Chengjun Zhang

姓　　名: 章成君, Chengjun Zhang

学　　科: 生物信息学, Bioinformatics

电子邮件: zhangcj[at]zafu.edu.cn

通讯地址: 浙江省杭州市临安区武肃街666号, 浙江农林大学亚热带森林培育国家重点实验室

ADDR: No. 88 Wushu Street, Linan Hangzhou 311300, Zhejiang, P.R. China.
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University. 

学习教育经历：

本科：

2001.9-2005.6 华中农业大学 生物技术

2003.3-2006.7 武汉大学（双学位） 计算机科学与技术 

硕博连读：

2005.9-2011.6 华中农业大学 生物化学与分子生物学

工作经历：

2011.9-2014.8 芝加哥大学 博士后

2014.8-2023.4 中科院昆明植物研究所 研究员，博导

2022.11-至今 浙江农林大学 教授，博导

代表性论文：

  1. Li K*, Wu Z*, et al., Zhang C#, Sun Q# (2022) R-loopAtlas: an integrated R-loop resource from 254 plant species sustained by a deep learning-based tool, Molecular Plant, doi: 10.1016/j.molp.2022.12.012.【PDF】
  2. Zhou Y, Zhang C#, Zhang L, Ye Q, Liu N, Wang M, Long G, Fan W, Long M#, Wing R# (2022) Gene Fusion as an Important Mechanism to Generate New Genes in the Genus Oryza, Genome Biology, 23:130.【PDF】
  3. Hu Y*, Wu X, Jin G, et al., Chuanzhu Fan#, Zhang C# (2021) Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications, Front. Plant Sci., doi: 10.3389/fpls.2021.772655.【PDF】
  4. Jin G*, Ma P*, Wu X, Gu L, Long M, Zhang C#, Li D# (2021) New Genes Interacted With Recent Whole-Genome Duplicates in the Fast Stem Growth of Bamboos, Molecular Biology and Evolution, 38(12):5752-5768. doi: 10.1093/ molbev/msab288.【PDF】
  5. Liu N, Zhang L, Zhaou Y, Tu M, Wu Z, Gui D, Ma Y, Wang J#, Zhang C# (2021) The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron, BMC Genomics, 22:376. DOI: 10.1186/s12864-021-07704-0.【PDF】
  6. Zhang C#*, Yang H, Yang H (2015) Evolutionary Character of Alternative Splicing in Plants, Bioinformatics and Biology Insights, 9(S1):1-6.DOI: 10.4137/BBI.S33716.【PDF】
  7. Zhang C, Gschwend RA, Ouyang Y, Long M (2014) , Evolution of gene structural complexity: An alternative-splicing based model accounts for intron-containing retrogenes, Plant Physiology, doi: 10.1104/pp.113.231696.【PDF】
  8. Zhang C, Wang J, Xie W, Zhou , Long M , Zhang Q (2011) Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method, Proc Natl Acad Sci USA, 2011, 108(19):7860-7865.【PDF】

发表全部论文：

2014-至今

  1. Zhang C#*, Yang H, Yang H (2015) Evolutionary Character of Alternative Splicing in Plants, Bioinformatics and Biology Insights, 9(S1):1-6.DOI: 10.4137/BBI.S33716【PDF】
  2. Ouyang Y#, Li G, Mi J, Xu C, Du H, Zhang C, Xie W, Li X, Xiao J, Song H, Zhang Q (2016) Origination and Establishment of a Trigenic Reproductive Isolation System in Rice, Molecular Plant, 9:1542-1545.DOI: 10.1016/j.molp.2016.07.008【PDF】
  3. 杜丽思，章成君，张靖，彭晟，杨静，刘林，李成云，杜云龙#（2016）两种生态型玛咖叶片的丛生芽诱导，云南农业科技，10.3969/j.issn.1000-0488.2016.02.001【PDF】
  4. Zhu Y, Chen L, Zhang C, Hao P, Jing X, Li X, (2017) Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in non-seed vascular plant Selaginella moellendorffii, BMC genomics, 18(1):1042.DOI: 10.1186/s12864-016-3266-1【PDF】
  5. Zhang L*, Xu P*, Cai Y*, Ma L*, et al., Zhang C, Gao Q, Wang J (2017) The draft genome assembly of Rhododendron delavayi Franch. var. delavayi, GigaScience, 6:1-11. DOI: 10.1093/gigascience/gix076【PDF】
  6. Chen J, Ni P, Li X, Han J, Jackovlic I, Zhang C and Zhao S# (2018) Population size may shape the accumulation of functional mutations following domestication, BMC Evolutionary Biology, 18(4). DOI: 10.1186/s12862-018-1120-6【PDF】
  7. Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K et al., Long M, Ware D, Wing RA# (2018) Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza, Nature Genetics, 50:285-296.【PDF】
  8. Li Y, Fang C, Fu Y et al., Zhang C, Li C# (2018) A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing, DNA Research, 25(4) 421-437.DOI: 10.1093/dnares/dsy014【PDF】
  9. Shi Y*, Su Z*, Yang H* et al., Xue R#, Zhang C# (2019) Alternative splicing coupled to nonsense-mediated mRNA decay contributes to the high-altitude adaptation of maca (Lepidium meyenii), Gene, 694:7-18.DOI: 10.1016/j.gene.2018.12.082【PDF】
  10. Shi Y, Yan X, Yin H et al., Zhang C#, Ma X# (2019) Divergence and hybridization in the desert plant Reaumuria soongarica, Journal of Systematics and Evolution, doi: 10.1111/jse.12490.【PDF】
  11. Zhou Y, Zhang C# (2019) Evolutionary patterns of chimeric retrogenes in Oryza species, Scientific Reports, 9:17733. doi: 10.1038/s41598-019-54085-2【PDF】
  12. Jin G, Zhou Y, Yang H, Hu Y, Shi Y, Li L, Abu N. Siddique, Liu C, Zhu A, Zhang C#, and Li D# (2019) Transposable element recruitment and de novo formation lead to the birth of orphan genes in the rice genome, Journal of Systematics and Evolution, doi: 10.1111/jse.12548.【PDF】
  13. Zhang L, Ren Y, Yang T et al., Zhang C, Zhang Y, Ouyang Y, Wing R#, Liu S#, Long M# (2019) Rapid evolution of protein diversity by de novo origination in Oryza, Nature Ecology & Evolution, 3:679-690. DOI: 10.1038/s41559-019-0822-5.【PDF】
  14. Li P*, Yang H*, Wang L, Liu H, Huo H, Zhang C, et al., Lin Y, Liu L# (2019) Physiological and transcriptome analyses reveal short-term responses and formation of memory under drought stress in rice, Frontiers in Genetics, doi: 10.3389/fgene.2019.00055.【PDF】
  15. 冷容、胡彦婷、周艳丽、金桂花、李玲、石勇、杨红、桂大萍、薛润光、章成君. 人参种胚不同后熟发育阶段比较转录组学分析[J]. 分子植物育种, 2020, v.18(17):112-123.【PDF】
  16. Yang H, Li P, Jin G, Gui D, Liu L#, Zhang C# (2020) Temporal regulation of alternative splicing events in rice memory under drought stress, Plant Diversity, doi: 10.1016/j.pld.2020.11.004.【PDF】
  17. Fang C, Gan X, Zhang C, He S# (2020) The new chimeric chiron genes evolved essential roles in zebrafish embryonic development by regulating NAD+ levels, Science China Life Sciences, doi: 10.1007/s11427-020-1851-0. 【PDF】
  18. Liu N, Zhang L, Zhaou Y, Tu M, Wu Z, Gui D, Ma Y, Wang J#, Zhang C# (2021) The Rhododendron Plant Genome Database (RPGD): a comprehensive online omics database for Rhododendron, BMC Genomics, 22:376. DOI: 10.1186/s12864-021-07704-0【PDF】
  19. Wang X*, Gao Y*, Wu X* et al., Zhang C#, Zhang L#, Xia Y# (2021) High-quality evergreen azalea genome reveals tandem duplication-facilitated low-altitude adaptability and floral scent evolution, Plant Biotechnol J, doi: 10.1111/pbi.13680.【PDF】
  20. Jin G*, Ma P*, Wu X, Gu L, Long M, Zhang C#, Li D# (2021) New Genes Interacted With Recent Whole-Genome Duplicates in the Fast Stem Growth of Bamboos, Molecular Biology and Evolution, 38(12):5752-5768. doi: 10.1093/ molbev/msab288.【PDF】
  21. Hu Y*, Wu X, Jin G, et al., Chuanzhu Fan#, Zhang C# (2021) Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications, Front. Plant Sci., doi: 10.3389/fpls.2021.772655.【PDF】
  22. Zhou Y*, Lu L, et al., Wang J#, Zhang C# (2021) Analysis of MYB genes in four plant species and the detection of those associated with drought resistance, Botany, doi: 10.1139/cjb-2020-0227.【PDF】
  23. Chen W, Wan H, Liu F, Du H, Zhang C#, Fan W#, Zhu A# (2022) Rapid evolution of T2/S-RNase genes in Fragaria linked to multiple transitions from self-incompatibility to self-compatibility, Plant Diversity, doi: 10.1016/j.pld.2022.04.003.【PDF】
  24. Zhou Y, Zhang C#, Zhang L, Ye Q, Liu N, Wang M, Long G, Fan W, Long M#, Wing R# (2022) Gene Fusion as an Important Mechanism to Generate New Genes in the Genus Oryza, Genome Biology, 23:130.【PDF】
  25. Li K*, Wu Z*, et al., Zhang C#, Sun Q# (2022) R-loopAtlas: an integrated R-loop resource from 254 plant species sustained by a deep learning-based tool, MP, doi: 10.1016/j.molp.2022.12.012.【PDF】
  26. Zhou Y, Zhang J, et al., Yang Y, Zhang C, Yang Y# (2022) Cold Tolerance of ScCBL6 Is Associated with Tonoplast Transporters and Photosynthesis in Arabidopsis, Current Issues in Molecular Biology, doi: 10.3390/cimb44110378.【PDF】
  27. Wu X*, Zhang L*, Wang X, et al., Ma Y#, Zhang C#, Wang J# (2023) Evolutionary history of two evergreen Rhododendron species as revealed by chromosome-level genome assembly, Front. Plant Sci., doi: 10.3389/fpls.2023.1123707.【PDF】

2011-2014（博士后阶段）

  1. Hu Y, Liu D, Zhong X, Zhang C, Zhang Q, Zhou DX (2012) CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome, Proc Natl Acad Sci USA, 109(15): 5773-5778.【PDF】
  2. Zhou G, Chen Y, Yao W, Zhang C, Xie W, Hua J, Xing Y, Xiao J, and Zhang Q (2012) Genetic composition of yield heterosis in an elite rice hybrid, Proc Natl Acad Sci USA, 109(39):15847-15852.【PDF】
  3. Zhang C*, Wang J*, Long M, Fan C (2013) gKaKs: The pipeline for genome level Ka/Ks calculation, Bioinformatics, doi: 10.1093/bioinformatics/btt009.【PDF】
  4. Yan W, Liu H, Zhou X, Li Q, Zhang J, Lu L, Liu T, Liu H, Zhang C, Zhang Z, Shen G, Yao W, Chen H, Yu S, Xie W, Xing Y (2013) Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice, Cell Research, doi: 10.1038/cr.2013.43.【PDF】
  5. Zhang C*, Wang J*, Marowsky NC, Long M, Rod AW, Fan C (2013) High Occurrence of Functional New Chimeric Genes in Survey of Rice Chromosome 3 Short Arm Genome Sequences, Genome Biology and Evolution, doi: 10.1093/gbe/evt071.【PDF】
  6. Zhang C, Gschwend RA, Ouyang Y, Long M (2014) , Evolution of gene structural complexity: An alternative-splicing based model accounts for intron-containing retrogenes, Plant Physiology, doi: 10.1104/pp.113.231696.【PDF】

2008-2011（博士生阶段）

  1. Nayidu NK, Wang L, Xie W, Zhang C, Fan C, Lian X, Zhang Q, Xiong L (2008) Comprehensive sequence and expression profile analysis of PEX11 gene family in rice. Gene 412:59-70.【PDF】
  2. Nuruzzaman M, Gupta M, Zhang C, Wang L, Xie W, Xiong L, Zhang Q and Lian X (2008) Sequence and expression analysis of the thioredoxin protein gene family in rice. MGG 280:139-151.【PDF】
  3. Gupta M, Qiu X, Wang L, Xie W, Zhang C, Xiong L, Lian X, Zhang Q (2008) KT/HAK/KUP potassium transporters gene family and their whole-life cycle expression profile in rice (Oryza sativa). MGG 280:437-52.【PDF】
  4. Xie W, Chen Y, Zhou G, Wang L, Zhang C, Zhang J, Xiao J, Zhu T, Zhang Q (2009) Single feature polymorphisms between two rice cultivars detected using a median polish method. Theor Appl Genet 119:151-164.【PDF】
  5. Xia J, Hu X, Shi F, Niu X and Zhang C (2010) Support vector machine method on predicting resistance gene against Xanthomonas oryzae pv. oryzae in rice. Expert Systems with Applications 37:5946-5950. 【PDF】
  6. Du H, Ouyang Y, Zhang C, Zhang Q (2011) Complex evolution of S5, a major reproductive barrier regulator, in the cultivated rice Oryza sativa and its wild relatives, New Phytologist, 2011, 191:275-287.【PDF】
  7. Zhang C, Wang J, Xie W, Zhou , Long M , Zhang Q (2011) Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method, Proc Natl Acad Sci USA, 2011, 108(19):7860-7865.【PDF】