Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals.
Potential efficacy of mitochondrial genes for animal DNA barcoding: a case study using eutherian mammals.
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线粒体基因对动物 DNA 条形码的潜在功效：使用真兽类哺乳动物的案例研究。
DOI：
10.1186/1471-2164-12-84
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发表时间：
2011-01-28
期刊：
影响因子：
4.4
通讯作者：
Zhu C
中科院分区：
文献类型：
--
作者：
Luo A;Zhang A;Ho SY;Xu W;Zhang Y;Shi W;Cameron SL;Zhu C
基因位点的明智选择是DNA条形码功效的核心。目前动物中的DNA条形码涉及使用线粒体细胞色素氧化酶1基因（CO1）的5'端来诊断和划分物种。然而，没有令人信服的先验原因，专门关注这一地区，它已被证明，它表现不佳的某些动物群体。为了探索替代的线粒体条形码区域，我们比较了通用CO1条形码区域与真兽目哺乳动物中其他线粒体蛋白编码基因的功效。四个标准用于此比较：恢复物种的数量，物种内和物种之间的序列变异性，分辨率以上的物种，和突变饱和度的分类水平。基于1，179个真兽目线粒体基因组，我们发现通用CO1条形码区域是线粒体基因整体的良好代表，因为高物种恢复率（> 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没有显著差异。然而，种内和种间变异之间的重叠仍然是所有线粒体基因的问题。我们的研究结果还表明，任何选择的线粒体基因的DNA条形码未能提供显着的分辨率在更高的分类水平。我们认为，CO1条形码区，通用的DNA条形码，是首选的线粒体蛋白质编码基因作为分子诊断至少真兽目物种鉴定。尽管如此，DNA条形码与此标记可能仍然是有问题的某些真兽目类群和我们的方法可以用来测试潜在的条形码基因座为这样的群体。
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.
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DOI：
10.1098/rsbl.2003.0025
发表时间：
2003-08-07
影响因子：
4.7
作者：
Hebert, PDN;Ratnasingham, S;deWaard, JR
通讯作者：
deWaard, JR
影响因子：
9.8
作者：
Hebert PD;Stoeckle MY;Zemlak TS;Francis CM
通讯作者：
Francis CM
影响因子：
4.4
作者：
Ficetola GF;Coissac E;Zundel S;Riaz T;Shehzad W;Bessière J;Taberlet P;Pompanon F
通讯作者：
Pompanon F
影响因子：
6.5
作者：
Cameron, Stephen;Rubinoff, Daniel;Will, Kipling
通讯作者：
Will, Kipling
影响因子：
3.7
作者：
Aliabadian M;Kaboli M;Nijman V;Vences M
通讯作者：
Vences M