陈明生

陈明生 男，博士，1966年生。研究员，博士生导师。

1988年南开大学生物系毕业；1991年获中科院遗传所硕士学位；1998年获Purdue University博士学位；1999-2000年在University of California, San Diego从事博士后研究；2001-2002年在Clemson University Genomics Institute任Research Assistant Professor；2002年至今任中科院遗传发育所研究员。2002年获国家杰出青年科学基金的资助；2009年入选新世纪百千万人才工程国家级人选；2013年享受政府特殊津贴。

实验室的主要研究方向是禾本科植物的比较基因组学、生物信息学以及农作物重要农艺性状基因的克隆和功能研究。近期的主要研究：

稻属的比较基因组学和基因组进化的研究：随着水稻基因组测序的完成和水稻功能基因组的发展，稻属已成为一个开展植物的生理生化、基因组进化、多倍体、人工驯化、适应性和基因功能等各个方面研究的独特模式系统。稻属包含十种不同的基因组类型，其中既有二倍体（AA、BB、CC、EE、FF、GG），也有四倍体（BBCC、CCDD、HHJJ、KKLL）。我们前期开展了稻属基因组的常染色质区域的比较分析，如Monoculm1, Adh1，Shattering 4和Hd1等等。目前我们参与了国际稻属基因组计划 (International Oryza Map Alignment Project, I-OMAP)，开展稻属基因组的着丝粒和异染色质区域的比较分析、短花药野生稻Oryza brachyantha（FF基因组）的全基因组测序和比较分析等等，以探讨稻属基因组的结构、功能和进化。

E-mail: mschen@genetics.ac.cn

Office Phone: 010-64806540

近期发表的代表性论文(*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.


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