A Survey of the SMR Gene Family in the Plant Kingdom, Using a Motif Oriented Search Tool

Next-generation sequencing has made genomes available at a faster rate. Consequently, effectively searching for homologous genes in a wide array of species has become increasingly important. The BLAST algorithm has been widely used to identify homologous sequences in taxa, based on sequence similarity. However, BLAST recovers a high frequency of false positives when identifying diverse sequences. I have developed a protein search method based on conserved motifs to detect homologous proteins with high sequence divergence. Initially, I developed this to search for the SMR protein family, cyclin-dependent kinase inhibitors specific to plants in cell cycle regulation and endoduplication. The SMR family proteins cannot be identifiable through BLAST because the conservation contains few short motifs. SMR loss of function mutants in Arabidopsis thaliana, the model angiosperm, can be complemented by the transgenic introduction of an SMR gene from the distantly related moss Physcomitrella patens. I searched for genome-wide SMR genes from twenty plant genomes using a Perl-based script that was developed to find conserved motifs in peptide sequences.  The algorithm I developed accounts for empirical evidence of essential residues in defined motifs. My algorithm was able to parse the entire A. thaliana genome and correctly identify only the 17 known SMR sequences. Candidate SMR protein sequences were aligned with BAli-Phy alignment program and a consensus tree was generated using RAxML. I will be presenting the SMR family divergence with relevance to gene family duplications, rapid radiation, and positive selection in 20 diverse plant lineages.