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The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae - PubMed

The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae

Rui Chen et al. PLoS One. 2012.

Erratum in

  • PLoS One. 2013;8(5). doi:10.1371/annotation/3595dc99-a0fc-47fc-b21b-b54003054ffd

Abstract

Background: The mitochondrial gene COI has been widely used by taxonomists as a standard DNA barcode sequence for the identification of many animal species. However, the COI region is of limited use for identifying certain species and is not efficiently amplified by PCR in all animal taxa. To evaluate the utility of COI as a DNA barcode and to identify other barcode genes, we chose the aphid subfamily Lachninae (Hemiptera: Aphididae) as the focus of our study. We compared the results obtained using COI with two other mitochondrial genes, COII and Cytb. In addition, we propose a new method to improve the efficiency of species identification using DNA barcoding.

Methodology/principal findings: Three mitochondrial genes (COI, COII and Cytb) were sequenced and were used in the identification of over 80 species of Lachninae. The COI and COII genes demonstrated a greater PCR amplification efficiency than Cytb. Species identification using COII sequences had a higher frequency of success (96.9% in "best match" and 90.8% in "best close match") and yielded lower intra- and higher interspecific genetic divergence values than the other two markers. The use of "tag barcodes" is a new approach that involves attaching a species-specific tag to the standard DNA barcode. With this method, the "barcoding overlap" can be nearly eliminated. As a result, we were able to increase the identification success rate from 83.9% to 95.2% by using COI and the "best close match" technique.

Conclusions/significance: A COII-based identification system should be more effective in identifying lachnine species than COI or Cytb. However, the Cytb gene is an effective marker for the study of aphid population genetics due to its high sequence diversity. Furthermore, the use of "tag barcodes" can improve the accuracy of DNA barcoding identification by reducing or removing the overlap between intra- and inter-specific genetic divergence values.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Basal nodes of the NJ tree based on distances obtained using the K2P model.

A, B, and C are the COI, COII and Cytb NJ trees, respectively. The number of identical samples is given in brackets.

Figure 2
Figure 2. NJ analysis of K2P distances in Lachnus siniquercus Zhang, L. tropicalis (van der Goot), L. roboris (Linnaeus) and L. yunlongensis Zhang.

A, B, and C are the COI, COII and Cytb NJ trees, respectively.

Figure 3
Figure 3. NJ analysis of K2P distances in Cinara piniarmandicola Zhang, Zhang & Zhong, C. bungeanae Zhang, Zhang & Zhong and C. orientalis (Takahashi).

A, B, and C are the COI, COII and Cytb NJ trees, respectively.

Figure 4
Figure 4. Frequency histogram of intra- and interspecific genetic divergence between C. formosana (Takahashi) and C. pinea (Zetterstedt) before (above) and after (below) using “tag barcodes.”

Genetic divergence was calculated using K2P model.

Figure 5
Figure 5. Frequency histogram of intra- and interspecific genetic divergence among Lachninae before (above) and after (below) using “tag barcodes.”

Genetic divergence was calculated using K2P model.

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Grants and funding

This work was funded by the National Natural Sciences Foundation of China (No. 30830017), National Science Funds for Distinguished Young Scientists (No. 31025024), National Science Fund for Fostering Talents in Basic Research (No. J0930004), and the Ministry of Science and Technology of the People's Republic of China (MOST Grant No. 2011FY120200). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.