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Open Access Highly Accessed Open Badges Research article

Expansion and diversification of the SET domain gene family following whole-genome duplications in Populus trichocarpa

Li Lei13, Shi-Liang Zhou1, Hong Ma2* and Liang-Sheng Zhang2*

Author Affiliations

1 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China

2 State Key Laboratory of Genetic Engineering, Institute of Plants Biology, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200433, China

3 Graduate University of the Chinese Academy of Sciences, Beijing 100039, China

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BMC Evolutionary Biology 2012, 12:51  doi:10.1186/1471-2148-12-51

Published: 12 April 2012



Histone lysine methylation modifies chromatin structure and regulates eukaryotic gene transcription and a variety of developmental and physiological processes. SET domain proteins are lysine methyltransferases containing the evolutionarily-conserved SET domain, which is known to be the catalytic domain.


We identified 59 SET genes in the Populus genome. Phylogenetic analyses of 106 SET genes from Populus and Arabidopsis supported the clustering of SET genes into six distinct subfamilies and identified 19 duplicated gene pairs in Populus. The chromosome locations of these gene pairs and the distribution of synonymous substitution rates showed that the expansion of the SET gene family might be caused by large-scale duplications in Populus. Comparison of gene structures and domain architectures of each duplicate pair indicated that divergence took place at the 3'- and 5'-terminal transcribed regions and at the N- and C-termini of the predicted proteins, respectively. Expression profile analysis of Populus SET genes suggested that most Populus SET genes were expressed widely, many with the highest expression in young leaves. In particular, the expression profiles of 12 of the 19 duplicated gene pairs fell into two types of expression patterns.


The 19 duplicated SET genes could have originated from whole genome duplication events. The differences in SET gene structure, domain architecture, and expression profiles in various tissues of Populus suggest that members of the SET gene family have a variety of developmental and physiological functions. Our study provides clues about the evolution of epigenetic regulation of chromatin structure and gene expression.