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Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals

BACKGROUND: The internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA is regarded as one of the candidate DNA barcodes because it possesses a number of valuable characteristics, such as the availability of conserved regions for designing universal primers, the ease of its amplificatio...

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Autores principales: Yao, Hui, Song, Jingyuan, Liu, Chang, Luo, Kun, Han, Jianping, Li, Ying, Pang, Xiaohui, Xu, Hongxi, Zhu, Yingjie, Xiao, Peigen, Chen, Shilin
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2948509/
https://www.ncbi.nlm.nih.gov/pubmed/20957043
http://dx.doi.org/10.1371/journal.pone.0013102
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author Yao, Hui
Song, Jingyuan
Liu, Chang
Luo, Kun
Han, Jianping
Li, Ying
Pang, Xiaohui
Xu, Hongxi
Zhu, Yingjie
Xiao, Peigen
Chen, Shilin
author_facet Yao, Hui
Song, Jingyuan
Liu, Chang
Luo, Kun
Han, Jianping
Li, Ying
Pang, Xiaohui
Xu, Hongxi
Zhu, Yingjie
Xiao, Peigen
Chen, Shilin
author_sort Yao, Hui
collection PubMed
description BACKGROUND: The internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA is regarded as one of the candidate DNA barcodes because it possesses a number of valuable characteristics, such as the availability of conserved regions for designing universal primers, the ease of its amplification, and sufficient variability to distinguish even closely related species. However, a general analysis of its ability to discriminate species in a comprehensive sample set is lacking. METHODOLOGY/PRINCIPAL FINDINGS: In the current study, 50,790 plant and 12,221 animal ITS2 sequences downloaded from GenBank were evaluated according to sequence length, GC content, intra- and inter-specific divergence, and efficiency of identification. The results show that the inter-specific divergence of congeneric species in plants and animals was greater than its corresponding intra-specific variations. The success rates for using the ITS2 region to identify dicotyledons, monocotyledons, gymnosperms, ferns, mosses, and animals were 76.1%, 74.2%, 67.1%, 88.1%, 77.4%, and 91.7% at the species level, respectively. The ITS2 region unveiled a different ability to identify closely related species within different families and genera. The secondary structure of the ITS2 region could provide useful information for species identification and could be considered as a molecular morphological characteristic. CONCLUSIONS/SIGNIFICANCE: As one of the most popular phylogenetic markers for eukaryota, we propose that the ITS2 locus should be used as a universal DNA barcode for identifying plant species and as a complementary locus for CO1 to identify animal species. We have also developed a web application to facilitate ITS2-based cross-kingdom species identification (http://its2-plantidit.dnsalias.org).
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spelling pubmed-29485092010-10-18 Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals Yao, Hui Song, Jingyuan Liu, Chang Luo, Kun Han, Jianping Li, Ying Pang, Xiaohui Xu, Hongxi Zhu, Yingjie Xiao, Peigen Chen, Shilin PLoS One Research Article BACKGROUND: The internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA is regarded as one of the candidate DNA barcodes because it possesses a number of valuable characteristics, such as the availability of conserved regions for designing universal primers, the ease of its amplification, and sufficient variability to distinguish even closely related species. However, a general analysis of its ability to discriminate species in a comprehensive sample set is lacking. METHODOLOGY/PRINCIPAL FINDINGS: In the current study, 50,790 plant and 12,221 animal ITS2 sequences downloaded from GenBank were evaluated according to sequence length, GC content, intra- and inter-specific divergence, and efficiency of identification. The results show that the inter-specific divergence of congeneric species in plants and animals was greater than its corresponding intra-specific variations. The success rates for using the ITS2 region to identify dicotyledons, monocotyledons, gymnosperms, ferns, mosses, and animals were 76.1%, 74.2%, 67.1%, 88.1%, 77.4%, and 91.7% at the species level, respectively. The ITS2 region unveiled a different ability to identify closely related species within different families and genera. The secondary structure of the ITS2 region could provide useful information for species identification and could be considered as a molecular morphological characteristic. CONCLUSIONS/SIGNIFICANCE: As one of the most popular phylogenetic markers for eukaryota, we propose that the ITS2 locus should be used as a universal DNA barcode for identifying plant species and as a complementary locus for CO1 to identify animal species. We have also developed a web application to facilitate ITS2-based cross-kingdom species identification (http://its2-plantidit.dnsalias.org). Public Library of Science 2010-10-01 /pmc/articles/PMC2948509/ /pubmed/20957043 http://dx.doi.org/10.1371/journal.pone.0013102 Text en Yao et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Yao, Hui
Song, Jingyuan
Liu, Chang
Luo, Kun
Han, Jianping
Li, Ying
Pang, Xiaohui
Xu, Hongxi
Zhu, Yingjie
Xiao, Peigen
Chen, Shilin
Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
title Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
title_full Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
title_fullStr Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
title_full_unstemmed Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
title_short Use of ITS2 Region as the Universal DNA Barcode for Plants and Animals
title_sort use of its2 region as the universal dna barcode for plants and animals
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2948509/
https://www.ncbi.nlm.nih.gov/pubmed/20957043
http://dx.doi.org/10.1371/journal.pone.0013102
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