张兴坦课题组

张兴坦课题组介绍

Zhang Xingtan Lab

　　课题组长

张兴坦，研究员、博导，热带作物生物育种全国重点实验室副主任，国家基金委优秀青年基金获得者，中国农科院农科英才领军人才B类。2009年于哈尔滨工业大学本科毕业，2015年于重庆大学获得植物学博士学位。长期从事植物基因组学研究，擅长植物复杂基因组的组装和生物信息学分析。近五年来，相关成果以第一或通讯作者（含共同）发表在Cell、Nature、Nature Genetics、Nature Plants等期刊。

　　工作经历

　　2020.10-至今           中国农业科学院深圳农业基因组研究所，研究员

　　2015.07-2020.10     福建农林大学，讲师/副教授

 

　　教育经历

　　2009.09 - 2015.06     重庆大学 植物学,  理学博士

　　2013.10 - 2014.10     J. Craig Venter Institute ,  访问博士生

　　2005.09 - 2009.06     哈尔滨工业大学 生物工程 ,  工学学士

 

　　研究方向

1. 复杂多倍体/高杂合二倍体基因组组装和分型方法的开发

2. 基于NGS或单分子测序技术开发生物信息分析算法和工具

3. 基于组学大数据挖掘植物重要功能基因并解析其生物学机制

　　研究进展

高精度的基因组组装不仅有助于解析物种演化、关键性状的产生等科学问题，也为推动农作物基因组辅助育种提供了必不可少的基础数据。然而许多植物基因组高度重复、高杂合和具有多份同源拷贝，同源染色体难以区分，为构建高精度的染色体水平的组装造成了极大的困难。目前主流的算法多针对人类或拟南芥、水稻等较为简单基因组开发，缺乏对植物复杂基因组的有效解决方案，尤其鲜有涉及多倍体染色体分型组装。多倍体繁杂多样，存在自身加倍（同源多倍体）、杂交加倍（异源多倍体）及两者之间的混合等多种形式，是基因组组装领域最难解决的问题之一。针对上述困难，团队开发了一系列创新性方法：1）基于已知性别的群体重测序数据和连锁SNP区块成功解决了榕树高度重复的性别决定区组装，并分型了X和Y性染色体（Cell封面，2020）；2）基于中低频的共享Kmer识别杂合基因组中的冗余序列，比传统方法提速3-18倍，解决了高杂合庞大基因组去冗余过程耗时耗费计算资源问题（Nature Genetics，2021）；3）基于消减信号和遗传算法首次解决了多倍体同源染色体分型组装难题，实现了多倍体分型组装从0到1的突破（Nature Genetics封面 2018; Nature Plants, 2019)。上述工作为动植复杂基因组项目提供了有效的算法工具和解决方案。

 

　　PI

　　Dr. Xingtan Zhang is a research professor and doctoral supervisor at the Agricultural Genomics Institute at Shenzhen (AGIS), Chinese Academy of Agricultural Sciences. He is also the deputy director of the National Key Laboratory for Tropical Crop Breeding and a recipient of the National Science Fund for Distinguished Young Scholars and the Chinese Academy of Agricultural Sciences' Leading Talent B. He graduated with a bachelor's degree from Harbin Institute of Technology (HIT) in 2009 and obtained a Ph.D. in Botany from Chongqing University in 2015. He has been engaged in research on plant genomics for a long time and is proficient in genome assembly and bioinformatics analysis of plant complex genomes. In the past five years, his relevant achievements have been published as first or corresponding author (including co-authorship) in journals such as Cell, Nature, Nature Genetics, and Nature Plants.

　　Working Experience

　　2020.10 - present      Agricultural Genomics Institute at Shenzhen-CAAS,   Research Professor

　　2015.07 - 2020.10     Fujian Agriculture and Forestry University,   research associate/associated professor

 

　　Education

　　2009.09 - 2015.06  Chongqing University, Ph.D in Plant Science

　　2013.10 - 2014.10  J. Craig Venter Institute, Visiting Ph.D student

　　2005.09 - 2009.06  Harbin Institute of Technology, Bachelor in Bio-engineering

 

　　Research Interest

1. Assembly and phasing of complex genomes, including polyploid and highly heterozygous diploid genomes.

2. Development of novel bioinformatics tools based on NGS and/or single-molecular sequencing technologies.

3. Data mining of functional genes underlying important roles in plant development and crop domestication 

　　

　　Major Achievement

Over the past two decades, significant advancements in sequencing technologies and computational algorithms have propelled plant genomic research into a flourishing era, with hundreds of genomes decoded, spanning from nonvascular plants to flowering plants. However, assembling complex genomes remains challenging and difficult to fully resolve using traditional sequencing and assembly methods, due to high heterozygosity, repetitive sequences, or high ploidy characteristics of complex genomes. To address these challenges, our group has developed a series of innovative methods:

1. Utilizing a resequenced population with characterized gender and linked SNP blocks, our team successfully assembled the highly repetitive sex-determining region of the fig tree genome with phased X and Y chromosomes (Cell, cover story, 2020).

2. We created a Kmer-based haplotype caller (Khaper) for identifying redundant sequences in heterozygous genomes, addressing the time-consuming and computationally expensive problem of de-redundancy in large heterozygous genomes (Nature Genetics, 2021).

3. Employing a novel prune algorithm in conjunction with a genetic algorithm, we resolved the challenge of homologous chromosome phasing and assembly in a sugarcane genome, achieving a breakthrough in polyploid haplotype-resolved assembly (Nature Genetics, cover story, 2018; Nature Plants, 2019).

The aforementioned work offers effective algorithmic tools and solutions for animal and plant complex genome projects.

 

Selected Publications

1. Zhang, Xingtan#, Gang Wang#, Shengcheng Zhang, Shuai Chen et al., 2020. “Genomes of banyan fig and pollinator wasp provide insights into fig-wasp coevolution.” Cell 183 (4): 875-889.https://doi.org/10.1016/j.cell.2020.09.043

2. Zhang, Xingtan#, Shuai Chen#, Longqing Shi#, Daping Gong#, Shengcheng Zhang, Qian Zhao et., al. 2021 “Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis”. Nature Genetics 53(8): 1250-1259. https://10.1038/s41588-021-00895-y

3. Zhang, Xingtan, Shengcheng Zhang, Qian Zhao, Ray Ming, and Haibao Tang*. 2019. “Assembly of Allele-Aware, Chromosomal-Scale Autopolyploid Genomes Based on Hi-C Data.” Nature Plants 5 (8): 833–45. https://doi.org/10.1038/s41477-019-0487-8.

4. Zhang, Liangsheng#, Fei Chen#, Xingtan Zhang#, Zhen Li#, Yiyong Zhao#, Rolf Lohaus, Xiaojun Chang, et al. 2020. “The Water Lily Genome and the Early Evolution of Flowering Plants.” Nature 577 (7788): 79–84. https://doi.org/10.1038/s41586-019-1852-5. (#co-first author)

5. Zhang, Jisen.#. Zhang Xingtan.#, Tang Haibao#., et al. Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L. Nature Genetics, doi:10.1038/s41588-018-0237-2 (2018). (co-first author)

6. Kong, W., Wang Y., Zhang, S., Yu, J., Zhang, X.* (2023). Recent Advances in Assembly of Plant Complex Genomes. Genomics Proteomics & Binformatics. https://doi.org/10.1016/j.gpb.2023.04.004

7. Wang, P., Gu, M., Yu, X., Shao, S., Du, J., Wang, Y., Wang, F., Chen, S., Liao, Z., Ye, N., Zhang, X.* (2022). Allele-specific expression and chromatin accessibility contribute to heterosis in tea plants ( Camellia sinensis ). Plant J., tpj.16004. 10.1111/tpj.16004.

8. Kong, W., Jiang, M., Wang, Y., Chen, S., Zhang, S., Lei, W., Chai, K., Wang, P., Liu, R., and Zhang, X.* (2022). Pan-transcriptome assembly combined with multiple association analysis provides new insights into the regulatory network of specialized metabolites in the tea plant Camellia sinensis. Hortic. Res. 9, uhac100. 10.1093/hr/uhac100.

9. Wang, G.#, Zhang, X.#, Herre, E.A., McKey, D., Machado, C.A., Yu, W.-B., Cannon, C.H., Arnold, M.L., Pereira, R.A.S., Ming, R., et al. (2021). Genomic evidence of prevalent hybridization throughout the evolutionary history of the fig-wasp pollination mutualism. Nat. Commun. 12, 718. 10.1038/s41467-021-20957-3. (#co-first author)

张兴坦课题组更新于2023年6月