黄颈亚马逊鹦鹉线粒体基因组全序列分析及系统进化

Mitochondrial Genome Sequence Analysis and Phylogenetic Evolution of Amazona auropalliata

黄颈亚马逊鹦鹉(Amazona auropalliata)属于《濒危野生动植物种国际贸易公约》附录Ⅱ监管物种。为了更好地了解黄颈亚马逊鹦鹉的起源、进化以及在鹦形目中的系统发育地位,本研究使用一代直接测序法获得了黄颈亚马逊鹦鹉的线粒体基因组序列,全长18679 bp,并针对全序列进行了结构分析。结果表明,黄颈亚马逊鹦鹉线粒体基因组中碱基含量具有明显的AT偏好性,包含13个蛋白编码基因、22个tRNA编码基因和2个rRNA编码基因,除了nad6在L链上以外,其他的蛋白编码基因都在H链上。黄颈亚马逊鹦鹉线粒体基因组有基因重叠现象且排列紧密,重叠序列长度范围从1 bp到6 bp,总长度共17 bp,共计8处;基因间隔序列的长度范围从1 bp到40 bp,总长度共154 bp,共计24处,有7处基因排列无间隙。基于线粒体基因序列分析发现,除了tRNA中trnC、trnF、trnG和trnH缺少反密码子环,trnP和trnQ缺少TΨC环,trnL-Ⅰ、trnS-Ⅱ和trnW呈短棒状,其他tRNA具有经典的三叶草二级结构。采用最大似然法(maximum likelihood method,ML)和近邻相接法(neighbor-joining method,NJ)对40种鹦形目物种线粒体全基因组序列构建系统进化树,结果表明黄颈亚马逊鹦鹉与黄冠亚马逊鹦鹉(Amazona ochrocephala)的亲缘关系最近。

Amazona auropalliata has been listed as a protected animal in AppendixⅡof the Convention on International Trade in Endangered Species of Wild Fauna and Flora.In order to better explore the origin,evolution,and phylogenetic status of Amazona auro-palliata in the order Psittaciformes,the direct sequencing method was used to obtain the complete mitochondrial genome sequence of Amazona auropalliata(18679 bp),and the structure analysis of the whole sequence was carried out in this study.The results showed that the base content of Amazona auropalliata mitochondrial genome had obvious AT preference,there were 13 protein-coding genes,22 tRNA-coding genes,and 2 rRNA-coding genes.Except for nad6 on the L chain,other protein-coding genes were on the H chain.The mitochondrial genome of Amazona auropalliata had gene overlap and was closely arranged.The length of the overlapping sequence ranged from 1 bp to 6 bp,and the total length was 17 bp,totaling 8 locations.The length of the intergenic sequence ranged from 1 bp to 40 bp,and the total length is 154 bp,there were a total of 24 locations,with 7 genes arranged without gaps.Based on the mitochondrial gene sequence,analysis found that except for trnC,trnF,trnG,and trnH in tRNA,which lack anticodon loops,trnP and trnQ lack TΨC loops,trnL-Ⅰ,trnS-Ⅱ,and TrnW were short rod-shaped,and other tRNAs had classic clover secondary structure.The phylogenetic tree was constructed using the maximum likelihood method(ML)and neighbor-joining method(NJ)based on the mitochondrial genome sequence of 40 species of Psittaciformes.The results showed that Amazona auropalliata had the closest genetic relationship with Amazona ochrocephala.