Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants

De Zhu Li, Lian Ming Gao, Hong Tao Li, Hong Wang, Xue Jun Ge, Jian Quan Liu, Zhi Duan Chen, Shi Liang Zhou, Shi Lin Chen, Jun Bo Yang, Cheng Xin Fu, Chun Xia Zeng, Hai Fei Yan, Yingjie Zhu, Yong Shuai Sun, Si Yun Chen, Lei Zhao, Kun Wang, Tuo Yang, Guang Wen Duan

Research output: Contribution to journalArticle

453 Citations (Scopus)

Abstract

A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1% of species, compared with only 49.7% with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.

Original languageEnglish (US)
Pages (from-to)19641-19646
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume108
Issue number49
DOIs
StatePublished - Dec 6 2011
Externally publishedYes

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Plastids
Seeds
Gymnosperms
Angiosperms
Intergenic DNA
Genetic Markers
Datasets

Keywords

  • Land plants
  • Nuclear ribosomal (nr) DNA
  • Species identification

ASJC Scopus subject areas

  • General

Cite this

Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. / Li, De Zhu; Gao, Lian Ming; Li, Hong Tao; Wang, Hong; Ge, Xue Jun; Liu, Jian Quan; Chen, Zhi Duan; Zhou, Shi Liang; Chen, Shi Lin; Yang, Jun Bo; Fu, Cheng Xin; Zeng, Chun Xia; Yan, Hai Fei; Zhu, Yingjie; Sun, Yong Shuai; Chen, Si Yun; Zhao, Lei; Wang, Kun; Yang, Tuo; Duan, Guang Wen.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 108, No. 49, 06.12.2011, p. 19641-19646.

Research output: Contribution to journalArticle

Li, DZ, Gao, LM, Li, HT, Wang, H, Ge, XJ, Liu, JQ, Chen, ZD, Zhou, SL, Chen, SL, Yang, JB, Fu, CX, Zeng, CX, Yan, HF, Zhu, Y, Sun, YS, Chen, SY, Zhao, L, Wang, K, Yang, T & Duan, GW 2011, 'Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants', Proceedings of the National Academy of Sciences of the United States of America, vol. 108, no. 49, pp. 19641-19646. https://doi.org/10.1073/pnas.1104551108
Li, De Zhu ; Gao, Lian Ming ; Li, Hong Tao ; Wang, Hong ; Ge, Xue Jun ; Liu, Jian Quan ; Chen, Zhi Duan ; Zhou, Shi Liang ; Chen, Shi Lin ; Yang, Jun Bo ; Fu, Cheng Xin ; Zeng, Chun Xia ; Yan, Hai Fei ; Zhu, Yingjie ; Sun, Yong Shuai ; Chen, Si Yun ; Zhao, Lei ; Wang, Kun ; Yang, Tuo ; Duan, Guang Wen. / Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. In: Proceedings of the National Academy of Sciences of the United States of America. 2011 ; Vol. 108, No. 49. pp. 19641-19646.
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abstract = "A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7{\%}), whereas ITS performed relatively well (79{\%}) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1{\%} of species, compared with only 49.7{\%} with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2{\%} of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.",
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AU - Ge, Xue Jun

AU - Liu, Jian Quan

AU - Chen, Zhi Duan

AU - Zhou, Shi Liang

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AU - Yang, Jun Bo

AU - Fu, Cheng Xin

AU - Zeng, Chun Xia

AU - Yan, Hai Fei

AU - Zhu, Yingjie

AU - Sun, Yong Shuai

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AU - Wang, Kun

AU - Yang, Tuo

AU - Duan, Guang Wen

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