Molecular evolution of chloroplast gene rps12 in ferns

Plant chloroplast genomes consist of an inverted repeat (IR) region and two single copy (SC) regions; however, the patterns of molecular evolution in the IR and SC regions differ. The rps12 gene encodes the ribosomal small subunit S12 protein, which is composed of 5'-rps12 (exon 1) and 3'-rps12 (exon 2-3), with the 3'-rps12 protein of different species located in different genomic regions. The rps12 genes of 68 species of ferns and two species of lycophytes were studied, in the phylogenetic background, combined with the maximum likelihood method, the evolution rate and selection pressure of this gene were analyzed with HyPhy and PAML software. Results showed that exon 2-3 was located in the IR region, and its substitution rate was significantly reduced. The substitution rate of the coding sequence of rps12 was also reduced, and the GC content in the third position of the codon of rps12 was significantly increased. During the evolution of ferns, 3'-rps12 tended to be located in the IR region to maintain a low substitution rate. Among the 123 amino acid sites encoded by rps12, four positive selection sites and 116 negative selection sites were detected. Results indicated that the gene translocated into the IR region showed decelerated substitution rates, and the strong negative selection pressure indicated that the RPS12 protein was highly conserved and the function and structure of rps12 were mostly stabilized.