奖学金、国家奖学金（2014和2017）、中国科学院大学三好学生标兵等奖励。

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, Peng., Yang, X., Zhu, L., Li, S.*, Liang, C.* 2017. Sequencing and de novo assembly of a near complete indica rice genome. Nature Communications, 8,15324. Du, H., Liang, C. 2019. Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads. Nature Communications, 10,5360. Liu, Y.#, Du, H.#, Li, P., Shen, Y., Peng, H., Liu, S., Zhou, G., Zhang, H., Liu, Z., Shi, M., Huang, X., Li, Y., Zhang, M., Wang, Z., Zhu, B., Han, B., Liang, C.*, Tian, Z.* 2020. Pan-Genome of Wild and Cultivated Soybeans. Cell, 182,162-176. 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.* 2020. 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. 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.* 2021. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell. 184(13):3542-3558 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, Bin., Zuccolo, A., Wing, R., Gao, C.*, Liang, C.*, Li, J.* 2021. A route to de novo domestication of wild allotetraploid rice. Cell, 184,1-15. Qiang He#; Dan Ma#; Wei Li; Longsheng Xing; Hongyu Zhang; Yu Wang; Cailian Du; Xuanzhao Li; Zheng Jia; Xiuxiu Li; Jianan Liu; Ze Liu; Yuqing Miao; Rui Feng; Yang Lv; Meijia Wang; Hongwei Lu; Xiaochen Li; Yao Xiao; Ruyu Wang; Hanfei Liang; Qinghong Zhou; Lijun Zhang*; Chengzhi Liang*; Huilong Du *; High-quality Fagopyrum esculentum genome provides insights into the flavonoid accumulation among different tissues and self-incompatibility , Journal of Integrative Plant Biology, 2023 近五年内其余论著： 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, Y., Wang, J.*, Cui, L.*, Liu, H.*, Liang, C.*, Qiao, Z.* 2017. The Tartary Buckwheat Genome Provides Insights into Rutin Biosynthesis and Abiotic Stress Tolerance. Molecular Plant, 10,1224-1237. Shen, Y.#, Du, H.#, Liu, Y., Ni, L., Wang, Z., Liang, C.*, Tian, Z.* 2019. Update soybean Zhonghuang 13 genome to a golden reference. Science China Life Sciences, 62,1257-1260. Xie, X.#, Du, H.#, Tang, H., Tang, J., Tan, X., Liu, W., Li, T., Lin, Z., Liang, C.*, Liu, Y.* 2020. A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice. Science China Life Sciences, 64,282-293. Ling, H.#*, 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.* 2018. Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature, 557,424-428. Peng, H., Wang, K., Chen, Z., Cao, Y., Gao, Q., Li, Y., Li, X., Lu, H., Du, H., Lu, M., Yang, X., Liang, C. 2020. MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice. Nucleic Acids Research, 48,1085-1092. 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.* 2020. Evolution and Domestication Footprints Uncovered from the Genomes of Coix. Molecular Plant, 13,295-308. Chen, Z., Li, X., Lu, H., Gao, Q., Du, H., Peng, H., Qin, P., Liang, C. 2020. Genomic atlases of introgression and differentiation reveal breeding footprints in Chinese cultivated rice. Journal of Genetics and Genomics, 47,637-649. 论著之外的研究成果和获得学术奖励： (1) 梁承志; 杜会龙; 一种构建超长连续DNA序列的基因组组装方法, 2018-06-08, 中国, ZL 2018 1 0588945.8. (专利) (2) 梁承志; 杜会龙; 一种基因组组装方法, 2021-7-30, 中国, ZL 2018 1 1062858.5 (专利专 )