陈玲玲 教授，博士,博士生导师/硕士生导师
E-mail: llchen@gxu.edu.cn
个人简介：
2004年毕业于天津大学生物物理专业，获理学博士学位。近些年主要从事作物多组学数据整合挖掘及生物信息工具开发，菌植互作多组学分析等方向的研究工作，作为生物信息负责人主导和参与了水稻、玉米、油菜、甜橙等多种作物基因组解析工作，所开发的植物单链导向RNA设计工具CRISPR-P系列得到了国内外研究者的广泛关注。近十年来在Nat. Genetics, Nat. Plants, PNAS，Nat. Commun., Science Advances, Nucleic Acids Res., Mol. Plant, Genome Biol.等国际顶级及知名期刊发表SCI论文110余篇，其中第一或通讯作者70余篇，他引9100余次。担任国际知名期刊Front. Plant Sci.的 Plant Bioinformatics分刊主编，SCI一区期刊 Hortic. Res.副主编，《基因组学与应用生物学》执行主编。主持国家十三五重点研发计划专项课题两项，国家自然科学基金六项，广西科技重大专项及创新群体项目。获国家级及省部级人才称号，获国务院政府特殊津贴。
教学和科研成果：
1、对水稻、玉米、油菜、甜橙等多种重要农作物、经济作物基因组进行了深入研究，首次构建了水稻T2T无空缺（gap-free）参考基因组及油菜泛基因组，助力作物遗传育种。得到了国内外专家高度评价，为作物基因组设计育种奠定了坚实基础。
2、开发了植物单链导向RNA设计CRISPR-P系列生物信息工具及数据库，是目前国际上最为通用的植物基因编辑sgRNA设计工具，为136个国家和地区的11万多研究人员提供了服务。
3、指导多名博士、硕士研究生及本科生获校级或省级优秀论文。
主持承担的主要科研项目：
广西自然科学基金创新研究团队项目（2024.4-2028.3）野生稻资源育种信息平台开发及种质创新利用（2023JJF130001），主持
国家自然科学基金面上项目（2023.1-2026.12），整合多组学数据及网络分析挖掘百香果抗冷关键调控因子及功能验证（32270712），主持
广西科技重大专项（2023.11-2026.10）广西特色优势水果土壤微生态调控、功能菌发掘及活性功能代谢物鉴定（桂科AA23062085），主持
十三五重点研发计划（2016.7-2020.12）水稻功能基因组研究与应用课题四（2016YFD0100904），主持
十三五重点研发计划（2018.7-2022.12）多年生园艺作物无性系变异和繁殖的基础与调控（2018YFD1000101），项目骨干成员
国家自然科学基金面上项目（2019.1-2022.12），利用核糖体印记识别可翻译的水稻短开放阅读框及初步功能研究（31871269），主持
研究方向：
1、作物多组学数据整合及挖掘
2、作物生物信息工具开发及数据库构建
3、作物微生物组及菌植互作多组学分析
代表性论文：
Zhong Y, Luo Y, Sun J, Qin X, Gan P, Zhou Z, Qian Y, Zhao R, Zhao Z, Cai W, Luo J*, Chen LL*, Song JM*. Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice. Plant Cell 2024, 36(6):2117-2139.
Zheng YY, Chen LH, Fan BL, Xu Z, Wang Q, Zhao BY, Gao M, Yuan MH, Tahir Ul Qamar M, Jiang Y, Yang L, Wang L, Li W, Cai W, Ma C, Lu L*, Song JM*, Chen LL*. Integrative multi-omics profiling of passion fruit reveals the genetic basis for fruit color and aroma. Plant Physiol. 2024, 194(4):2491-2510.
Xie WZ, Zheng YY, He W, Bi F, Li Y, Dou T, Zhou R, Guo YX, Deng G, Zhang W, Yuan MH, Sanz-Jimenez P, Zhu XT, Xu XD, Zhou ZW, Zhou ZW, Feng JW, Liu S, Li C, Yang Q, Hu C, Gao H, Dong T, Dang J, Guo Q, Cai W, Zhang J, Yi G, Song JM, Sheng O, Chen LL*. Two haplotype-resolved genome assemblies for AAB allotriploid bananas provide insights into banana subgenome asymmetric evolution and Fusarium wilt control. Plant Commun. 2024, 5(2):100766.
Zhu XT, Zhou R, Che J, Zheng YY, Tahir Ul Qamar M, Feng JW, Zhang J, Gao J, Chen LL. Ribosome profiling reveals the translational landscape and allele- specific translational efficiency in rice. Plant Commun. 2023, 4(2):100457.
Feng JW, Han L, Liu H, Xie WZ, Liu H, Li L*, Chen LL*. MaizeNetome: A multi-omics network database for functional genomics in maize. Mol Plant. 2023, 16(8):1229-1231.
Xu XD, Zhao RP, Xiao L, Lu L, Gao M, Luo YH, Zhou ZW, Ye SY, Qian YQ, Fan BL, Shang X, Shi P, Zeng W, Cao S, Wu Z, Yan H, Chen LL, Song JM. Telomere-to-telomere assembly of cassava genome reveals the evolution of cassava and divergence of allelic expression. Hortic Res. 2023, 10(11):uhad200.
Liu H, Wang X, Liu S, Huang Y, Guo YX, Xie WZ, Liu H, Tahir Ul Qamar M, Xu Q*, Chen LL*. Citrus Pan-genome to Breeding Database (CPBD): A comprehensive genome database for citrus breeding. Mol Plant 2022, 15(10):1503-1505.
Wang S, Xiao Y, Zhou ZW, Wang X, Chen LL*, Luo J*. Cocos nucifera (coconut). Trends Genet. 2022, 38(10):1096-1097.
Wang S, Xiao Y, Zhou ZW, Yuan J, Guo H, Yang Z, Yang J, Sun P, Sun L, Deng Y, Xie WZ, Song JM, Qamar MTU, Xia W, Liu R, Gong S, Wang Y, Wang F, Liu X, Fernie AR, Wang X*, Fan H*, Chen LL*, Luo J*. High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height. Genome Biol. 2021, 22(1):304.
He C#, Liu H#, Chen D, Xie WZ, Wang M, Li Y, Gong X, Yan W*, Chen LL*. CRISPR-Cereal: a guide RNA design tool integrating regulome and genomic variation for wheat, maize and rice. Plant Biotechnol J. 2021, 19(11):2141-2143.
Song JM, Xie WZ, Wang S, Guo YX, Koo DH, Kudrna D, Gong C, Huang Y, Feng JW, Zhang W, Zhou Y, Zuccolo A, Long E, Lee S, Talag J, Zhou R, Zhu XT, Yuan D, Udall J, Xie W, Wing RA, Zhang Q, Poland J*, Zhang J*, Chen LL*. Two Gap-free Reference Genomes and a Global View of the Centromere Architecture in Rice. Mol Plant 2021, 14(10):1757-1767.
Zhang Q, Hu J, Feng JW, Hu XT, Wang T, Gong WX, Huang K, Guo YX, Zou Z, Lin X, Zhou R, Yuan YQ, Zhang AD, Wei H, Cao G, Liu C*, Chen LL*, Jin ML*. Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection. Genome Biol. 2020, 21(1):99.
Song JM, Guan Z, Hu J, Guo C, Yang Z, Wang S, Liu D, Wang B, Lu S, Zhou R, Xie WZ, Cheng Y, Zhang Y, Liu K*, Yang QY*, Chen LL*, Guo L*. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat Plants 2020, 6(1):34-45.
Sturtevant D, Lu S, Zhou ZW, Shen Y, Wang S, Song JM, Zhong J, Burks DJ, Yang ZQ, Yang QY, Cannon AE, Herrfurth C, Feussner I, Borisjuk L, Munz E, Verbeck GF, Wang X, Azad RK, Singleton B, Dyer JM, Chen LL*, Chapman KD*, Guo L*. The genome of jojoba (Simmondsia chinensis): A taxonomically isolated species that directs wax ester accumulation in its seeds. Sci Adv. 2020, 6(11):eaay3240.
Sun J, Liu H, Liu J, Cheng S, Peng Y, Zhang Q, Yan J, Liu HJ*, Chen LL*. CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes. Bioinformatics 2019,35(14): 2501-2503.
Song JM, Lei Y, Shu CC, Ding Y, Xing F, Liu H, Wang J, Xie W, Zhang J*, Chen LL*. Rice Information GateWay: a comprehensive boinformatics platform for indica rice genomes. Mol. Plant 2018, 11(3): 505-507.
Yang N, Xu XW, Wang RR, Peng WL, Cai L, Song JM, Li W, Luo X, Niu L, Wang Y, Jin M, Chen L, Luo J, Deng M, Wang L, Pan Q, Liu F, Jackson D, Yang X, Chen LL*, Yan J*. Contributions of Zea mays subspecies mexicana haplotypes to modern maize. Nat Commun. 2017, 8(1):1874.
Liu H, Ding Y, Zhou Y, Jin W, Xie K*, Chen LL*. CRISPR-P 2.0: An Improved CRISPR-Cas9 Tool for Genome Editing in Plants. Mol. Plant 2017, 10: 530-532.
Zhang J#, Chen LL#, Xing F#, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song JM, Xie W, Lee S, Talag J, Shao L, An Y, Zhang CL, Ouyang Y, Sun S, Jiao WB, Lv F, Du B, Luo M, Maldonado CE, Goicoechea JL, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou ZW, Hurtado BE, Danowitz A, Wing RA*, Zhang Q*. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc Natl Acad Sci USA 2016, 113(35):E5163-71.
Xu Q#, Chen LL#, Ruan X#, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX*, Ruan Y*. The draft genome of sweet orange (Citrus sinensis). Nat Genet. 2013, 45(1):59-66.
