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Evolutionary Genomics of Eukaryotic Cells

Dr. Jian-Fan Wen, Principal Investigator, Vice Director of the State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, CAS. His group is mainly interested in the origin and evolution of eukaryotic cells. Taking the protists, which occupy key positions in the eukaryotic cell evolution, as models, and combining with the data of prokaryotes and multicellular organisms, they study the biodiversity, origin and evolution of the structures, functions, genes, gene families, gene groups of functional pathways and genomes of the eukaryotic cells. They also study the adaptive evolution of parasites and unicellular algae to explore both the novel ways of harmful organism controlling (e.g. parasitic protozoa and schistosomes) and the new applications of the effective and specific metabolic pathways of beneficial organism (e.g. algae).

1. Identification of the nucleolar protein genome in Giardia lamblia and the origin and evolution of eukaryotic SSU processome

Here, we identified the first nucleolar protein genome in G. lamblia, and established the first nucleolar protein genome in protist; then we compared it with the Eukaryotic Basic Nucleolar Protein Genome (EBNPG) to reveal the real evolutionary position of G. lamblia. All these results indicate the probably primitive feature of nucleolus in G. lamblia and the 憆ibosome related?is the primary function of nucleolus in the early eukaryotes, and various other nucleolar functions arose at later point after the divergence of G. lamblia from the eukaryotic trunk. Besides, we have charted the picture of the origin and evolutionary history of SSU processome for the first time: a rudimentary SSU processome had likely arisen in archaea; then a complex SSU processome had formed in LECA through ancient gene duplication, de novo eukaryotic protein innovations, and recruiting prokaryote-original protein domains to form novel proteins; finally, during the divergence of various eukaryotic lineages from LECA, lineage-specific and species-specific gene duplications, lineage-specific gene innovations, and lineage-specific and species-specific gene losses, have complicated this complex further in diverse extant eukaryotes.

2. Proposition and verification of the hypothesis that Giardia is the combination of extreme primitiveness and highly parasitic adaptation

It is still controversial whether Giardia is a most primitive eukaryotic cell or a highly evolved parasite. Based on our previous studies, we proposed that this organism might be a combination of extreme primitiveness and highly parasitic adaptation. To test this hypothesis, we re-identified and confirmed the genes involved in glycerophospholipid biosynthesis pathway in Giardia, and reconstructed the pathway in the organism. We found that compared with typical eukaryotic, Giardia抯 Kennedy pathway and PA pathway are both incomplete. After we investigated the evolutionary history of the whole glycerophospholipid biosynthesis pathway in many representatives of the three domains of life, the following findings were observed: Giardia has not developed a complete Kennedy pathway as prokaryotes; but the PA pathway probably has been partly lost due to the adaption to its parasitic lifestyle. Our phylogenetic analysis of all the genes involved in the pathway indicated that 8 giardial genes are the earliest-branching ones among eukaryotic homologs, while the other 3 giardial genes are probably acquired through horizontal gene transfer. Therefore Giardia glycerophospholipid biosynthesis pathway itself might be a combination of primitiveness and parasitic adaptation. Thus our results support the hypothesis.

Highlights in 2013

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

2. Zhang YJ, Yang CL, Hao YJ, Li Y, Chen B*, Wen JF*. Macroevolutionary trends of atomic composition and related functional group proportion in eukaryotic and prokaryotic proteins. 2013. Gene, S0378-1119(13)01510-2.

3. Xiong J, Lu YM, Feng JM,..., Miao W*. Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics. DATABASE-OXFORD, 2013. doi: 10.1093/database/bat008. (co-authors)

4. Xu J, Cheng YQ, Chen B,? Wen JF, ? Depression in systemic lupus erythematosus patients is associated with link-polymorphism but not methylation status of the 5HTT promoter region. 2013. Lupus,. 22(10):1001-10.

5. Gao S, Xiong J, ? Wen JF, ? Miao W, and Liu YF. Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation. 2013. Genes Dev, 27(15):1662-79.

6. Sun GL, Yang YF, Xie FL, Wen JF, ? Deep Sequencing Reveals Transcriptome Re-Programming of Taxus ?media Cells to the Elicitation with Methyl Jasmonate. 2013. PLoS ONE,8(4):e62865.

7. Xie GQ, Chen B, Wen JF*. Research progress on the mechanisms of immune evasion of parasitic flatworms such as schistosoma. Acta Parasitologica Et Medica Entomologica Sinica, 2013, 20(3):194-201.


Lab Staff:

Bing Chen, Research Assistant,;

Jing-Ru Shao, Experimentalist,

Graduate Students:

Qing-Qing Ye 2010; Yu-Jin Li 2011; Gang-Qin Xie 2011; Wen-Min Wang 2011; You-Xu Yao 2012; Hai-Bo Huang 2013; Min Xue 2013


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32 Jiaochang Donglu Kunming, Yunnan 650223
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