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

<h4>Background</h4>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 ani...

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Autores principales:	Rui Chen, Li-Yun Jiang, Ge-Xia Qiao
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/53a56b8937c44ab98179803c04f6dee1
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spelling	oai:doaj.org-article:53a56b8937c44ab98179803c04f6dee12021-11-18T08:13:23ZThe effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae.1932-620310.1371/journal.pone.0046190https://doaj.org/article/53a56b8937c44ab98179803c04f6dee12012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23056258/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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.Rui ChenLi-Yun JiangGe-Xia QiaoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 10, p e46190 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rui Chen Li-Yun Jiang Ge-Xia Qiao The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae.
description	<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions/significance</h4>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.
format	article
author	Rui Chen Li-Yun Jiang Ge-Xia Qiao
author_facet	Rui Chen Li-Yun Jiang Ge-Xia Qiao
author_sort	Rui Chen
title	The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae.
title_short	The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae.
title_full	The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae.
title_fullStr	The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae.
title_full_unstemmed	The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae.
title_sort	effectiveness of three regions in mitochondrial genome for aphid dna barcoding: a case in lachininae.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/53a56b8937c44ab98179803c04f6dee1
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The effectiveness of three regions in mitochondrial genome for aphid DNA barcoding: a case in Lachininae.

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