We are the Marine Ecological Genomics team of the School of Oceanology, Sun Yat-sen University.

The Marine ecological Genomics team uses genomics methods to study Marine ecological issues, clarify the mechanisms of Marine organisms’ adaptation to extreme environments (cold seepage, hydrothermal vents, deep sea areas), and explore the relevant functions of important economic traits of Marine organisms such as sex determination, disease resistance, growth, pigmentation, etc., through genetic data analysis, so as to integrate with the industry.

Our work includes:

（1）Adaptation mechanism, evolutionary model and sex regulation mechanism of Marine fishes to different habitats;

（2）Regulatory mechanisms of functional gene adaptation to extreme environments (cold springs and hydrothermal regions).

（3）Effects of Marine microorganisms on methane gas transport mechanism in hydrate-rich sea area;

（4）Marine ecological adaptation mechanisms in deep, ultra-deep and abyssal waters;

（5）Adaptation mechanisms of Marine organisms in coastal wetland mangrove ecosystems.

• Lu J*, et al. DupScan: predicting and visualizing vertebrate genome duplication database. Nucleic Acids Res. 2022. 1区Top, IF=19.16
• Fang W … Lu J*. Identification of pigment genes (melanin, carotenoid and pteridine) associated with skin color variant in red tilapia using transcriptome analysis. Aquaculture. 2022. 1区Top
• Genmei Lin … Jianguo Lu*. Response of gut microbiota and immune function to hypoosmotic stress in the yellowfin seabream (Acanthopagrus latus). Science of the Total Environment, 2020. 1区Top
• Genmei Lin, Xianbiao Lin*. Bait input altered microbial community structure and increased greenhouse gases production in coastal wetland sediment. Water Research, 2022. 1区Top
• Lu, J*.et al. Chromosome-level Genome Assembly of Acanthopagrus latus Provides Insights into Salinity Stress Adaptation of Sparidae. Mar Biotechnol 24, 655–660 (2022).
• Lin G … Lu J*. 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

 

A one-stop multi-omics analysis platform DupScan database was built by integrating 106 high-quality multi-omics data of vertebrates

Technical breakthrough ：

1. Multi-omics fusion technology
2. Mining and application of trait function genes

Main Advantage :

1. Designed for polyploid analysis of fish
2. The data collected are more comprehensive
3. Visualization, interaction, and coordination
4. Friendly interface
5. Accompanying video and text tutorials

Technical breakthrough:

In this paper, a core technique for mining the functional genes related to sex dimorphism and sex reversal was established in the main economic aquatic species of Pelteobagrus pelteobagrus, yellowfin bream, red tilapia and semi-slippery cynoglossus.

Dong Gao, Min Zheng, Genmei Lin, Wenyu Fang, Jing Huang, Jianguo Lu*, Xiaowen Sun. Construction of high-density genetic map and mapping of sex determination loci in the yellow catfish (Pelteobagrus fulyidraco)

Shizhu Li, Genmei Lin, Wenyu Fang, Peilin Huang, Dong Gao, Jing Huang, Jingui Xie, Jianguo Lu*. Gonadal transcriptome analysis of sex-related genes in the protandrous yellowfin seabream (Acanthopagrus latus). Frontiers in Genetics, 2020, 11.

Wenyu Fang, Junrou Huang, Shizhu Li, Jianguo Lu*. Identification of pigment genes (melanin, carotenoid and pteridine) associated with skin color variant in red tilapia using transcriptome analysis. Aquaculture, 2021, 547: 737429.

Genmei Lin, Shizhu Li, Junrou Huang, Dong Gao, Jianguo Lu*. 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, 47: 1725-1738.
Genmei Lin, Min Zheng, Dong Gao, Shizhu Li, Wenyu Fang, Jing Huang, Jingui Xie, Jingxiong Liu, Yijing Liu, Zhaohong Li, Jianguo Lu*. Hypoosmotic stress induced tissue-specific immune responses of yellowfin seabream (Acanthopagrus latus) revealed by transcriptomic analysis. Fish & Shellfish Immunology, 2020, 99: 473-482.

Genmei Lin, Dong Gao, Jianguo Lu*, Xiaowen Sun. 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.

Jianguo Lu, Wenyu Fang, Junrou Huang, Shizhu Li. The application of genome editing technology in fish. Marine Life Science & Technology, 2021, 3: 326-346.

李石竹, 方文宇, 骆明飞, 卢建国*. 黄颡鱼GnRHR基因的克隆和表达及CRISPR/Cas9构建GnRHR基因敲除突变体. 大连海洋大学学报, 2021, 36(3): 383-392.

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[J]. BMC Genomics, 2022, 23(S1).

Jianguo Lu, Dong Gao, Ying Sims, Wenyu Fang, Joanna Collins, James Torrance, Genmei Lin, et al. Chromosome-level Genome Assembly of Acanthopagrus latus Provides Insights into Salinity Stress Adaptation of Sparidae. Mar Biotechnol, 2022,24: 655-660.

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[J]. Aquaculture, 2022, 547: 737429.

Marco Podobnik, Ajeet P. Singh, Zhenqiang Fu, Christopher M. Dooley, Hans Georg Frohnhöfer, Magdalena Firlej, Sarah J. Stednitz, Hadeer Elhabashy, Simone Weyand, John R. Weir, Jianguo Lu, Christiane Nüsslein-Volhard, Uwe Irion. kcnj13 regulates pigment cell shapes in zebrafish and has diverged by cis-regulatory evolution between Danio species[J]. Development, 2023, 150(16).

In this paper, the adaptive strategies of Marine fishery organisms to the stressed environment were studied by using deep-sea mussels, deep-sea shrimp and yellowfin bream in deep-sea special habitats and traditional culture environments.

Genmei Lin, Min Zheng, Shizhu Li, Jingui Xie, Wenyu Fang, Dong Gao, Jing Huang, Jianguo Lu*. Response of gut microbiota and immune function to hypoosmotic stress in the yellowfin seabream (Acanthopagrus latus). Science of the Total Environment, 2020, 745: 140976.

Genmei Lin, Jianguo Lu*, Zhilei Sun, Jingui Xie, Junrou Huang, Ming Su, Nengyou Wu*. 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.

Genmei Lin, Jing Huang, Jianguo Lu, Ming Su, Bangqi Hu, Xianbiao Lin*. Geochemical and microbial insights into vertical distributions of genetic potential of N-cycling processes in deep-sea sediments. Ecological Indicators, 2021, 125: 107461.

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).

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.

Through culture experiment and multi-omics sequencing analysis, the effects of environmental microbial communities on the symbiotic microbial community structure of Marine organisms were studied.

Genmei Lin, Yongni He, Jianguo Lu, Hui Chen, Jianxiang Feng*. 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.

Hualin Liu, Vimalkumar Prajapati*, Shobha Prajapati, Harsh Bais, Jianguo Lu. Comparative genome analysis of Bacillus amyloliquefaciens focusing on phylogenomics, functional traits, and prevalence of antimicrobial and virulence genes. Frontiers in Genetics, 2021, 12: 724217.

Liu H, Lin G, Gao D, 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, 85(1): 121-136.

Genmei Lin, Xianbiao Lin*. Bait input altered microbial community structure and increased greenhouse gases production in coastal wetland sediment. Water Research, 2022, 218: 118520.

Genmei Lin, Jianguo Lu, Kunwen Luo, Yunxin Fang, Jiawei Liu, Xiang Ji, Shutong Ge, Jia Liu, Ming Su*. Characterization of bacterial and archaeal community structure in deep subsurface sediments in the Shenhu area, northern South China Sea. Marine and Petroleum Geology, 2022, 136: 105468.

Lin X, Lin G, Zheng Y, et al. Nitrogen mineralization and immobilization in surface sediments of coastal reclaimed aquaculture ecosystems[J]. Frontiers in Marine Science, 2023, 9.

Hualin Liu, Xueyu Cai, Kunwen Luo, Sihan Chen, Ming Su, Jianguo Lu. Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology[J]. Microbiology Spectrum, 2023, 11(2).