Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China.
BMC Genomics. 2011 Jan 28;12:84. doi: 10.1186/1471-2164-12-84.
A well-informed choice of genetic locus is central to the efficacy of DNA barcoding. Current DNA barcoding in animals involves the use of the 5' half of the mitochondrial cytochrome oxidase 1 gene (CO1) to diagnose and delimit species. However, there is no compelling a priori reason for the exclusive focus on this region, and it has been shown that it performs poorly for certain animal groups. To explore alternative mitochondrial barcoding regions, we compared the efficacy of the universal CO1 barcoding region with the other mitochondrial protein-coding genes in eutherian mammals. Four criteria were used for this comparison: the number of recovered species, sequence variability within and between species, resolution to taxonomic levels above that of species, and the degree of mutational saturation.
Based on 1,179 mitochondrial genomes of eutherians, we found that the universal CO1 barcoding region is a good representative of mitochondrial genes as a whole because the high species-recovery rate (> 90%) was similar to that of other mitochondrial genes, and there were no significant differences in intra- or interspecific variability among genes. However, an overlap between intra- and interspecific variability was still problematic for all mitochondrial genes. Our results also demonstrated that any choice of mitochondrial gene for DNA barcoding failed to offer significant resolution at higher taxonomic levels.
We suggest that the CO1 barcoding region, the universal DNA barcode, is preferred among the mitochondrial protein-coding genes as a molecular diagnostic at least for eutherian species identification. Nevertheless, DNA barcoding with this marker may still be problematic for certain eutherian taxa and our approach can be used to test potential barcoding loci for such groups.
知情选择遗传基因座是 DNA 条码有效性的核心。目前动物 DNA 条码使用线粒体细胞色素氧化酶 1 基因（CO1）的 5' 端来诊断和界定物种。然而，没有令人信服的先验理由将注意力仅仅集中在这个区域，并且已经表明它在某些动物群体中的表现不佳。为了探索替代的线粒体条码区域，我们比较了通用 CO1 条码区域与真兽类哺乳动物其他线粒体蛋白编码基因的有效性。使用了四个标准进行比较：回收物种的数量、物种内和物种间的序列变异性、分类学水平的分辨率以及突变饱和程度。
基于 1179 个真兽类动物的线粒体基因组，我们发现通用 CO1 条码区域是整个线粒体基因的良好代表，因为高物种回收率（>90%）与其他线粒体基因相似，并且基因之间的种内或种间变异性没有显著差异。然而，所有线粒体基因的种内和种间变异性之间仍然存在重叠问题。我们的结果还表明，任何选择线粒体基因进行 DNA 条码都未能在更高的分类学水平上提供显著的分辨率。
我们建议，在真兽类物种鉴定中，作为分子诊断，CO1 条码区，即通用 DNA 条码，在所有线粒体蛋白编码基因中是首选。然而，使用此标记的 DNA 条码对于某些真兽类分类群仍然可能存在问题，并且我们的方法可用于测试此类群体的潜在条码基因座。
