張興坦課題組介紹

Zhang Xingtan Lab

　　課題組長(zhǎng)

張興坦，研究員,、博導(dǎo),，熱帶作物生物育種全國(guó)重點(diǎn)實(shí)驗(yàn)室副主任。2009年于哈爾濱工業(yè)大學(xué)本科畢業(yè),，2015年于重慶大學(xué)獲得植物學(xué)博士學(xué)位,。長(zhǎng)期從事植物基因組學(xué)研究，擅長(zhǎng)植物復(fù)雜基因組的組裝和生物信息學(xué)分析,。近五年來,，相關(guān)成果以第一或通訊作者（含共同）發(fā)表在Cell、Nature,、Nature Genetics,、Nature Plants等期刊,。

　　工作經(jīng)歷

　　2020.10-至今           中國(guó)農(nóng)業(yè)科學(xué)院深圳農(nóng)業(yè)基因組研究所，研究員

　　2015.07-2020.10     福建農(nóng)林大學(xué),，講師/副教授

 

　　教育經(jīng)歷

　　2009.09 - 2015.06     重慶大學(xué) 植物學(xué),  理學(xué)博士

　　2013.10 - 2014.10     J. Craig Venter Institute ,  訪問博士生

　　2005.09 - 2009.06     哈爾濱工業(yè)大學(xué) 生物工程 ,  工學(xué)學(xué)士

 

　　研究方向

1. 復(fù)雜多倍體/高雜合二倍體基因組組裝和分型方法的開發(fā)

2. 基于NGS或單分子測(cè)序技術(shù)開發(fā)生物信息分析算法和工具

3. 基于組學(xué)大數(shù)據(jù)挖掘植物重要功能基因并解析其生物學(xué)機(jī)制

　　研究進(jìn)展

高精度的基因組組裝不僅有助于解析物種演化,、關(guān)鍵性狀的產(chǎn)生等科學(xué)問題，也為推動(dòng)農(nóng)作物基因組輔助育種提供了必不可少的基礎(chǔ)數(shù)據(jù),。然而許多植物基因組高度重復(fù),、高雜合和具有多份同源拷貝，同源染色體難以區(qū)分,，為構(gòu)建高精度的染色體水平的組裝造成了極大的困難,。目前主流的算法多針對(duì)人類或擬南芥、水稻等較為簡(jiǎn)單基因組開發(fā),，缺乏對(duì)植物復(fù)雜基因組的有效解決方案，尤其鮮有涉及多倍體染色體分型組裝,。多倍體繁雜多樣,，存在自身加倍（同源多倍體）、雜交加倍（異源多倍體）及兩者之間的混合等多種形式,，是基因組組裝領(lǐng)域最難解決的問題之一,。針對(duì)上述困難，團(tuán)隊(duì)開發(fā)了一系列創(chuàng)新性方法：1）基于已知性別的群體重測(cè)序數(shù)據(jù)和連鎖SNP區(qū)塊成功解決了榕樹高度重復(fù)的性別決定區(qū)組裝,，并分型了X和Y性染色體（Cell封面,，2020）；2）基于中低頻的共享Kmer識(shí)別雜合基因組中的冗余序列,，比傳統(tǒng)方法提速3-18倍,，解決了高雜合龐大基因組去冗余過程耗時(shí)耗費(fèi)計(jì)算資源問題（Nature Genetics，2021）,；3）基于消減信號(hào)和遺傳算法首次解決了多倍體同源染色體分型組裝難題,，實(shí)現(xiàn)了多倍體分型組裝從0到1的突破（Nature Genetics封面 2018; Nature Plants, 2019)。上述工作為動(dòng)植復(fù)雜基因組項(xiàng)目提供了有效的算法工具和解決方案,。

 

　　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)

張興坦課題組更新于2023年6月