Evolutionary Genomics of Eukaryotic Cells

At the molecular and cellular levels, the aim is to explore the diversity of eukaryotic cells and its formation mechanisms, including the origin and evolution of the architectures, cellular machineries, metabolic pathways, and their corresponding genes, gene families, and the whole genomes of the eukaryotic cell, also including adaptive evolution of some organisms occupying different evolutionary positions. We mainly focus on a series of single-celled protozoa (such as Giardia) and algae (such as single-celled green algae, Euglena, etc.) that occupy key evolutionary positions, trace back to prokaryotes, and trace upward to multicellular organisms , using cell biology, molecular biology, biochemistry, multi-omics, bioinformatics, and evolutionary biology and other multidisciplinary carry out researches on the following aspects: 1) The diversity and its evolutionary forming of important structures of eukaryotic cells (such as nuclear skeleton, nuclear lamina, chromatin, and nucleolus, etc.); 2) The diversity and its evolution of important functional mechanisms of eukaryotic cells (such as nuclear division, protein directional transport system, various metabolic pathways such as glycolysis, tricarboxylic acid cycle, Calvin cycle, gluconeogenesis and lipid metabolism, etc.); 3) The diversity and evolution of important genes, gene families, functional pathway gene groups and subgenomes (such as nucleolar genome) related to the former two aspects; 4) The cellular, molecular, and genomic basis of specific adaptations and adaptive radiations of some interesting organisms, and to discover the specific control targets of harmful organisms (such as parasites) and develop and utilize efficient and special biological metabolic pathways of algae for algae engineering and synthetic biology.

Recently, we mainly focus on carrying out synthetic biology research such as the construction of minimal genome and chassis cells based on the minimal genome and special metabolic pathways of certain protists, aiming to construct eukaryotic chassis with basic research value and broad application prospects and efficient engineered microalgae strains with mixotrophic ability.

1. Feng JM, Yang CL, Tian HF, Wang JX, Wen JF*. 2020. Identification and evolutionary analysis of the nucleolar proteome of Giardia lamblia. BMC Genomics, 21(1), 269.

2. Lyu ZX, Shao JR , Xue M, Ye QQ , Chen B, Qin Y, Wen JF*. 2018. A new species of Giardia Künstler, 1882 (Sarcomastigophora: Hexamitidae) in hamsters. Parasites & Vectors, 11(1), 202.

3. Xue M, Chen B, Ye QQ, Shao JR, Lyu ZX, Wen JF*. 2018. Sense-antisense gene overlap is probably a cause for retaining the few introns in Giardia genome and the implications. Biology Direct, 13, 23.

4. Ye QQ, Tian HF, Chen B, Shao JR, Qin Y, Wen JF*. 2017. Giardia’s primitive GPL biosynthesis pathways with parasitic adaptation ‘patches’: implications for Giardia’s evolutionary history and for finding targets against Giardiasis. Sci Rep, 7(1), 9507.

5. Feng JM, Tian HF, Wen JF*. 2013. Origin and Evolution of the Eukaryotic SSU Processome Revealed by a Comprehensive Genomic Analysis and Implications for the Origin of the Nucleolus. Genome Biol Evol, 5(12), 2255-67.

6. Gao S, Xiong J, Zhang CC, Berquist BR, Yang RD, Zhao M, Molascon AJ, Kwiatkowski SY, Yuan DX, Qin ZH, Wen JF, Kapler G-M, Andrews P-C, Miao W*, Liu Y-F*. 2013. Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation. Genes Dev, 27(15), 1662-79.

7. Tian HF, Feng JM, Wen JF*. 2012. The evolution of cardiolipin biosynthesis and maturation pathways and its implications to the evolution for eukaryotes. BMC Evol. Biol, 12, 32.

8. Jiang YH, Wang DY, Wen JF*. 2012. The independent prokaryotic origins of eukaryotic fructose-1 6-bisphosphatase and sedoheptulose-1 7-bisphosphatase and the implications of their origins for the evolution of eukaryotic Calvin cycle. BMC Evol. Biol, 12, 208.

9. Sun J, Jiang HF, Flores R, Wen JF*. 2012. Gene duplication in the genome of parasitic Giardia lamblia. BMC Evol. Biol, 10, 49.

10. Ni T, Yue JP, Sun GL, Zou Y, Wen JF*, Hang J-L*. 2012. Ancient gene transfer from algae to animals: Mechanisms and evolutionary significance. BMC Evol. Biol, 12, 83.

11. Zhang YJ, Tian HF, Wen JF*. 2009. The evolution of YidC/Oxa/Alb3 family in the three domains of life: a phylogenomic analysis. BMC Evol. Biol, 9, 137.

12. Xin DD, Wen JF*, He D, Lu SQ. 2005. Identification of a Giardia krr1 homolog gene and the secondarily anucleolate condition of Giardia lamblia. Mol. Biol. Evol, 22(3), 391-394.  

13. Sun GL, Shen W, Wen JF*, 2008. Triosephosphate isomerase (TIM) genes in two trophic modes of euglenoids (Euglenophyceae) and their phylogenetic analysis. J. Eukaryot. Microbiol. 55 (3): 170-177.  

14. He D, Wen JF*, Chen WQ, Lu SQ, Xin DD. 2005. Identification, Characteristic and Phylogenetic Analyses of Type II DNA topoisomerase Gene in Giardia lamblia. Cell Res. 15(6): 474-482.  

15. Wen JF*, 2000. The Nuclear Matrix of Euglena gracilis (Euglenophyta): A stage of nuclear matrix evolution? Biol. Cell 28(5): 125-131.   

1. Genomic basis for the function and evolution of the two-equal-nuclei system in the special eukaryotic lineage diplomonads, the Natural Science Foundation of China ( 32270463), preside.

2. The Construction of Minimal Genome and Chassis Cells Based on the Small Genome of Giardia lamblia, the Natural Science Foundation of China (32070419), preside.

3. Nucleolar functional genomics of the extremely primitive protozan--Giardia and the origin and evolution of the nucleolus, the Key Projects of the Natural Science Foundation of China (30830018), preside.

4. Selection and evolution of genes and gene family/group functions, the National Key Basic Research Development Program of the Ministry of Science and Technology (973 Program) (2007CB815705), preside.

5. Molecular Evolution and Evolutionary Genomics, Scientific Fund for Innovative Research Groups of the Natural Science Foundation of China (30021004), Research Backbone (the 2nd).

6. Exploration of the evolution of sexual reproduction via comparative genomics study of Giardia lamblia and its close relatives, the Natural Science Foundation of China (31772452), preside.

7. Comparative genomics of the extreme primitiveness and the secondary parasitic adaptation of Giardia lamblia, the Natural Science Foundation of China (31572256), preside.

8. Genomics of the Adaptive Evolution of Energy Metabolic Pathways in Several Parasitic Protozoa, the Natural Science Foundation of China (31172081), preside.