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Genome sequencing has uncovered tremendous sequence variation within and between species. In plants, in addition to large variations in genome size, a great deal of sequence polymorphism is also evident in several large multi-gene families, including those involved in the ubiquitin-26S proteasome protein degradation system. However, the biological function of this sequence variation is yet not clear. In this work, we explicitly demonstrated a single origin of retroposed  Arabidopsis Skp1-Like  ( ASK ) genes using an improved phylogenetic analysis. Taking advantage of the 1,001 genomes project, we here provide several lines of polymorphism evidence showing both adaptive and degenerative evolutionary processes in  ASK  genes. Yeast two-hybrid quantitative interaction assays further suggested that recent neutral changes in the  ASK2  coding sequence weakened its interactions with some F-box proteins. The trend that highly polymorphic upstream regions of  ASK1  yield high levels of expression implied negative expression regulation of  ASK1  by an as-yet-unknown transcriptional suppression mechanism, which may contribute to the polymorphic roles of Skp1-CUL1-F-box complexes. Taken together, this study provides new evolutionary evidence to guide future functional genomic studies of SCF-mediated protein ubiquitylation.

Adaptive and degenerative evolution of theS-Phase Kinase-Associated Protein 1-Likefamily inArabidopsis thaliana