Background The mitochondrial genome (mitogenome) has been extensively used for phylogenetic and evolutionary analysis in Diptera, but the study of mitogenome is still scarce in the family Chironomidae. Methods Here, the first complete mitochondrial genomes of four Chironomid species representing Diamesinae, Orthocladiinae, Prodiamesinae and Tanypodinae are presented. Coupled with published mitogenomes of two, a comparative mitochondrial genomic analysis between six subfamilies of Chironomidae was carried out. Results Mitogenomes of Chironomidae are conserved in structure, each contains 37 typical genes and a control region, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, the control region displayed the highest A + T content. All protein coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the phylogenetic analysis covering six subfamilies within Chironomidae was conducted. The monophyly of Chironomidae is strongly supported. However, the topology of six subfamilies based on mitogenomes in this study is inconsistent with previous morphological and molecular studies. This may be due to the high mutation rate of the mitochondrial genetic markers within Chironomidae. Our results indicate that mitogenomes showed poor signals in phylogenetic reconstructions at the subfamily level of Chironomidae.

中文翻译：

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Diamesinae、Orthocladiinae、Prodiamesinae、Tanypodinae（双翅目：摇蚊科）的第一个完整线粒体基因组及其在系统发育中的意义

背景 线粒体基因组（线粒体基因组）已广泛用于双翅目的系统发育和进化分析，但在摇蚊科中线粒体基因组的研究仍然很少。方法在这里，提出了代表 Diamesinae、Orthocladiinae、Prodiamesinae 和 Tanypodinae 的四个摇蚊物种的第一个完整线粒体基因组。结合已发表的两个线粒体基因组，对摇蚊科六个亚科之间的线粒体基因组进行了比较分析。结果摇蚊科线粒体基因组结构保守，每个基因组包含37个典型基因和一个控制区，所有基因的排列顺序与祖先昆虫线粒体基因组相同。核苷酸组成存在很大偏差，对照区域显示最高的 A + T 含量。所有蛋白质编码基因都处于纯化选择之下，并且ATP8以最快的速度进化。此外，还对摇蚊科六个亚科进行了系统发育分析。摇蚊科的单系性得到强烈支持。然而，本研究中基于线粒体基因组的六个亚科的拓扑结构与之前的形态学和分子研究不一致。这可能是由于摇蚊科线粒体遗传标记的高突变率所致。我们的结果表明，丝裂基因组在摇蚊科亚科水平的系统发育重建中显示出较差的信号。