Thanks to the development of high‐throughput sequencing technologies, target enrichment sequencing of nuclear ultraconserved DNA elements (UCEs) now allows routine inference of phylogenetic relationships from thousands of genomic markers. Recently, it has been shown that mitochondrial DNA (mtDNA) is frequently sequenced alongside the targeted loci in such capture experiments. Despite its broad evolutionary interest, mtDNA is rarely assembled and used in conjunction with nuclear markers in capture‐based studies. Here, we developed MitoFinder, a user‐friendly bioinformatic pipeline, to efficiently assemble and annotate mitogenomic data from hundreds of UCE libraries. As a case study, we used ants (Formicidae) for which 501 UCE libraries have been sequenced whereas only 29 mitogenomes are available. We compared the efficiency of four different assemblers (IDBA‐UD, MEGAHIT, MetaSPAdes, and Trinity) for assembling both UCE and mtDNA loci. Using MitoFinder, we show that metagenomic assemblers, in particular MetaSPAdes, are well suited to assemble both UCEs and mtDNA. Mitogenomic signal was successfully extracted from all 501 UCE libraries, allowing us to confirm species identification using CO1 barcoding. Moreover, our automated procedure retrieved 296 cases in which the mitochondrial genome was assembled in a single contig, thus increasing the number of available ant mitogenomes by an order of magnitude. By utilizing the power of metagenomic assemblers, MitoFinder provides an efficient tool to extract complementary mitogenomic data from UCE libraries, allowing testing for potential mitonuclear discordance. Our approach is potentially applicable to other sequence capture methods, transcriptomic data and whole genome shotgun sequencing in diverse taxa. The MitoFinder software is available from GitHub (https://github.com/RemiAllio/MitoFinder).

中文翻译：

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MitoFinder：在靶标丰富的系统发育组学中高效自动地大规模提取线粒体基因组数据。

得益于高通量测序技术的发展，核超保守DNA元素（UCE）的靶标富集测序现在可以从数千个基因组标记中常规推断出系统发育关系。最近，已经表明在这样的捕获实验中，线粒体DNA（mtDNA）经常与靶基因座一起测序。尽管具有广泛的进化兴趣，但在基于捕获的研究中，mtDNA很少被组装并与核标记结合使用。在这里，我们开发了MitoFinder，这是一种用户友好的生物信息流水线，可以有效地组装和注释来自数百个UCE库的线粒体数据。作为案例研究，我们使用已对501个UCE文库进行了测序的蚂蚁（Formicidae），而只有29个有丝分裂基因组可用。我们比较了四种不同的组装器（IDBA-UD，MEGAHIT，MetaSPAdes和Trinity）组装UCE和mtDNA位点的效率。使用MitoFinder，我们显示了宏基因组组装器，尤其是MetaSPAdes，非常适合组装UCE和mtDNA。从所有501个UCE库中成功提取了线粒体信号，这使我们能够使用CO1条形码。此外，我们的自动化程序检索了296个线粒体基因组组装在一个重叠群中的案例，从而使可用的蚂蚁有丝分裂基因组的数量增加了一个数量级。通过利用宏基因组组装器的功能，MitoFinder提供了一种有效的工具，可以从UCE库中提取互补的细胞基因组数据，从而可以测试潜在的微核不一致性。我们的方法可能适用于其他序列捕获方法，转录组数据和不同分类群中的全基因组shot弹枪测序。可从GitHub（https://github.com/RemiAllio/MitoFinder）获得MitoFinder软件。