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

• Published in: PloS one 2012-10, Vol.7 (10), p.e46190-e46190
• Main Authors: Chen, Rui, Jiang, Li-Yun, Qiao, Ge-Xia
• Format: Article
• Language: English
• Subjects: Animal species; Animals; Aphididae; Aphids; Aphids - anatomy & histology; Aphids - classification; Aphids - genetics; Bar codes; Biology; Comparative analysis; CytB gene; Cytochrome; Cytochromes b - classification; Cytochromes b - genetics; Data analysis; Deoxyribonucleic acid; Divergence; DNA; DNA barcoding; DNA Barcoding, Taxonomic - methods; DNA, Mitochondrial - chemistry; DNA, Mitochondrial - genetics; Electron Transport Complex IV - classification; Electron Transport Complex IV - genetics; Ephemeroptera; Evolution; Gene sequencing; Genes; Genetic research; Genetic Variation; Genetics; Genome, Mitochondrial - genetics; Genomes; Genomics; Hemiptera; Hymenoptera; Identification; Insect Proteins - classification; Insect Proteins - genetics; Insects; Interspecific; Laboratories; Lepidoptera; Mitochondria; Mitochondrial DNA; Molecular biology; Morphology; Next-generation sequencing; Nucleotide sequence; Phylogenetics; Phylogeny; Polymerase chain reaction; Population genetics; Population studies; Protein Subunits - classification; Protein Subunits - genetics; Reproducibility of Results; Sequence Analysis, DNA; Species; Species Specificity; Taxa; Trees; Trends; Zoology
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0046190

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. 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. 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.