Education Background

• D.in Fish Genetics & Genomics, Auburn University, Auburn, AL, August, 2012
  • DISSERTATION: “Understanding Teleost Genome Structure and Organization: AlternativeSplicing, Gene Duplication, and Whole Genome Assembly”
• M. S. in CSSE, Auburn University, Auburn, AL, May 2011
  • THESIS: “MPI-Velvet: A Next Generation Sequence Assembler”
• M. S. in Molecular Ecology,Nankai University, Tianjin, China, June 2006
• B. S. in Plant Ecology, Inner Mongolia University, Huhehot, China, June 2003

 

Professional Experiences 

• 2023.6–Present  Professor/Director/PI

Marine Ecological Genomics Institute

School of Marine Sciences, Sun Yat-Sen University

RESEARCH INTERESTS:

• Marine Ecological Genomics.
• Genomic Resources Discovery & Utilization of Marine Species.
• Big Data in FishSpecies Omics Data.
• Population Genetics and Evolutionary Genomics.
• Fish Species Sex Determination Mechanism.

 

• 2017–Present  Associate  Professor/Director/PI

Marine Ecological Genomics Institute

School of Marine Sciences, Sun Yat-Sen University

RESEARCH INTERESTS:

• Marine Ecological Genomics.
• Genomic Resources Discovery & Utilization of Marine Species.
• Big Data in FishSpecies Omics Data.
• Population Genetics and Evolutionary Genomics.
• Fish Species Sex Determination Mechanism.

 

• 2012–2017  Associate Professor/ Associate Director

National and Local United Engineering Lab for Freshwater fish breeding, Harbin, China

RESEARCH INTERESTS:

• Successfully completedthe yellow catfish whole genome sequencing using NGS approach. Including genome assembly, high definition linkage map, sex chromosomal evolutionary pattern, and teleost specific genome duplication event.
• Investigate sex determination/differential genes by analyzing high-throughput transcriptomic sequencing of yellow catfish at different growth stages and elucidate the sex determination mechanism of yellow catfish.
• Collaborating with collages on common carp whole genome project, curcian carp whole genome project, and Amur Ide whole genome project.

 

• 2007–2012  Graduate Research Assistant

Auburn Fisheries & Allied Aquacultures,

Fish Genetics & Genomics Lab, Auburn AL

RESEARCH INTERESTS:

• Investigate alternative splicing and gene duplication pattern on teleost fish species using comparative genomics
• Successfully completedcatfish whole genome sequencing using next-generation sequencing technology
• Collaborated with five visiting scholars and advised 15 graduate students on their projects and journal papers

 

• 2006 – 2007 Assistant Professor

Heilongjiang River Fisheries Research Institute, CAFS

RESEARCH INTERESTS:

• Constructed common carp cDNA normalization library and cloned five economically related genes
• Initiated projects for five graduate students and advised them on their journal papers

 

Rewards and Honors

• “100 Young talents”in Sun Yat-sen University, 2017
• “Young Talents Scientist ”in Chinese Academy of Fisheries Sciences, 2015
• H. S. Swingle Award, Auburn University, 2011
• Outstanding International Graduate Student Award, Auburn University, 2011
• NRSP-8 Travel Fellowship, 18^thPlant and Animal Genome Conference, 2010
• NRSP-8 Travel Fellowship, 19^thPlant and Animal Genome Conference, 2011
• Graduate Research Scholars Program (GRSP) Scholarship, Alabama EPSCoR, 2011
• Graduate Research Scholars Program (GRSP) Scholarship, Alabama EPSCoR, 2012
• Chinese Scholarship Council Fellowship, 2007-2010

 

Peer-Reviewed Publication:

1. Lu J*, Huang P, Sun J, Liu J. DupScan: predicting and visualizing vertebrate genome duplication database. Nucleic Acids Res. 2022 Aug. IF=19.16
2. Fang W, Huang J, Li S, Lu J*. Identification of pigment genes (melanin, carotenoid and pteridine) associated with skin color variant in red tilapia using transcriptome analysis. Aquaculture. 2022. IF=4.242
3. Lu, J*., Gao, D., Sims, Y. et al. Chromosome-level Genome Assembly of Acanthopagrus latus Provides Insights into Salinity Stress Adaptation of Sparidae. Mar Biotechnol 24, 655–660 (2022). 
4. Genmei Lin, Junrou Huang, Kunwen Luo, Xianbiao Lin, Ming Su, Jianguo Lu*. Bacterial, archaeal, and fungal community structure and interrelationships of deep-sea shrimp intestine and the surrounding sediment. Environmental Research, 2022, 205: 112461.
5. Gao, D., Huang, J., Lin, G, Lu J*. A time-course transcriptome analysis of gonads from yellow catfish (Pelteobagrus fulvidraco) reveals genes associated with gonad development. BMC Genomics 23 (Suppl 1), 409 (2022).
6. Huang, J., Huang, P., Lu J*. et al. Gene expression profiles provide insights into the survival strategies in deep-sea mussel (Bathymodiolus platifrons) of different developmental stages. BMC Genomics 23 (Suppl 1), 311 (2022).
7. Liu, H., Lin, G., Gao, D. et al Lu J*. Geographic Scale Influences the Interactivities Between Determinism and Stochasticity in the Assembly of Sedimentary Microbial Communities on the South China Sea Shelf. Microb Ecol 2022
8. Lin G, Lu J*, Sun Z, Xie J, Huang J, Su M, Wu N*. Characterization of tissue-associated bacterial community of two Bathymodiolus species from the adjacent cold seep and hydrothermal vent environments. Science of the Total Environment. 2021, 796: 149046.
9. Lin G, Huang J, Lu J, Su M, Hu B, Lin X*. Geochemical and microbial insights into vertical distributions of genetic potential of N-cycling processes in deep-sea sediments. Ecological Indicators. 2021, 125: 107461.
10. Lin G, Li S, Huang J, Gao D, Lu J*. Hypoosmotic stress induced functional alternations of intestinal barrier integrity, inflammatory reactions, and neurotransmission along gut-brain axis in the yellowfin seabream (Acanthopagrus latus). Fish Physiology and Biochemistry. 2021.
11. Liu H, Prajapati V*, Prajapati S, Bais H, Lu J. Comparative genome analysis of Bacillus amyloliquefaciens focusing on phylogenomics, functional traits, and prevalence of antimicrobial and virulence genes. Frontiers in Genetics. 2021.
12. Lin G, Gao D, Lu J*, Sun X. Transcriptome profiling insights the sexual dimorphism of gene expression patterns during gonad differentiation in the half-smooth tongue sole (Cynoglossus semilaevis). Marine Biotechnology. 2021, 23: 18-30.
13. Lu J*, Fang W, Huang J, Li S. The application of genome editing technology in fish. Marine Life Science & Technology. 2021, 3: 326-346.
14. Lin G, He Y, Lu J, Chen H, Feng J*. Seasonal variations in soil physicochemical properties and microbial community structure influenced by Spartina alterniflora invasion and Kandelia obovata restoration. Science of the Total Environment. 2021, 797: 149213. 1区Top, IF=7.963
15. GaoD, Zheng M, Lin G, Fang W, Huang J, Lu J*, Sun Construction of high-density genetic map and mapping of sex-related loci in the yellow catfish (Pelteobagrus fulyidraco). Marine Biotechnolgy.2020. DOI: 10.1007/s10126-019-09928-4.
16. Zheng M#, Lu J#, Lin G, Su H, Sun J, Luan T. Dysbiosis of gut microbiota bydietary exposure of three graphene-family materials in zebrafish (Danio rerio). Environ Pollut. 2019 Nov;254(Pt A):112969.
17. Jiang L, Feng J, Ying R, Yin F, Pei S, Lu J, Cao Y, Guo J, Li Z. Individualand combined effects of ammonia-N and sulfide on the immune function and intestinal microbiota of Pacific white shrimp Litopenaeus vannamei. Fish Shellfish Immunol. 2019 Sep;92:230-240.
18. Zheng M, Lu J, Zhao D. Toxicity and Transcriptome Sequencing (RNA-seq) Analyses of Adult Zebrafish in Response to Exposure Carboxymethyl Cellulose Stabilized Iron Sulfide Nanoparticles. Sci Rep. 2018 May 24;8(1):8083.
19. Zheng M, Lu J, Zhao D. Effects of starch-coating of magnetite nanoparticles on cellular uptake, toxicity and gene expression profiles in adult zebrafish. Sci Total Environ. 2018 May 1;622-623:930-941.
20. Lu, P. Luan, X. Zhang, S. Xue, L. Peng, S. Mahbooband, X Sun. (2014) Gonadal transcriptomic analysis of yellow catfish (Pelteobagrus fulvidraco): identification of sex-related genes and genetic markers. Physiol Genomics. 1;46(21):798-807.
21. Lu J, Zheng M, Zheng J, et al. Transcriptomic Analyses Reveal Novel Genes with Sexually Dimorphic Expression in Yellow Catfish (Pelteobagrus fulvidraco) Brain[J]. Marine Biotechnology, 2015, 17(5): 613-623.
22. Wang P, Zheng M, Liu J, Liu Y, Lu J*., Sun XSexually Dimorphic Gene Expression Associated with Growth and Reproduction of Tongue Sole (Cynoglossus semilaevis) Revealed by Brain Transcriptome Analysis. Int J Mol Sci. 2016 Aug 26;17(9).
23. Lu, P. Luan, X. Zhang, S. Xue, L. Peng, S. Mahbooband, X Sun. (2014) Gonadal transcriptomic analysis of yellow catfish (Pelteobagrus fulvidraco): identification of sex-related genes and genetic markers. Physiol Genomics. 1;46(21):798-807.
24. Liu Y, Liu J, Lu J, Peng J, Juan L, Zhu X, Li B, Wang Y. Joint detection of copy number variations in parent-offspring trios. Bioinformatics. 2016 Apr 15;32(8):1130-7.
25. Tang, H., Zhang, X., Miao, C., Zhang, J., Ming, R., Schnable, J. C., & Lu, J.(2015). ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biology, 16(1), 3.
26. Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, Koren S, Jiang Y, Zimin A, Xu P, Phillippy AM, Geng X, Song L, Sun F, Li C, Wang X, Chen A, Jin Y, Yuan Z, Yang Y, Tan S, Peatman E, Lu J, Waldbieser GC. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nat Commun. 2016 Jun 2;7:11757. （SCI IF: 11.329）
27. Peng, J. Lu,XW Sun . Mitochondrial DNA sequence of Lampetra morri. Mitochondrial DNA. 2014 Aug 12:1-2.
28. TB Huo, L. Peng, Lu*, ZF Jiang. Complete mitochondrial genome of the Lampetra japonica. Mitochondrial DNA. 2014 Aug 11:1-2.
29. TB Huo, L. Peng, ZF Jiang, Lu*. Complete mitochondrial genome of the Lampetra reissneri. Mitochondrial DNA. 2014 Aug 8:1-2.
30. PX Luan, JG Lu*, SQ Xue, XF Zhang, LN Peng, Sun XW. Mitochondrial DNA genome sequence of Ili marinka (Schizothorax pseudoaksaiensis). Mitochondrial DNA. 2014 Sep 10:1-2
31. Lu, E. Peatman, H. Tang, J. Lewis, and Z. Liu (2012) Profiling of gene duplication patterns of teleost genomes: Evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications. BMC Genomics. 13:246.
32. Li, Y. Zhang, R. Wang, J. Lu, S. Nandi, S. Mohanty, J. Terhune, J. Liu, and E. Peatman. (2012) RNA-seq Analysis of Mucosal Immune Responses Reveals Signatures of Intestinal Barrier Disruption and Pathogen Entry Following Edwardsiella ictaluri Infection in Channel Catfish, Ictalurus punctatus. Fish & Shellfish Immunology. doi: 10.1016/j.fsi.2012.02.004.
33. Jiang, J. Lu, E. Peatman, H. Kucuktas, S. Liu, S. Wang, F. Sun, and Z. Liu. (2012) A Pilot Study for Channel Catfish Whole Genome Sequencing and de novo Assembly. BMC Genomics. 12(1):629.
34. Zhou, H. Liu, S, Liu, F. Sun, E. Peatman, H. Kucuktas, L. Kaltenboeck, T. Feng, H. Zhang, D. Niu, J. Lu, G. Waldbieser, and Z. Liu. (2012) Alternative complement pathway of channel catfish (Ictalurus punctatus): Molecular characterization, mapping and expression analysis of factors Bf/C2 and Df. Fish Shellfish Immunol. 32(1):186-95.
35. Lu,E. Peatman, Q. Yang, S. Wang, Z. Hu, J. Reecy, H. Kucuktas, and Z. Liu. (2011) The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish. Nucleic Acids Research. D815-21.
36. Lu and Z. Liu (2011) Chapter 2: Copy number variations. Next Generation Sequencing and Whole Genome Selection in Aquaculture. 21-33. Wiely-Blackwell.
37. Wong, E. Peatman, J. Lu,H. Kucuktas, S. He, C. Zhou, U. Na-Nakorn, and Z. Liu. (2011) DNA barcoding of catfish: species authentication and phylogenetic assessment. PLoS One. 15; 6(3):e17812.
38. Liu, Z. Zhou, J. Lu, F. Sun, S. Wang, H. Liu, Y. Jiang, H. Kucuktas, L. Kaltenboeck, E. Peatman, and Z. Liu. (2011) Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics. 21:53.
39. Niu, E. Peatman, H. Liu, J. Lu, H. Kucuktas, S. Liu, F. Sun, H. Zhang, T. Feng, Z. Zhou, J. Terhune, G. Waldbieser, J. Li, and Z. Liu. (2011) Microfibrillar-associated protein 4 (MFAP4) genes in catfish play a novel role in innate immune responses. Dev Comp Immunol. 35(5): 568-79.
40. Liu, E. Peatman, W. Wang, J. Abernathy, S. Liu, H. Kucuktas, J. Lu, DH. Xu, P. Klesius, G. Waldbieser, and Z. Liu. Molecular responses of calreticulin genes to iron overload and bacterial challenge in channel catfish (Ictalurus punctatus). Dev Comp Immunol. 35(3): 267-72.
41. Lu, E. Peatman, W. Wang, Q. Yang, J. Abernathy, S. Wang, H. Kucuktas, and Z. Liu. (2010) Alternative splicing in teleost fish genomes: same-species and cross-species analysis and comparisons. Mol Genet Genomics. 283(6):531-9.
42. Abernathy, J. Lu, H. Liu, H. Kucuktas, and Z. Liu. (2009) Molecular characterization of complement factor I reveals constitutive expression in channel catfish. Fish and Shellfish Immunology. 27(3):529-34.
43. Wang, E. Peatman, J. Abernathy, G. Waldbieser, E. Lindquist, P. Richardson, S. Lucas, M. Wang, P. Li, J. Thimmapuram, L. Liu, D. Vullaganti, H. Kucuktas, C. Murdock, B.C. Small, M. Wilson, H. Liu, Y. Jiang, Y. Lee, F. Chen, J. Lu, W. Wang, P. Xu, B. Somridhivej, P. Baoprasertkul, J. Quilang, Z. Sha, B. Bao, Y. Wang, Q. Wang, T. Takano, S. Nandi, S. Liu, L. Wong, L. Kaltenboeck, S. Quiniou, E. Bengten, N. Miller, J. Trant, D. Rokhsar, Z. Liu and the catfish genome consortium. (2010) Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biology 11(1):R8.
44. Lu, H. Wang, X. He, Y. Gao. (2006) Responses of Artemisia ordosica population to soil moisture spatial heterogeneity on semi-fixed dune of Mu Us sandy land. Chin J Appl Ecol. 17 (8). 1469 -74.
45. Lu, X. He, Y. Gao. (2006) Study on the trade-off between nutrition growth and reproduction growth of Artemisia ordosica. Digest of annual symposium paper of China Ecology Association in 2006. 65.

 

Abstracts presented at scientific meetings

1. Lu, E. Peatman, H. Tang, J. Lewis, and Z. Liu (Jan. 2012) Genome Expansion in Zebrafish is Mediated by Recent Tandem Duplications. 20th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
2. Zhang, J. Lu, H. Zhang, C. Li, and J. Liu (Jan. 2012) Comparative Genomic Analysis of Catfish Linkage Group 28 with Teleost Species Genomes. 20th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
3. Li, Y. Zhang, R. Wang, J. Lu, S. Nandi, S. Mohanty, J. Terhune, J. Liu, and E. Peatman. (Jan. 2012) RNA-seq Analysis of Mucosal Immune Responses Reveals Signatures of Intestinal Barrier Disruption and Pathogen Entry Following Edwardsiella ictaluriInfection in Channel Catfish, Ictalurus punctatus. 20th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
4. Liu, Y. Zhang, Z. Zhou, G. Waldbieser, F. Sun, J. Lu, et. al.(Jan. 2012) Comprehensive Annotation of the Transcriptome of Channel Catfish (Ictalurus punctatus) by Paired-end RNA-Seq. 20th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
5. Wang, S. Liu, F. Sun, J. Zhang, H. Liu, J. Lu, et. al.(Jan. 2012) Identification of GenesAssociated With Heat Tolerance in CatfishExposed to Chronic Thermal Stress Using RNA-Seq. 20th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
6. Lu, E. Peatman, Q. Yang, S. Wang, Z. Hu, J. Reecy, H. Kucuktas, and Z. Liu. (March 2011) Development of cBARBEL, A Catfish Genome Database. 2011 World Aquaculture Society Conference. New Orleans, LA. Poster Presentation
7. Peatman, J. Lu, S. Liu, LL. Wong (March 2011) Progress in catfish genomics: aiming for impact at the pond bank. 2011 World Aquaculture Society Conference. New Orleans, LA. Poster Presentation
8. Wong, E. Peatman, J. Lu, H. Kucuktas, S. He, C. Zhou, U. Na-Nakorn, and Z. Liu. (2011) Catfish species authentication using DNA barcoding and Lab-on-a-chip-based PCR-RFLP assays. 2011 World Aquaculture Society Conference. New Orleans, LA. Poster Presentation.
9. Lu, E. Peatman, Q. Yang, S. Wang, Z. Hu, J. Reecy, H. Kucuktas, and Z. Liu. (Jan 2011) Development of cBARBEL, A Catfish Genome Database. 19th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
10. Lu, E. Peatman, Q. Yang, H. Tang, H. Kucuktas, and Z. Liu. (Jan 2011) Genome-wide Gene Duplication in Teleost Fish: Same-species and Cross-species Analysis and Comparisons. 19th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
11. Liu, Z. Zhou, J. Lu, F. Sun, S. Wang, H. Liu, Y. Jiang, H. Kucuktas, L. Kaltenboeck, E. Peatman, and Z. Liu. (Jan 2011) Genome-Scale Gene-Associated SNPs in Catfish for the Construction of a High-density SNP Array. 19th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
12. Niu, E. Peatman, H. Liu, J. Lu, H. Kucuktas, S. Liu, F. Sun, H. Zhang, T. Feng, Z. Zhou, J. Terhune, G. Waldbieser, J. Li, and Z. Liu. (2011) Microfibrillar-associated protein 4 (MFAP4) genes in catfish play a novel role in innate immune responses. 19th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
13. Zhou, H. Liu, S. Liu, F. Sun, T. Feng, E. Peatman, H. Kucuktas, H. Zhang, D. Niu, J. Lu, G. Waldbieser, and Z. Liu. (Jan 2011) Alternative complement pathway of channel catfish Ictalurus punctatus: molecular characterization and expression analysis of factors B and D. 19th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
14. Lu, E. Peatman, W. Wang, Q. Yang, J. Abernathy, S. Wang, and Z. Liu. (Jan 2010) Alternative splicing in teleost fish genomes: Cross-species analysis and comparisons. 18th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation
15. Abernathy, J. Lu, H. Liu, Z. Sha, and Z. Liu. (Jan 2009) Complement control factor I in catfish immunity: molecular characterization and gene expression after bacterial challenge. 17th Annual Plant and Animal Genome Conference. San Diego, CA. Poster Presentation