Bioengineering Research Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
Department of Bioengineering and Technology, Gauhati University Institute of Science and Technology (GUIST), Gauhati University, Guwahati, Assam, India.
Sci Rep. 2022 Apr 29;12(1):7028. doi: 10.1038/s41598-022-10547-8.
Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.
乌兹蝇（蝇科）是一种寄生于鳞翅目昆虫的内寄生蝇，在全球范围内给丝绸业造成了重大经济损失。在这里，我们首次报道了鳞翅目寄生蜂小眼蝇属（Acc：KY644698，15080bp，A+T=78.41%）的完整线粒体基因组，小眼蝇属是在印度阿萨姆邦和梅加拉亚邦发现的大蚕蛾（Antheraea assamensis）的寄生蝇。这项研究证实，小眼蝇属的线粒体基因组基因含量和排列与其他双翅目蝇科和肿腿蜂科的 Oestroidea 超级科相似，这是祖先进化的双翅目特征。尽管丽蝇科和皮蝇科的 tRNA 发生了易位和插入，形成了独特的基因间区（IGS）和重叠区（OL），但其中一些（IGS、OL）在 Oestroidea 蝇科中得到了保守。与 Oestroidea 相对应的，Tachinidae 线粒体基因组在其蛋白质编码基因（PCGs）中具有更高的 AT 含量和 AT 偏向密码子。在这个新物种的所有 3722 个密码子中，大约有 92.07%的密码子在第三位密码子位置具有 A/T。控制区（CR）中高比例的 AT 和重复序列会影响序列覆盖度，从而导致 CR 较短（小眼蝇属：168bp）和较小的双翅目蝇科线粒体基因组。我们的研究揭示了那些具有高 AT 含量的基因，其有效密码子数减少，导致密码子使用偏好性较高。中性检验表明，自然选择对密码子使用偏好性的影响强于定向突变压力。这项研究还表明，较长的 PCGs（如 nad5、cox1）比较短的 PCGs（如 atp8、nad4l）具有更高的密码子使用偏好性。当第三位密码子位置的 AT 含量增加时，分歧率呈非线性增加，同义分歧率高于非同义分歧率，导致强烈的纯化选择。系统发育分析表明，小眼蝇属非常适合于食虫性双翅目蝇科幼虫。在 Tachinidae 科中，偏倚密码子的使用可能会减少有效密码子的数量，而纯化选择保留了其线粒体基因组的核心功能，这有助于其内寄生生活方式和生存策略的有效代谢。
