林木生物信息学-蛋白组学研究中心

林木生物信息学 ( Plant Bioinformatics )

主任(PI): 顾连峰（Lianfeng Gu, PhD）

团队成员(Members)：张航晓（Hangxiao Zhang,PhD），王汇源（Huiyuan Wang），王慧慧（Huihui Wang），张泽宇（Zeyu Zhang），刘旭庆（Xuqing Liu），赵良真（Liangzhen Zhao）

PI简介(PI Introduction)：

顾连峰，博士生导师。2012年获得中国科学院生物信息学博士学位，2015年从美国加州大学河滨分校访学回国，受聘为福建农林大学林学中心全职教授。第十四届林业青年科技奖获得者。2016年入选福建省C类引进高层次人才，2017年获福建农林大学“金山学者”荣誉称号。以福建农林大学为依托单位主持2015年国家自然科学基金面上项目“自毒胁迫下杉木可变剪接与microRNA相互调控网络研究”，承担2016 年国家重点研发专项“林业资源培育及高效利用技术创新”课题六“林木次生生长的分子调控和环境胁迫机制”子课题；承担2018 年国家重点研发专项“竹资源高效培育关键技术研究”中课题一“竹子生长发育机制与性状评价”子课题；在PNAS、Cell Research、Plant Journal、Bioinformatics等权威期刊上发表相关文章三十篇。目前主要从事生物信息学和林木遗传改良相关研究。

实验室网址：www.bioinfor.org

电子邮箱：lfgu@fafu.edu.cn
研究领域（Research focus）:
开发生物信息学软件解析来自高通量技术所产生的大批量数据，从基因组、转录组和蛋白质组等组学数据中挖掘林木次生生长的规律。结合二代和三代高通量测序及蛋白组学数据开展重要速生树种（毛竹、杉木和杨树）的基因表达调控网络研究。并深入开展转录后调控网络研究，为林木遗传改良提供理论依据。

Developing bioinformatics methods and computational tools to analyze large-scale datasets from high throughput technologies to understand the massive amounts of information at system level including genome, transcriptome and proteome. Application of next-generation sequencing technologies, proteomics, and bioinformatics on crop species, including bamboo, China fir, rice and maize, to infer gene regulatory networks by integrating omics data. Investigation of the interplay between different post-transcriptional regulation mechanisms to provide theoretical basis for improving production of important crop species.

发表文章(Publications):

2023

Jin Y,Wang B,Bao M,Li Y,Xiao S,Wang Y,Zhang J,Zhao L,Zhang H,Hsu Y,Li M,Gu L. (2023) Development of an efficient expression system with large cargo capacity for interrogation of gene function in bamboo based on bamboo mosaic virus. J Integr Plant Biol.https://doi.org/10.1111/jipb.13468.

Wang Y,Wang H,Wang H,Zhou R,Wu J,Zhang Z,Jin Y,Li T,Kohnen M,Liu X,Wei W,Chen K,Gao Y,Ding J,Zhang H,Liu B,Lin C,Gu L. (2023) Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis). Genomics, Proteomics & Bioinformatics. https://doi.org/10.1016/j.gpb.2023.01.007.

Zhang Y,Wei Y,Meng J,Wang Y,Nie S,Zhang Z,Wang Y,Gao Y,Wu J,Li T,Liu X,Zhang H,Gu L. (2023) Chromosome-scale de novo genome assembly and annotation of three representative Casuarina species: C. equisetifolia, C. glauca, and C. cunninghamiana . Plant Journal. https://doi.org/10.1111/tpj.16201 .

Liao J,Deng B,Yang Q,Li Y,Zhang Y,Cong J,Wang X,Kohnen M,Liu Z,Lu M,Lin D,Gu L,Liu B.(2023) Insights into Cryptochrome Modulation of ABA Signaling to Mediate Dormancy Regulation in Marchantia polymorpha. New Phytol.238(4):1479-1497.

2022

Gao Y,Liu X,Jin Y,Wu J,Li S,Li Y,Chen B,Zhang Y,Wei L,Li W,Li R,Lin C,Reddy A,Jaiswal R,Gu L.(2022) Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa. Plant Physiology. https://doi.org/10.1093/plphys/kiac272.

Li T,Wang H,Zhang Y,Wang H,Zhang Z,Liu X,Zhang Z,Liu K,Yang D,Zhang H,Gu L.(2022) Comprehensive profiling of epigenetic modifications in fast-growing moso bamboo shoots. Plant Physiology. https://doi.org/10.1093/plphys/kiac525.

Zhang Z,Wang H,Wu J,Jin Y,Xiao S,Li T,Liu X,Zhang H,Zhang Z,Su J,Liu J,Wang X,Gao Y,Ma X and Gu L. (2022) Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata.Frontiers in Genetics. https://doi.org/10.3389/fgene.2022.843269.

Zheng Y,Yang D,Rong J,Chen L,Zhu Q,He T,Chen L,Ye J,Fan L,Gao Y,Zhang H,Gu L.(2022) Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma Bamboo (Dendrocalamus latiflorus Munro). Journal of Integrative Plant Biology. https://doi.org/10.1111/jipb.13217.

2021

Wang X, Jiang B, Gu L, Chen Y, Mora M, Zhu M, Noory E, Wang Q, Lin C.(2021) A photoregulatory mechanism of the circadian clock in Arabidopsis.Nature Plants.7(10):1397-1408.

Zhang Z, Wang H, Wang Y, Xi F, Wang H, Kohnen MV, Gao P, Wei W, Chen K, Liu X, Gao Y, Han X, Hu K, Zhang H, Zhu Q, Zheng Y, Liu B, Ahmad A, Hsu YH, Jacobsen SE, Gu L. (2021) Whole genome characterization of chronological age-associated changes in methylome and circular RNAs in moso bamboo (Phyllostachys edulis) from vegetative to floral growth. Plant J. doi: 10.1111/tpj.15174. Gao Y, Liu X, Wu B, Wang H, Xi F, Kohnen MV, Reddy ASN, Gu L. (2021) Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing. Genome Biol.22(1):22. doi: 10.1186/s13059-020-02241-7.

2020

Wang Y, Wang H, Xi F, Wang H, Han X, Wei W, Zhang H, Zhang Q, Zheng Y, Zhu Q, Kohnen MV, Reddy ASN, Gu L. (2020) Profiling of circular RNA N6 -methyladenosine in moso bamboo (Phyllostachys edulis) using nanopore-based direct RNA sequencing. J Integr Plant Biol. 62(12):1823-1838.

2018-2019

Gao Y, Xi F, Zhang H, Liu X, Wang H, Zhao L, Reddy A, Gu L.(2019) Single-molecule real-time (SMRT) isoform sequencing (Iso-Seq) in plants: The status of the bioinformatics tools to unravel the transcriptome complexityCurrent Bioinformatics （14）:566-573.

Wang Q, Zuo Z, Wang X, Liu Q, Gu L, Oka Y, Lin C.(2018) Beyond the photocycle – how cryptochromes regulate photoresponses in plants?Current Option in Plant Biology45:120-126.
Zhang H, Wang H, Zhu Q, Gao Y, Wang H, Zhao L, Wang Y, Xi F, Wang W, Yang Y, Lin C, Gu L.(2018) Transcriptome characterization of moso bamboo (Phyllostachys edulis) seedlings in response to exogenous gibberellin applicationsBMC plant biology18(1):125. doi: 10.1186/s12870-018-1336-z.

2017

Taotao Wang , Huiyuan Wang, Dawei Cai, Yubang Gao, Hangxiao Zhang,Yongsheng Wang , Chentao Lin , Liuyin Ma , Lianfeng Gu .(2017) Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis) The Plant Journal doi: 10.1111/tpj.13597.

2016

Wang Q,Zuo Z C,Wang X,Gu L F, Yoshizumi T,Yang,Z H,Liu Q,Liu W,Han Y J,Liu B, Wohlschlegel J A, Matsui M, Oka Y and Lin C.(2016) Photoactivation and inactivation mechanisms of Arabidopsis cryptochrome2 Science354:343-347.

Li C, Gu L, Gao L, Chen C, Wei C, Qiu Q, Chien C, Wang S, Jiang L, Chen C, Yang S, Nguyen V, Snyder M, Burlingame A, Kohalmi S, Huang S, Cao X, Wang Z, Wu K, Chen X, Cui Y. (2016) Concerted genomic targeting of histone H3 lysine 27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis Nature genetics48(6):687-693.
      Wu, Z, Zhu D, Lin X, Miao L, Gu L, Deng X, Yang Q, Sun K, Zhu D, Cao X, TSUGE T, Dean C, Aoyama T, Gu H, Qu L. (2016) RNA-binding proteins At RZ-1B and At RZ-1C play a critical role in regulation of pre-mRNA splicing and gene expression during Arabidopsis development The Plant Cell28(1):55-73.
      Yan H, Zhang H, Wang Q, Jian H, Qiu X, Baudino S, Just J, Raymond O, Gu L, Jihua W, Bendahmane M and Tang K. (2016) The Rosa chinensis cv. Viridiflora phyllody phenotype is associated with misexpression of flower organ identity genes Front Plant Sci (12)7:996. doi: 10.3389/fpls.
      Li S, Zhang G, Zhang X, Yuan J, Deng C, Gu L, Gao W.( 2016) DPTEdb, an integrative database of transposable elements in dioecious plants Database 5(12) baw078 doi:10.1093/database/baw078.
     Cui X, Lu F, Qiu Q, Zhou B, Gu L, Zhang S, Kang Y, Cui X, Ma X, Yao Q, Ma J, Zhang X, Cao X. (2016) REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis Nature genetics48(6):694-699.
     Deng X, Lu T, Wang L, Gu L, Sun J, Kong X, Liu C, Cao X. (2016) Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5 PNAS 113(19):5447-5452.
     Zhang S, Xu M, Qiu Z, Wang K, Du Y, Gu L, Cui X.(2016) Spatiotemporal transcriptome provides insights into early fruit development of Solanum lycopersicum Sci Rep18;6, 23173; doi: 10.1038/srep23173.

2015

Zhang Y, Gu, L, Hou, Y, Wang L, Deng, X, Hang, R, Chen, D, Zhang, X, Zhang, Y, Liu, C, and Cao, X. (2015) Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein， regulates plant flowering by targeted alternative polyadenylation Cell Research25(7):864-876.

2014
      Zhou H, Zhou M, Yang Y, Li J, Zhu L, Jiang D, Dong J, Liu Q, Gu L, Zhou L., Cao X, Zhuang C. (2014) RNAase Zs1 processes UBL40 mRNA and controls thermo-sensitive genic male sterility in rice NATURE COMMUNICATIONSdoi:10.1038/ncomms5884.
      Wei L, Gu L, Song X, Cui X, Lu Z, Zhou M, Wang L, Hu F, Zhai J, Meyer B, Cao X. (2014) Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice Proc Natl Acad Sci U S A111: 3877-3882.
      Wu B, Suo F, Lei, W and Gu, L.(2014) Comprehensive Analysis of Alternative Splicing in Digitalis purpurea by Strand-Specific RNA-Seq PLoS One9, e106001.

Before 2014
      Cui X, Jin P., Cui X, Gu L, Lu Z, Xue Y, Wei L, Qi J, Song X, Luo M, Gynheung An, Cao X. (2013) Control of Transposon Activity by a Histone H3K4 Demethylase in Rice Proc Natl Acad Sci U S A110(5):1953-1958.
      Wang L, Song X, Gu L, Li X, Cao S, Chu C, Cui X, Chen X, and Cao X. (2013) NOT2 proteins promote polymerase II-dependent transcription and interact with multiple MicroRNA biogenesis factors in Arabidopsis Plant Cell25: 715-727.
      Zhang L, Cheng Z, Qin R, Qiu Y, Wang J, Cui X, Gu L, Zhang X, Guo X, Wang D, Jiang L, Wu C, Wang H, Cao X, Wan J. (2012) Identification and Characterization of an Epi-1 allele of OsFIE1 Reveals a Regulatory Linkage between two Epigenetic Marks in Rice Plant Cell24: 4407-4421.
      Deng X, Gu L, Liu C, Lu T, Lu F, Lu Z, Cui P, Pei Y, Wang B, Hu S, and Cao X. (2010) Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing Proc Natl Acad Sci U S A 107: 19114-19119.
      Zhou M, Gu L, Li P, Song X, Wei L, Chen Z. and Cao X. (2010) Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica) Front. Biol5: 67–90.
      Gu,L and Guo,R.(2007) Genome-wide detection and analysis of alternative splicing for nucleotide binding site-leucine-rich repeats sequences in rice J Genet Genomics34: 247-257.