Abstract
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 rps12 gene encodes ribosomal protein small subunit 12, which is composed of 5′-rps12 (exon 1) and 3′-rps12 (exon 2–3); 3′-rps12 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 rps12 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 rps12 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 rps12 gene.
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Acknowledgements
The authors wish to thank Ziying Liang, and Xiuqin Ma for technical assistance and sharing opinions, ShanShan Liu for the sample. This work was funded by the National Natural Science Foundation of China (31670200, 31770587, 31872670 and 32071781).
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Online Resource 1. Plastomes sampled in this study.
Online Resource 2. Alignment of the complete chloroplast genome sequences used in this study.
Online Resource 3. Alignment of the tandem data set of rbcL and matK sequences used in this study.
Online Resource 4. Alignment of the rps12-CDS sequences used in this study.
Online Resource 5. Alignment of the exon1 sequences used in this study.
Online Resource 6. Alignment of the exon2-3 sequences used in this study.
Online Resource 7. Maximum likelihood (ML) tree constructed based on the complete chloroplast genome.
Online Resource 8. Maximum likelihood (ML) tree constructed based on concatenated data sets of rbcL and matK.
Online Resource 9. Distribution of exon 1 and exon 2-3 values for each species in IR-109.
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Ping, J., Li, A., Feng, P. et al. The highly conserved rps12 gene in ferns provides strong evidence for decreased substitution rates in the inverted repeat region. Plant Syst Evol 307, 26 (2021). https://doi.org/10.1007/s00606-021-01750-7
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DOI: https://doi.org/10.1007/s00606-021-01750-7