21个禾本科物种线粒体基因组特征与系统进化分析

Mitochondrial Genomic Characteristics and Phylogenetic Analysis of 21 Species of Poaceae

不同物种线粒体基因组有其特异的组成结构和进化方式,本研究基于NCBI-Genome数据库已公布的21个禾本科(Poaceae)物种线粒体基因组,利用比较基因组学方法对其线粒体基因组序列特征及亲缘关系进行了比较分析。结果显示,21个禾本科物种的线粒体基因组大小为443~705 kb,(A+T)含量为50%~70%,表现出明显的碱基偏倚现象。不同禾本科物种线粒体基因组所含的开放阅读框(open reading frame,ORF)数目、RNA编辑位点、编码蛋白、tRNA及重复序列类型不尽相同,且同一类编码蛋白、tRNA及重复序列类型在不同物种间的拷贝数也存有差异。不同禾本科物种线粒体基因组间,蛋白编码基因在使用密码子上具备一定的偏好性,偏好于使用AGA(R)、UCU(S)、CUU(L)、ACU(T)和GCU(A)。同时,各蛋白编码基因在禾本科物种线粒体遗传进化过程中遭受了不同方向和程度的遗传选择,其中mttB、ccmFn及rpl16等18种蛋白编码基因受到了不同程度的纯化(负)选择(K_(a)/K_(s)<1)。线粒体基因组共线性结果和邻接法构建的系统发育进化树结果表明,稻属(Oryza)与簕竹属(Bambusa)物种间,山羊草属(Aegilops)、小麦属(Triticum)、大麦属(Hordeum)和黑麦草属(Lolium)物种间,玉蜀黍属(Zea)、高粱属(Sorghum)、摩擦禾属(Tripsacum)、香根草属(Chrysopogon)、甘蔗属(Saccharum)及穇属(Eleusine)物种间存在较近的亲缘关系。本研究也为进一步揭示禾本科物种进化过程中的线粒体基因组结构变化和功能研究提供了参考。

The mitogenomes of different plants have their unique genomic characteristics and evolutionary patterns.Based on the NCBI-Genome database,the comparative genomics method was used to analyze the genomic characteristics and phylogenetic relationships of 21 Poaceae mitogenomes.The results showed that the mitogenomes of 21 Poaceae species ranged in size from 443 to 705 kb,with(A+T)content ranging from 50%to 70%,exhibiting significant base bias.The number of open reading frame(ORF),RNA editing sites,coding proteins,tRNA,and repeat sequences varied in different Poaceae mitogenomes,meanwhile the copy numbers of the same type of coding protein,tRNA,and repeat sequence also vary among different mitogenomes.Among different Poaceae mitogenomes,the codon usage of protein-coding genes prefer using AGA(R),UCU(S),CUU(L),ACU(T),and GCU(A).Meanwhile,the protein-coding genes were also subjected to different directions and degrees of genetic selection during the mitochondrial genetic evolution in Poaceae,among which,18 protein coding genes such as mttB,ccmFn,and rpl16 were subjected to different degrees of purification(negative)selection(K_(a)/K_(s)<1).The results of mitogenome collinearity and phylogenetic evolutionary tree constructed by neighbor joining method,which indicate that there are close phylogenetic relationships among the species from genus Oryza and Bambusa,the species from Aegilops,Triticum,Hordeum,and Lolium genus,as well as the species from Zea,Sorghum,Tripsacum,Chrysopogon,Saccharum,and Eleusine genus.The results provide a reference for further revealing the structural variations and functional studies of mitogenomes during the evolutionary process of Poaceae.