The highly conserved rps12 gene in ferns provides strong evidence for decreased substitution rates in the inverted repeat region

The typical chloroplast genome consists of two inverted repeat (IR) and two single-copy (SC) regions. Each region has its own pattern of molecular evolution. Many studies have shown that the IR region has a low substitution rate. The plastid rps 12 gene encodes ribosomal protein small subunit 12, which is composed of 5′- rps 12 (exon 1) and 3′- rps 12 (exon 2–3); 3′- rps 12 is near the IR region and enters or leaves the IR region as it expands and contracts, enabling study of the variation in its substitution rate. We analyzed the evolutionary rate and adaptive evolution of the rps 12 genes of 118 ferns and 2 lycophytes in a phylogenetic context using the maximum likelihood method. We found that the substitution rate of exon 2–3 was significantly lower in the IR region than in the LSC (1–11 times higher in the LSC), and also lower than that of exon 1 in the LSC region (1.9–6.7 times higher for exon 1). In addition, there was more GC content at the third codon position, and the rps 12 gene encoded 123 amino acids, with 107 negative selection sites and 4 positive selection sites. These results prove that the substitution rate decreases after the sequence fragments enter the IR region and demonstrate the highly conserved nature of the rps 12 gene.