Mingsheng Chen

 

Dr. Mingsheng Chen graduated from Nankai University, Tianjin, China in 1988. He received a Master Degree from the Institute of Genetics, Chinese Academy of Sciences, Beijing, China in 1991 and a Ph. D. from Purdue University, West Lafayette, Indiana, USA in 1998. He conducted a postdoctoral research in University of California, San Diego, USA from 1999 to 2001. Then he worked as a Research Assistant Professor in Clemson University Genomics Institute, Clemson, South Carolina, USA for approximately one year. He was hired as a Principal Investigator by the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences in 2002. Dr. Chen’s main research areas are plant comparative and evolutionary genomics, bioinformatics and molecular cloning of genes of agronomic import.

 

Email: mschen@genetics.ac.cn

 

Tel: (86-10) 64806540

Comparative Genomics in the Genus Oryza: The wild rice species are tremendous reservoirs for genes with respect to production, quality, and resistance to diseases and insects, and have furnished genes for the hybrid rice revolution, yield enhancing traits, and tolerance to biotic and abiotic stress. The genus Oryza comprises ten different genome types, including six diploid genomes (AA, BB, CC, EE, FF and GG) and four allotetraploid genomes (BBCC, CCDD, HHJJ and KKLL). The genus Oryza is an ideal system to study gene function, genome evolution, domestication, polyploidy, and ecological adaptation. We performed comparative sequence analysis of several orthologous euchromatic regions across the genus Oryza, such as MOC1, Adh1, Hd1, and Shattering-4. Currently we are focusing on comparative genomic analysis of heterochromatic regions across the genus Oryza, whole genome sequencing and comparative analysis of Oryza brachyantha (FF), and etc.

 

RECENT REPRESENTATIVE PUBLICATIONS(*Corresponding author or Co-corresponding author)

 

1.  Tian, P., Zhang, X., Xia, R., Liu, Y., Wang, M., Li, B., Liu, T., Shi, J., Wing, R.A., Meyers, B.C. *, and Chen, M. * (2021). Evolution and diversification of reproductive phased small interfering RNAs in Oryza species. New Phytol 229, 2970-2983.

 

2.  Liao, Y., Zhang, X., Li, B., Liu, T., Chen, J., Bai, Z., Wang, M., Shi, J., Walling, J.G., Wing, R.A., Jiang, J., and Chen, M.* (2018). Comparison of Oryza sativa and Oryza brachyantha Genomes Reveals Selection-Driven Gene Escape from the Centromeric Regions. Plant Cell 30, 1729-1744.

 

3.  Li, B.*, Kremling, K.A.G., Wu, P., Bukowski, R., Romay, M.C., Xie, E., Buckler, E.S., and Chen, M.* (2018). Coregulation of ribosomal RNA with hundreds of genes contributes to phenotypic variation. Genome Res 28, 1555-1565.

 

4.  Stein, J.C., Yu, Y., Copetti, D., Zwickl, D.J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J.L., Wei, S., Wang, J., Liao, Y., and et al. (2018). Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet 50, 285-296.

 

5.  Bai, Z., Chen, J., Liao, Y., Wang, M., Liu, R., Ge, S., Wing, R.A., and Chen, M.* (2016). The impact and origin of copy number variations in the Oryza species. BMC Genomics 17, 261.

 

6.  Wang, M., Yu, Y., Haberer, G., Marri, P.R., Fan, C., Goicoechea, J.L., Zuccolo, A., Song, X., Kudrna, D., Ammiraju, J.S., Cossu, R.M., Maldonado, C., Chen, J., Lee, S., Sisneros, N., de Baynast, K., Golser, W., Wissotski, M., Kim, W., Sanchez, P., Ndjiondjop, M.N., Sanni, K., Long, M., Carney, J., Panaud, O., Wicker, T., Machado, C.A., Chen, M.*, Mayer, K.F.*, Rounsley, S.*, and Wing, R.A.* (2014). The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet. (*Co-corresponding authors)

 

7.  Sui, Y., Li, B., Shi, J., and Chen, M.* (2014). Genomic, regulatory and epigenetic mechanisms underlying duplicated gene evolution in the natural allotetraploid Oryza minuta. BMC Genomics 15, 11.

 

8.  Chen, J., Huang, Q., Gao, D., Wang, J., Lang, Y., Liu, T., Li, B., Bai, Z., Luis Goicoechea, J., Liang, C., Chen, C., Zhang, W., Sun, S., Liao, Y., Zhang, X., Yang, L., Song, C., Wang, M., Shi, J., Liu, G., Liu, J., Zhou, H., Zhou, W., Yu, Q., An, N., Chen, Y., Cai, Q., Wang, B., Liu, B., Min, J., Huang, Y., Wu, H., Li, Z., Zhang, Y., Yin, Y., Song, W., Jiang, J., Jackson, S.A., Wing, R.A., and Chen, M.* (2013). Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Communications 4, 1595.

 

9.  Yang, L., Liu, T., Li, B., Sui, Y., Chen, J., Shi, J., Wing, R.A., and Chen, M.* (2012). Comparative sequence analysis of the Ghd7 orthologous regions revealed movement of Ghd7 in the grass genomes. PLoS One 7, e50236.

 

10.Gao, D., Chen, J., Chen, M., Meyers, B.C., and Jackson, S. (2012). A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PLoS One 7, e32010.

 

11.Sanyal, A., Jetty, A.S., Lu, F., Yu, Y., Rambo, T., Currie, J., Kollura, K., Kim, H.R., Chen, J., Ma, J., San Miguel, P., Chen, M.*, Wing, R.A.*, and Jackson, S.A.* (2010). Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in sorghum. Mol Biol Evol 27, 2487.

 

12.Chen, M.*, Lu, F., Jackson, S.A., and Wing, R.A. (2010). Dynamic Genome Evolution of Oryza, - A Genus-Wide Comparative Analysis. In DARWIN’S HERITAGE TODAY: Proceedings of the Darwin 200 Beijing International Conference, M. Long, H. Gu, and Z. Zhou, eds. (Beijing, Higher Education Press), pp. 76-83.

 

13.Wang, C., Chen, J., Zhi, H., Yang, L., Li, W., Wang, Y., Li, H., Zhao, B., Chen, M.*, and Diao, X.* (2010). Population genetics of foxtail millet and its wild ancestor. BMC Genet 11, 90.

 

14.Ammiraju, J.S., Fan, C., Yu, Y., Song, X., Cranston, K.A., Pontaroli, A.C., Lu, F., Sanyal, A., Jiang, N., Rambo, T., Currie, J., Collura, K., Talag, J., Bennetzen, J.L., Chen, M., Jackson, S., and Wing, R.A. (2010). Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza. Plant J 63, 430.

 

15.Lu, F., Ammiraju, J. S., Sanyal, A., Zhang, S., Song, R., Chen, J., Li, G., Sui, Y., Song, X., Cheng, Z., de Oliveira, A. C., Bennetzen, J. L.*, Jackson, S.*, Wing, R. A.*, and Chen, M*. (2009). Comparative sequence analysis of the MONOCULM1 orthologous regions in fourteen Oryza genomes. Proc Natl Acad Sci U S A 106, 2071-2076.

 

16.Ammiraju, J. S., Lu, F., Sanyal, A., Yu, Y., Song, X., Jiang, N., Pontaroli, A. C., Rambo, T., Currie, J., Collura, K., Talag, J., Fan, C., Goicoechea, J. L., Zuccolo, A., Chen, J., Bennetzen, J. L., Chen, M.*, Jackson, S.*, and Wing, R. A.* (2008). Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set. Plant Cell 20, 3191-3209.