Rach Jessica, Bergmann Tjard, Paknia Omid, DeSalle Rob, Schierwater Bernd, Hadrys Heike
ITZ, Ecology & Evolution, TiHo Hannover, Hannover, D-30559, Germany.
Sackler Institute of Comparative Genomics, American Museum of Natural History, New York, NY 10024, United States of America.
PLoS One. 2017 Apr 13;12(4):e0174842. doi: 10.1371/journal.pone.0174842. eCollection 2017.
The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent "Folmer region", a 648 basepair fragment at the 5' end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the "Folmer region", the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the "Folmer region" using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic "environment", this new marker will further enhance the discrimination power at the species level.
DNA条形码技术用于识别单一物种和表征物种组成的潜力在很大程度上取决于标记的选择。著名的“福尔默区域”，即线粒体CO1基因5'端的一个648碱基对片段，传统上一直被用作后生动物的通用DNA条形码区域。为了找到一种适合用于蜻蜓目（蜻蜓和豆娘）生物监测的标记，我们在此探索CO1基因的一个新区域（CO1B），用于对23种蜻蜓和豆娘的51个种群进行DNA条形码分析。我们比较了“福尔默区域”、线粒体ND1基因（烟酰胺腺嘌呤二核苷酸脱氢酶1）和新的CO1区域在以下方面的表现：（i）序列生成的速度和可重复性，（ii）平行进化的程度，以及（iii）用于区分亲缘关系密切的姐妹分类单元和种群的诊断特征数量。这些基因区域在这些标准方面的表现差异很大。CO1B和ND1的扩增都具有高度可重复性，并且CO1B在区分不同分类水平的姐妹分类单元方面显示出最高的潜力。相比之下，使用通用引物扩增“福尔默区域”很困难，并且该片段的第三个密码子位置已经经历了核苷酸替代饱和。最重要的是，探索CO1基因的这个新条形码区域发现，在亲缘关系密切的姐妹分类单元之间具有更高的区分能力。连同设计适合特定分类“环境”的分层条形码方法，这个新标记将进一步提高物种水平的区分能力。
