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

• Main Authors: Lei Li, Zhou Shi-Liang, Ma Hong, Zhang Liang-Sheng
• Format: Article
• Language: English
• Published: BMC 2012-04-01
• Series: BMC Evolutionary Biology
• Online Access: http://www.biomedcentral.com/1471-2148/12/51

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>We identified 59 <it>SET </it>genes in the <it>Populus </it>genome. Phylogenetic analyses of 106 <it>SET </it>genes from <it>Populus </it>and <it>Arabidopsis </it>supported the clustering of <it>SET </it>genes into six distinct subfamilies and identified 19 duplicated gene pairs in <it>Populus</it>. The chromosome locations of these gene pairs and the distribution of synonymous substitution rates showed that the expansion of the <it>SET </it>gene family might be caused by large-scale duplications in <it>Populus</it>. 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 <it>Populus SET </it>genes suggested that most <it>Populus SET </it>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.</p> <p>Conclusions</p> <p>The 19 duplicated <it>SET </it>genes could have originated from whole genome duplication events. The differences in <it>SET </it>gene structure, domain architecture, and expression profiles in various tissues of <it>Populus </it>suggest that members of the <it>SET </it>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.</p>