摘要
叶绿体rps12基因是所有叶绿体基因中最特殊的,由在基因组上相距甚远的两部分组成,含有3个外显子,经反式剪接作用编码核糖体小亚基S12蛋白.探究该基因的分子进化式样有助于理解该基因的进化过程及基因组特征.应用二代测序技术对南洋杉和柏木的叶绿体基因组进行测序;共选取78种裸子植物和2种蕨类植物,在系统发育背景下结合最大似然法,对rps12基因的进化速率、选择压力和适应性进化进行分析.结果显示,外显子3发生独立的碱基插入事件,发生插入的序列受到了更强的负选择作用;外显子2~3位于反向重复区,它们的替换率显著低于外显子1, rps12编码序列受到更强的负选择作用;适应性进化分析没有检测到正选择位点.结果表明,在裸子植物的进化过程中rps12基因结构稳定,并保持着相对较低的进化速率且表现出高度的保守特性;这为反向重复区具有降低的替换率提供了更多的证据,同时也揭示了裸子植物中存在的进化速率异质性现象.
The chloroplast rps12 gene is a very distinct chloroplast gene that consists of two parts widely separated in the chloroplast genome. It has three exons and encodes the small ribosomal subunit S12 protein via trans-splicing. A typical chloroplast genome consists of two inverted-repeat(IR) regions and two single-copy(SC) regions. The IR regions play an important role in the evolution of genome structure and sequence. Some genes enter or leave the IR region as it expands or contracts.Most studies have shown that the IR region has a low substitution rate, and the rps12 gene is considered to be the best representative for studying the evolutionary rate of sequences in the IR region due to its distribution pattern on the genome.Molecular evolutionary studies of rps12 genes in ferns led to the discovery of the loss of introns from the rps12 gene, the reduced substitution rate of the IR region, and three sites undergoing positive selection. Gymnosperms include gnetophytes, cycads, ginkgo, and conifers. Unlike the small-scale changes in the IR region of ferns, the IR region of conifers has been markedly reduced or lost, which may affect the rate of sequence evolution. And the rps12 gene may exhibit different molecular evolutionary patterns in gymnosperms. The chloroplast genomes of Araucaria cunninghamii and Callitropsis funebris were sequenced via second-generation sequencing. Using the sequences of 78 gymnosperms and two ferns, the evolutionary rate and adaptive evolution of, as well as the selection pressure on the rps12 gene were analyzed with the maximum-likelihood method. The results showed that exon 3 of gnetophytes and Araucariales had a base insertion, but its substitution rate did not change. The selection pressure analysis indicated that the gene was under strong negative selection pressure. The rps12 genes of the gymnosperms tend to have stable structures, and all contain introns. The rps12 gene encodes 126 amino acids with 81 identical positions;the amino-acid sequence encoded by rps12 in the IR region has 9
作者
平晶耀
冯佩沛
郝静
栗锦烨
苏应娟
王艇
Jingyao Ping;Peipei Feng;Jing Hao;Jinye Li;Yingjuan Su;Ting Wang(College of Life Sciences,South China Agricultural University,Guangzhou 510642,China;School of Life Sciences,Sun Yat-sen University,Guangzhou 510275,China;Research Institute of Sun Yat-sen University in Shenzhen,Shenzhen 518057,China)
出处
《科学通报》
EI
CAS
CSCD
北大核心
2021年第24期3182-3193,共12页
Chinese Science Bulletin
基金
国家自然科学基金(31670200,31770587,31872670,32071781)资助。
