Professor Lingling Chen, Ph.D., Doctoral and Master's Supervisor

Contact

E-mail: llchen@gxu.edu.cn

Biography

Professor Lingling Chen graduated from Tianjin University in 2004 with a Ph.D. in Biophysics. In recent years, her research has primarily focused on bioinformatics, including plant genome assembly and annotation, transcriptome data analysis, and functional gene identification. As the head of bioinformatics, she has participated in the genomic analysis of rice, maize, and sweet orange. The plant single-guide RNA design tool CRISPR-P developed by her group have received widespread attention from researchers both domestically and internationally. Over the past decade, she has published more than 110 SCI papers in top-tier and well-known international journals, including Nature Genetics, Nature Plants, PNAS, Nature Communications, Science Advances, Nucleic Acids Research, Molecular Plant, and Genome Biology, with 72 of these as the first or corresponding author. Her work has been cited over 9100 times. She has led two special projects under the National Key R&D Program of China and six projects under the National Natural Science Foundation of China. She has received the national and provincial level talent awards and the State Council's special government allowance.

Teaching and Research Achievements

1. We have conducted in-depth research on the genomes of various important and economic crops such as rice, corn, rapeseed, and sweet orange. We have constructed a gap free reference genome for rice T2T and a pan genome for rapeseed for the first time to assist in crop genetic breeding. Highly praised by domestic and foreign experts, it has laid a solid foundation for crop genome design and breeding.

2. Developed the CRISPR-P series of bioinformatics tools and databases for plant single stranded RNA design, which is currently the most widely used plant gene editing sgRNA design tool internationally, providing services to over 110,000 researchers in 136 countries and regions.

3. Guide multiple doctoral, master's, and undergraduate students to obtain excellent academic papers at the university or provincial level.

Fundings

1.    Guangxi Natural Science Foundation (2024.4-2028.3): Development of Wild Rice Resource Breeding Information Platform and Innovative Utilization of Germplasm (2024GXNSFGA010003)

2.    National Natural Science Foundation of China (2023.1-2026.12): Integrating multiple omics data and network analysis to mine key regulatory factors and functional validation of cold resistance in passion fruit (32270712)

3.    Guangxi Science and Technology Major Program (2023.11-2026.10): Microecological regulation of soil, exploration of functional bacteria, and identification of active functional metabolites in Guangxi's characteristic and advantageous fruits (AA23062085)

4.    National Key R&D Program (2016.7-2020.12): Project 4 of Rice Functional Genomics Research and Application (2016YFD0100904)

5.    National Key R&D Program (2018.7-2022.12): Basic Research and Regulation of Clonal Variation and Propagation in Perennial Horticultural Crops (2018YFD1000101)

6.    National Natural Science Foundation of China (2019.1-2022.12): Identification and Preliminary Functional Study of Translatable Short Open Reading Frames in Rice Using Ribosome Footprinting (31871269)

Research Interests

1. Integration and mining of crop multi omics data

2. Development of crop bioinformatics tools and database construction

3. Multiomics analysis of crop microbiome and microbial plant interaction

Selected Publications

1.    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.

2.    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.

3.    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.

4.    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.

5.    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.

6.    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.

7.    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.

8.    Wang S, Xiao Y, Zhou ZW, Wang X, Chen LL*, Luo J*. Cocos nucifera (coconut). Trends Genet. 2022, 38(10):1096-1097.

9.    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.

10.    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.

11.    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.

12.    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.

13.    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.

14.    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.

15.    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.

16.    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.

17.    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.

18.    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.

19.    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.

20.    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.