Unraveling the Distribution and Evolution of miR156-targeted SPLs in Plants by Phylogenetic Analysis

Abstract

Squamosa promoter-binding protein-like genes (SPLs) are critical during plant development and mostly regulated by miR156. However, little is known about phylogenetic distribution and evolutionary patterns of miR156-targeted SPLs. In this study, 183 SPLs from nine genome-sequenced species representing algae, bryophytes, lycophyte, monocots, and eudicots were computationally analyzed. Our results showed that miR156 responsive elements (MREs) on SPLs were present in land plants but absent from unicellular green algae. Phylogenetic analysis revealed that miR156-targeted SPLs only distributed in group II not group I of land plants, suggesting they originated from a common ancestor. In addition, group II were further divided into seven subgroups (IIa-IIg) and miR156-targeted SPLs distributed in some specific members of SPLs from six subgroups except subgroup IId. Such distribution pattern was well elucidated by gene structure evolution of miR156-targeted SPLs based on the correlation of phylogenetic classification and gene structure. They could suffer from the exon loss events combined with MREs loss during evolution. Moreover, gene duplication contributed to the abundance of miR156-targeted SPLs, which had significantly increased after angiosperms and lower plants split. With Arabidopsis as the model species, we found segmental and tandem gene duplications predominated during miR156-targeted SPLs expansion. Taken together, these results provide better insights in understanding the function diversity and evolution of miR156-targeted SPLs in plants.