Chuanzhu Fan

Chuanzhu Fan

Research interest(s)/area of expertise

 molecular evolution, genomics, epigenomics, population genetics/genomics, plant biology

Research

My laboratory investigates genetics and epigenetics underlying the evolution of genes and genomes in plants, especially origination and functionalization of the genomic novelties. Our approach to these problems will be combining our investigations in the model organism Arabidopsis and the critical crop plant species Oryza. By integrating computational and high-throughput experiments based on comparative transcriptomes, DNA methylation manipulation, state-of-the-art phenotyping, our research aims to determine how genetics and epigenomic divergences give rise to phenotypic differentiation for evolutionary novelties, especially the newly evolving genes in recent evolutionary times.

Education

• Ph.D. 2003. North Carolina State University
• Post-Doc. 2006. University of Chicago

Selected publications

1. Feng Tao, Vishwanath Sollapura, Laurian S Robert, and Chuanzhu Fan. 2023. Neofunctionalization of tandem duplicate genes encoding putative beta-L-arabinofuranosidases in Arabidopsis. Plant Physiology 192: 2855–2870
2. Feng Tao, Chuanzhu Fan, Yimin Liu, Subashini Sivakumar, Kurt P. Kowalski, and Edward M. Golenberg. 2023. Optimization and application of non-native Phragmites australis transcriptome assemblies. PLoS One 18(1):e0280354.
3. Jianhai Chen, Jie Zhong, Xuefei He, Ivan Jakovlić, Yong Zhang, Hao Yang, Younan Chen, Guang Yang, Chuanzhu Fan, and Bairong Shen. 2022. The nanopore sequencing of a Chinese rhesus macaque revealed patterns of methylation, recombination, and selection for structural variations. bioRxiv: doi: https://doi.org/10.1101/2022.10.21.513306
4. Jingjing Li, Jinyan Xu, Tingting Yang, Jianhai Chen, Fuping Li, Bairong Shen, and Chuanzhu Fan. 2022. Genome-wide methylation analyses of human sperm unravel novel differentially methylated regions in asthenozoospermia. Epigenomics 14: 951-964.  https://doi.org/10.2217/epi-2022-0122
5. Yanting Hu, Xiaopei Wu, Guihua Jin, Junchu Peng, Rong Leng, Ling Li, Daping Gui, Chuanzhu Fan, and Chengjun Zhang. 2022. Rapid genome evolution and adaptation of Thlaspi arvense mediated by recurrent RNA-based and tandem gene duplications. Frontiers in Plant Science 12: 772655. https://doi.org/10.3389/fpls.2021.772655
6. Yuan Huang, Jiahui Chen, Chuan Dong, Dylan Sosa, Shengqian Xia, Yidan Ouyang, Chuanzhu Fan, Dezhu Li, Emily Mortola, Manyuan Long, and Joy Bergelson. 2021. Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection. Plant Cell 34: 802-817. https://doi.org/10.1093/plcell/koab291
7. Xueting Li, Riwen Fei, Zhijing Chen, Chuanzhu Fan, and Xiaomei Sun. 2020. Plant hormones changes and differential expression profiling reveal seed dormancy removal process in double dormant plant-herbaceous peony. PLoS One 15: e0231117.
8. Xueting Li, Ping Liu, Panpan Yang, Chuanzhu Fan, and Xiaomei Sun. 2018. Characterization of glycerol-3-phosphate acyltransferase gene and its real-time expression under cold stress in Paeonia lactiflora Pall. PLoS One 13: e0202168.
9.  Joshua C. Stein, Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, Dongying Gao, Aiko Iwata, Jose Luis Goicoechea, Sharon Wei, Jun Wang, Yi Liao, Muhua Wang, Julie Jacquemin, Claude Becker, Dave Kudrna, Jianwei Zhang, Carlos E.M. Londono, Xiang Song, Seunghee Lee, Paul Sanchez, Andrea Zuccolo, Jetty S.S. Ammiraju, Jayson Talag, Ann Danowitz, Luis F. Rivera, Andrea R. Gschwend, Christos Noutsos, Cheng-chieh Wu, Shu-min Kao, Jhih-wun Zeng, Fu-jin Wei, Qiang Zhao, Qi Feng, Moaine El Baidouri, Marie-Christine Carpentier, Eric Lasserre, Richard Cooke, Daniel da Rosa Farias, Luciano Carlos da Maia, Railson S. dos Santos, Kevin G. Nyberg, Kenneth L. McNally, Ramil Mauleon, Nickolai Alexandrov, Jeremy Schmutz, Dave Flowers, Chuanzhu Fan, Detlef Weigel, Kshirod K. Jena, Thomas Wicker, Mingsheng Chen, Bin Han, Robert Henry, Yue-ie C. Hsing, Nori Kurata, Antonio Costa de Oliveira, Olivier Panaud, Scott A. Jackson, Carlos A. Machado, Michael J. Sanderson, Manyuan Long, Doreen Ware, and Rod A. Wing. 2018. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nature Genetics 50: 285-296.
10. Yuan Huang*, Jun Wang*, Yongping Yang, Chuanzhu Fan, and Jiahui Chen. 2017. Phylogenomic analysis and dynamic evolution of chloroplast genomes in Salicaceae. Frontiers in Plant Science 8: 1050.
11. Jun Wang*, Feng Tao*, Nicholas C. Marowsky, and Chuanzhu Fan. 2016. Evolutionary fates and dynamic functionalization of young duplicate genes in Arabidopsis genomes. Plant Physiology 172: 427-440.
12. Jun Wang, Yeisoo Yu, Feng Tao, Jianwei Zhang, Dario Copetti, Dave Kudrna, Jayson Talag, Seunghee Lee, Rod A. Wing, and Chuanzhu Fan. 2016. DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. Genome Biology 17: 92.
13. Jun Wang and Chuanzhu Fan. 2015. A neutrality test for detecting selection on DNA methylation using single methylation polymorphism frequency spectrum. Genome Biology and Evolution 7: 154-171.
14. Jun Wang, Nicholas C. Marowsky, and Chuanzhu Fan. 2014. Divergence of gene body DNA methylation and evolution of plant duplicate genes. PLoS One 9: e110357.
15. Chengjun Zhang*, Jun Wang*, Manyuan Long, and Chuanzhu Fan. 2013. gKaKs: The pipeline for genome level Ka/Ks calculation. Bioinformatics 29: 645-646.
16. Jun Wang, Nicholas C. Marowsky, and Chuanzhu Fan. 2013. Divergent evolutionary and expression patterns between lineage specific new duplicate genes and their parental paralogs in Arabidopsis thaliana. PLoS One 8: e72362.
17. Chengjun Zhang*, Jun Wang*, Nicholas C. Marowsky, Manyuan Long, Rod A.Wing, and Chuanzhu Fan. 2013. High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences. Genome Biology and Evolution 5: 1038-1048.
18. Muhua Wang*, Yeisoo Yu*, Georg Haberer*, Pradeep R. Marri*, Chuanzhu Fan; Jose L. Goicoechea, Andrea Zuccolo; Xiang Song; Dave Kudrna; Jetty S.S. Ammiraju; Rosa M. Cossu; Carlos Maldonado; Jinfeng Chen; Seunghee Lee; Nick Sisneros; Kristi de Baynast; Wolfgang Golser; Marina Wissotski; Woojin Kim; Paul Sanchez; Marie-Noelle Ndjiondjop; Kayode Sanni; Manyuan Long; Judith Carney; Olivier Panaud; Thomas Wicker; Carlos A. Machado; Mingsheng Chen; Klaus F.X. Mayer; Steve Rounsley; and Rod A. Wing. 2014. The genome of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics 46: 982-988.
19. Dario Copetti, Jianwei Zhang, Moaine El Baidouri, Dongying Gao, Jun Wang, Elena Barghini, Rosa M. Cossu, Angelina Angelova, Carlos E. Maldonado L., Stefan Roffler, Hajime Ohyanagi, Thomas Wicker, Chuanzhu Fan, Andrea Zuccolo, Mingsheng Chen, Antonio Costa de Oliveira, Bin Han, Robert Henry, Yue-ie Hsing, Nori Kurata, Wen Wang, Scott A. Jackson, Olivier Panaud, and Rod A. Wing. 2015. RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 16: 538.
20. Chuanzhu Fan*, Jason Walling*, Jianwei Zhang, Cory Hirsch, Jiming Jiang, and Rod Wing. 2011. Conservation and purifying selection of transcribed genes located in a rice centromere. Plant Cell 23: 2821-2830.

Courses taught by Chuanzhu Fan

Fall Term 2024 (future)

• BIO3070 - Genetics

Winter Term 2024 (current)

• BIO7300 - Communication of Research
• BIO8995 - Graduate Seminar in Biology

Fall Term 2023

• BIO3070 - Genetics

Winter Term 2023

• BIO5150 - Genomics
• BIO7150 - Genomics

Fall Term 2022

• BIO3070 - Genetics