Data from: Mitochondrial capture enriches mito-DNA 100 folds enabling PCR-free mitogenomics biodiversity analysis

Biodiversity analyses based on Next Generation Sequencing (NGS) platforms have developed by leaps and bounds in recent years. A PCR-free strategy, which can alleviate taxonomic bias, was considered as a promising approach to delivering reliable species compositions of targeted environments. The major impediment of such a method is the lack of appropriate mitochondrial DNA enrichment ways. Because mitochondrial genomes (mitogenomes) make up only a small proportion of total DNA, PCR-free methods will inevitably result in a huge excess of data (> 99%). Furthermore, the massive volume of sequence data is highly demanding on computing resources. Here, we present a mitogenome enrichment pipeline via a gene capture chip that was designed by virtue of the mitogenome sequences of the 1000 Insect Transcriptome Evolution project (1KITE, www .1kite . org). A mock sample containing 49 species was used to evaluate the efficiency of the mitogenome capture method. We demonstrate that the proportion of mitochondrial DNA can be increased by ca. 100-fold (from the original 0.47% to 42.52%). Variation in phylogenetic distances of target taxa to the probe set could in principle result in bias in abundance. However, the frequencies of input taxa were largely maintained after capture (R2=0.81). We suggest that our mitogenome capture approach coupled with PCR-free shotgun sequencing could provide ecological researchers an efficient NGS method to deliver reliable biodiversity assessment.

近年来，基于下一代测序（Next Generation Sequencing, NGS）平台的生物多样性分析研究发展迅猛。无PCR扩增策略可减轻分类学偏差，被视为获取目标环境可靠物种组成的极具前景的方法。该方法的主要障碍在于缺乏适配的线粒体DNA富集手段：由于线粒体基因组（mitogenomes）仅占总DNA的极小比例，无PCR扩增策略不可避免地会产生远超需求的测序数据（占比超99%）。此外，海量的测序数据对计算资源有着极高的要求。本研究依托千种昆虫转录组进化项目（1KITE, www.1kite.org）的线粒体基因组序列设计基因捕获芯片，开发了一套线粒体基因组富集流程。我们使用包含49个物种的模拟样本对该线粒体基因组捕获方法的效率进行了评估。结果显示，线粒体DNA的占比可提升约100倍（从初始的0.47%提升至42.52%）。理论上，目标类群与探针组之间的系统发育距离差异可能会导致丰度偏差，但捕获后输入样本的类群频率整体得以保留（决定系数R²=0.81）。我们认为，本研究开发的线粒体基因组捕获方法结合无PCR扩增鸟枪法测序，可为生态领域研究者提供一套高效的NGS技术方案，以实现可靠的生物多样性评估。