The complete mitochondrial genome sequence of Remiz consobrinus was determined using long PCR and conserved primers walking approaches. Based on the results of assembling and annotation, the structure, sequence composition and codon usage of the genome protein-coding genes were analyzed, and the prediction of the secondary structure of 22 tRNA and 2 rRNA, the control region structure, and the phylogeny were also conducted, which provided new information for phylogenetic studies of passerine birds. The entire mitochondrial genome of Remiz consobrinus was 16 737 bp in length, the accession number was KC463856 and the content of A, T, C, and G were 27.8%, 21.5%, 35.4%, and 15.3%, respectively. The genome harbored the same gene order with that of other birds, and contained 13 protein coding genes (PCGs), 22 tRNA, 2 rRNA, and a non-coding control region. There were 77 bp intergenic intervals between 18 pair genes and 30 bp overlaps between 7 pair genes. Except for ND3 gene, which used ATT as the initiation codon, all other PCGs started with the typical ATG codon. Except for COIII and ND4, which used incomplete termination codon T, the other 11 PCGs used standard TAA, TAG, AGA or AGG as termination codons. The tRNAs all formed typical cloverleaf secondary structure, except for tRNASer-AGN, which lost the DHU arm in its structure. A total of 27 base mismatches appeared, with 19 common G-U mismatches. The predicted secondary structure of SrRNA and LrRNA contained 3 domains with 47 helices and 6 domains with 60 helices, respectively. Besides F-box, D-box, C-box, and B-box, Bird similarity-box and CSB1-box were also found in the control region of Remiz consobrinus, as found in other bird species. Our results suggest Remizidae as a separate family. The monophyly of Sylviidae and Remizidae was supported.
该研究使用长PCR扩增和引物步移法测定了中华攀雀 (Remiz consobrinus) 线粒体基因组全序列,在对序列进行拼接和注释的基础上,分析了其结构、序列组成及蛋白编码基因密码子使用情况等,并对22个tRNA和2个rRNA的二级结构以及控制区结构进行了预测及系统发育分析,为雀形目鸟类的系统发育研究提供了新信息。中华攀雀线粒体基因组全长16 737 bp,GenBank登录号 KC463856,碱基A、T、C、G的含量分别为27.8%、21.5%、35.4%及15.3%, 37个基因排列顺序与已报道的其他鸟类基本一致,包含13个蛋白编码基因、22个tRNA基因、2个rRNA基因及1个非编码的控制区 (D-loop),有18对基因间共存在77 bp的间隔,7对基因间共存在30 bp的重叠。除ND3基因的起始密码子为ATT外,其余均为标准的ATG,11个蛋白编码基因的终止密码子为TAA、TAG、AGA或AGG,2个为不完全终止密码子T (COⅢ、ND4)。除tRNASer-AGN DHU臂缺失外,其余21个tRNA均可形成典型的三叶草结构,在出现的27处碱基错配中有19处为常见的G-U错配。SrRNA和LrRNA二级结构分别包含3个结构域47个茎环结构和6个结构域60个茎环结构,与所发表的其他鸟类rRNA二级结构大体一致。中华攀雀控制区发现了同样存在于其他鸟类控制区的保守框F-box、D-box、C-box、B-box、Bird similarity-box和CSB1-box。该研究支持将攀雀科作为独立的科,同时,支持莺总科与攀雀科的单系性。
Keywords: Complete mitochondrial genome; Control region; Protein-coding genes; Remiz consobrinus; rRNA secondary structure; tRNA secondary structure.