Silin Zhong Lab | Plant Functional Genomics CUHK

EG12 Science Centre East
School of Life Sciences
The Chinese University of Hong Kong
Tel: 3943 6280

home    lab members    publications    fruitENCODE    C3C4    Hi-C   



Representative work (full_list, Google Scholar, ORCiD)


Fruit development and ripening:

Lv P, Yu S, Zhu N, Chen Y, Zhou B, Pan Y, Tzeng D, Fabi J, Argyris J, Garcia-Mas J, Ye N, Zhang J, Grierson D,Xiang J, Fei Z, Giovannoni J, and Zhong S. (2018) Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening. Nature Plants. 4:784-791.

Zhong S., Fei Z., Chen Y.C., Zheng Y., Huang M., Vrebalov J., Gapper N., McQuinn R. Liu B., Xiang J., Shao, Y. and Giovannoni J. (2013) Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nature Biotechnology. 31:154-159.

Zhong S., Lin Z. and Grierson D. (2008) Tomato ethylene receptor interaction: visualization of NEVER-RIPE interaction with multiple CTRs at the endoplasmic reticulum. Journal of Experimental Botany. 59:965-972.

Photosynthesis and C4 evolution:

Liang, Z., Zhu, N., Mai, K., Liu, Z., Tzeng, D., Osteryoung, K., Zhong, S., Staehelin, A.,& Kang, B. (2018) Thylakoid-bound polysomes and a dynamin-related protein, FZL, mediate critical stages of the linear chloroplast biogenesis program in greening Arabidopsis cotyledons. The Plant Cell. 30, 1476-1495.

Ding Z, Weissmann S, Wang M, Du B, Huang L, Wang L, Tu X, Zhong S, Myers C, Brutnell T, Qi S, and Li P (2015) Identification of Photosynthesis-Associated C4 Candidate Genes through Comparative Leaf Gradient Transcriptome in Multiple Lineages of C3 and C4 Species, PLoS ONE, 10/2015.

Nguyen CV, Vrebalov JT, Gapper NE, Zheng Y, Zhong S, Fei Z and Giovannoni J (2014) Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening. The Plant Cell. 26:585-601.


Epigenome and 3D chromatin architecture:

Dong P, Tu X, Li H, Zhang J, Grierson D, Li P & Zhong S (2019) Tissue‐specific Hi‐C analyses of rice, foxtail millet and maize suggest non‐canonical function of plant chromatin domains. JIPB. 10.1111/jipb.12809.

Dong P, Tu X, Chu PY, Lv P, Zhu N, Grierson D, Du B, Li P and Zhong S. (2017). 3D chromatin architecture of large plant genomes determined by local A/B compartments. Molecular Plant. 10, 1497-1509.

Hu L, Li N, Xu C, Zhong S, Lin X, Yang J, Zhou T, Yuliang A, Wu Y, Chen YR, Cao X, Zemach A, Rustgi S, Wettstein D and Liu B (2014) Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. PNAS. 111:10642-7.


Genome sequencing:


Cassava Genome Consortium (2014) Cassava Genome from a Wild Ancestor to Cultivated Varieties. Nature Communications. 5:5110 .

Kiwifruit Genome Consortium (2013) The Draft Genome of Kiwifruit Actinidia chinensis. Nature Communications. 4:2640.

Watermelon Genome Consortium (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nature Genetics. 45:51-58.

Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature. 485:635-641.