Zhang Nai-Xin, Yu Guo, Li Ting-Jing, He Qi-Yi, Zhou Yong, Si Feng-Ling, Ren Shuang, Chen Bin
Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, 401331, China.
PLoS One. 2015 Oct 1;10(10):e0139736. doi: 10.1371/journal.pone.0139736. eCollection 2015.
Delia antiqua is a major underground agricultural pest widely distributed in Asia, Europe and North America. In this study, we sequenced and annotated the complete mitochondrial genome of this species, which is the first report of complete mitochondrial genome in the family Anthomyiidae. This genome is a double-stranded circular molecule with a length of 16,141 bp and an A+T content of 78.5%. It contains 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) and a non-coding A+T rich region or control region. The mitochondrial genome of Delia antiqua presents a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All of the 13 protein-coding genes use ATN as an initiation codon except for the COI gene that starts with ATCA. Most protein-coding genes have complete termination codons but COII and ND5 that have the incomplete termination codon T. This bias is reflected in both codon usage and amino acid composition. The protein-coding genes in the D. antiqua mitochondrial genome prefer to use the codon UUA (Leu). All of the tRNAs have the typical clover-leaf structure, except for tRNASer(AGN) that does not contain the dihydrouridine (DHU) arm like in many other insects. There are 7 mismatches with U-U in the tRNAs. The location and structure of the two rRNAs are conservative and stable when compared with other insects. The control region between 12S rRNA and tRNAIle has the highest A+T content of 93.7% in the D. antiqua mitochondrial genome. The control region includes three kinds of special regions, two highly conserved poly-T stretches, a (TA)n stretch and several G(A)nT structures considered important elements related to replication and transcription. The nucleotide sequences of 13 protein-coding genes are used to construct the phylogenetics of 26 representative Dipteran species. Both maximum likelihood and Bayesian inference analyses suggest a closer relationship of D. antiqua in Anthomyiidae with Calliphoridae, Calliphoridae is a paraphyly, and both Oestroidea and Muscoidea are polyphyletic.
葱蝇是一种主要的地下农业害虫，广泛分布于亚洲、欧洲和北美洲。在本研究中，我们对该物种的完整线粒体基因组进行了测序和注释，这是花蝇科完整线粒体基因组的首次报道。该基因组是一个双链环状分子，长度为16141 bp，A+T含量为78.5%。它包含37个基因（13个蛋白质编码基因、22个tRNA和2个rRNA）以及一个富含A+T的非编码区或控制区。葱蝇的线粒体基因组在核苷酸组成上呈现出明显的偏向性，具有正的AT偏斜和负的GC偏斜。除了起始密码子为ATCA的COI基因外，其余13个蛋白质编码基因均以ATN作为起始密码子。大多数蛋白质编码基因具有完整的终止密码子，但COII和ND5具有不完整的终止密码子T。这种偏向性在密码子使用和氨基酸组成中均有体现。葱蝇线粒体基因组中的蛋白质编码基因倾向于使用密码子UUA（亮氨酸）。除了tRNASer(AGN) 外，所有tRNA均具有典型的三叶草结构，tRNASer(AGN) 不像许多其他昆虫那样含有二氢尿嘧啶（DHU）臂。tRNA中有7个U-U错配。与其他昆虫相比，两个rRNA的位置和结构保守且稳定。在葱蝇线粒体基因组中，12S rRNA和tRNAIle之间的控制区A+T含量最高，为93.7%。该控制区包括三种特殊区域、两个高度保守的多聚T序列、一个(TA)n序列以及几个被认为是与复制和转录相关的重要元件的G(A)nT结构。利用13个蛋白质编码基因的核苷酸序列构建了26种代表性双翅目物种的系统发育树。最大似然法和贝叶斯推断分析均表明，花蝇科中的葱蝇与丽蝇科关系更近，丽蝇科是并系群，狂蝇总科和蝇总科均为多系群。
