Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)
Beyond barcoding: A mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae)
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DOI：
10.1016/j.gene.2012.09.103
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发表时间：
2012-12-15
期刊：
影响因子：
3.5
通讯作者：
Cameron, Stephen L.
中科院分区：
文献类型：
--
作者：
Nelson, Leigh A.;Lambkin, Christine L.;Cameron, Stephen L.
丽蝇科（丽蝇）的成员对于医疗和兽医管理具有重要意义，因为某些物种能够以幼虫的形式食用活体肉，并且由于其他物种能够在尸体中发育，因此对于法医调查也具有重要意义。由于难以准确识别绿头苍蝇幼虫的物种，因此需要对该科进行基于 DNA 的诊断，但广泛使用的 DNA 条形码标记 cox1 已被证明对该科内的几个类群失败。此外，丽丽科内的许多系统发育关系仍未解决，特别是更深层次的关系。整个 mt 基因组测序已被证明是识别信息最丰富的诊断标记和解决系统发育关系的有效方法。对 27 个完整或接近完整的 mt 基因组进行了测序，代表 13 个物种、7 个属和 4 个丽蝇亚科以及相关的寄蝇科 (Tachinidae) 的成员。为对一种丽蝇物种进行测序而开发的 PCR 和测序引物可以重复用于对同一超科内的相关物种进行测序，成功率范围为 61% 至 100%，这证明了 mt 基因组数据集组装的速度和效率。在一系列分类学尺度上对 13 个蛋白质编码基因和 2 个核糖体 RNA 基因中每一个的分子差异进行比较，确定了开发为诊断标记的新目标，这些标记比以前在丽蝇中使用的标记多变 117-200%。对整个 mt 基因组序列的系统发育分析为科和亚科水平关系提供了更有力的支持。 Calliphoridae 是多系的，其中 Polleninae 与 Tachinidae 关系更近，而 Sarcophagidae 是其余 Calliphorids 的姐妹群。在 Calliphoridae 中，人们强烈支持 Chrysomyinae 和 Luciliinae 的单系以及 Luciliinae 与 Calliphorinae 的姐妹群。 Chrysomya内部的关系没有得到很好的解决。完整的mt基因组数据支持了先前证明的铜绿蝇相对于丝光藻的并系性，并让我们得出结论，这是由于现代丝光藻种群最后一个共同祖先之前的杂交渐渗，而不是由于最近的杂交、核假基因或不完整的谱系排序。 (C) 2012 Elsevier B.V. 保留所有权利。
Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117-200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting. (C) 2012 Elsevier B.V. All rights reserved.