蕨类植物叶绿体rps12基因的分子进化研究

Molecular evolution of chloroplast gene rps12 in ferns

以68种蕨类植物和2种石松类植物的rps12基因为对象,在系统发育背景下,结合最大似然法,使用HyPhy和PAML软件对该基因进行进化速率和适应性进化研究。结果显示:位于IR区的外显子2~3,其替换率明显降低,rps12基因编码序列的替换率也随之降低,且rps12基因密码子第3位的GC含量明显升高;在蕨类植物的进化过程中,3′-rps12更倾向定位于IR区,以保持较低的替换率;rps12基因编码的123个氨基酸位点中,共检测到4个正选择位点和116个负选择位点。研究结果表明基因序列进入到IR区后,显示出降低的替换率;强烈的负选择压力表明RPS12蛋白的高度保守性以及rps12基因的功能和结构已经趋于稳定。

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.