Diversification of SQUAMOSA promoter binding protein-like (SPL) genes by changes of miR156/529 binding sites in land plants

Gene duplication can increase functional diversity of a gene family. SQUAMOSA promoter binding protein-like (SPL) genes encode plant-specific transcription factors. The SPL genes are regulated by miR156 and miR529 microRNA families. However, little is known about how and if duplicated SPL genes (paralogs) have retained active miR156/529 binding sites. Here, we analyzed 136 SPL genes from eight representative land plants, in which 70 of them originated from several large-scale duplication events, 40 ones constituted 32 duplicated target pairs. In this study, these target pairs were divided into divergent pattern (D-type) and same pattern (S-type). The D-pattern included loss/gain of miRNA binding sites on one paralog (D-1) and the mutation on miRNA binding sequences (D-2). Further study indicated that D-type gene pairs had the higher sequence divergence and evolutionary rate than S-type ones. Meanwhile, D-type gene pairs exhibited the different expression patterns, whereas S-type gene pairs had the similar expression patterns. These results revealed that the different divergence of miR156/529 binding sites after gene duplication might contribute to increasing functional diversity of SPL genes. In addition, gene structural analysis suggested that exonization/pseudoexonization and indel were two main mechanisms to gain/loss and shift the miR156/529 binding sites after gene duplications, and the latter might easily introduce the mutation when miRNA binding sites shifted from the coding region to untranslated region. Therefore, this study provides the better understanding the functional diversity of SPL genes in land plants.