Expedient identification of Magnoliaceae species by DNA barcoding

Hua Yu, Kongyun Wu, Jingyuan Song, Yingjie Zhu, Hui Yao, Kun Luo, Yong Dai, Shijun Xu, Yulin Lin

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Magnoliaceae species have high ornamental and medicinal importance, but they are morphologically similar. DNA barcoding has been regarded as a rapid and effective approach for species identification. To determine the efficiency of expedient identification in Magnoliaceae species by DNA barcoding, in this study, we collected 83 samples belonging to 68 species in 10 genera of Magnoliaceae. Candidate DNA regions (i.e.,psbA-trnH, matK, rbcL, ITS, ITS2, rpoB, and rpoC1) were amplified and sequenced for the evaluation of their PCR amplification, sequencing efficiency, intra-and inter-specific divergence and barcoding gap by sequence alignment and Kimura 2-Parameter (K2P) distance analysis, and the rate of correct identification was assessed by BLAST analysis. The results showed that psbA-trnH and matK exhibited high performance in efficiency of PCR amplification and the rate of successful sequencing, followed by rbcL. Associated with the analysis of 199 sequences for 96 species in 9 genera of Magnoliaceae retrieved from GenBank, it was discovered that psbA-trnH was highest in inter-specific divergence and rate of correct identification, indicating its efficiency in the identification of Magnoliaceae species. Besides, matK was also easy to amplify and had high rate of correct identification, suggesting its potential to distinguish Magnoliaceae species. This study indicates that DNA barcoding provides an effective technique for the expedient identification of morphologically similar species, and it is a powerful aid to the conventional methods for species identification.

Original languageEnglish (US)
Pages (from-to)47-53
Number of pages7
JournalPlant OMICS
Volume7
Issue number1
StatePublished - Feb 21 2014
Externally publishedYes

Fingerprint

Magnoliaceae
DNA barcoding
barcoding
sequence alignment
sequence analysis
DNA
methodology

Keywords

  • Candidate DNA region
  • DNA barcoding
  • Intra-and inter-specific divergence
  • Magnoliaceae species
  • Plant identification

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Plant Science

Cite this

Yu, H., Wu, K., Song, J., Zhu, Y., Yao, H., Luo, K., ... Lin, Y. (2014). Expedient identification of Magnoliaceae species by DNA barcoding. Plant OMICS, 7(1), 47-53.

Expedient identification of Magnoliaceae species by DNA barcoding. / Yu, Hua; Wu, Kongyun; Song, Jingyuan; Zhu, Yingjie; Yao, Hui; Luo, Kun; Dai, Yong; Xu, Shijun; Lin, Yulin.

In: Plant OMICS, Vol. 7, No. 1, 21.02.2014, p. 47-53.

Research output: Contribution to journalArticle

Yu, H, Wu, K, Song, J, Zhu, Y, Yao, H, Luo, K, Dai, Y, Xu, S & Lin, Y 2014, 'Expedient identification of Magnoliaceae species by DNA barcoding', Plant OMICS, vol. 7, no. 1, pp. 47-53.
Yu H, Wu K, Song J, Zhu Y, Yao H, Luo K et al. Expedient identification of Magnoliaceae species by DNA barcoding. Plant OMICS. 2014 Feb 21;7(1):47-53.
Yu, Hua ; Wu, Kongyun ; Song, Jingyuan ; Zhu, Yingjie ; Yao, Hui ; Luo, Kun ; Dai, Yong ; Xu, Shijun ; Lin, Yulin. / Expedient identification of Magnoliaceae species by DNA barcoding. In: Plant OMICS. 2014 ; Vol. 7, No. 1. pp. 47-53.
@article{1846151ab1c84988ac662daa7d732b63,
title = "Expedient identification of Magnoliaceae species by DNA barcoding",
abstract = "Magnoliaceae species have high ornamental and medicinal importance, but they are morphologically similar. DNA barcoding has been regarded as a rapid and effective approach for species identification. To determine the efficiency of expedient identification in Magnoliaceae species by DNA barcoding, in this study, we collected 83 samples belonging to 68 species in 10 genera of Magnoliaceae. Candidate DNA regions (i.e.,psbA-trnH, matK, rbcL, ITS, ITS2, rpoB, and rpoC1) were amplified and sequenced for the evaluation of their PCR amplification, sequencing efficiency, intra-and inter-specific divergence and barcoding gap by sequence alignment and Kimura 2-Parameter (K2P) distance analysis, and the rate of correct identification was assessed by BLAST analysis. The results showed that psbA-trnH and matK exhibited high performance in efficiency of PCR amplification and the rate of successful sequencing, followed by rbcL. Associated with the analysis of 199 sequences for 96 species in 9 genera of Magnoliaceae retrieved from GenBank, it was discovered that psbA-trnH was highest in inter-specific divergence and rate of correct identification, indicating its efficiency in the identification of Magnoliaceae species. Besides, matK was also easy to amplify and had high rate of correct identification, suggesting its potential to distinguish Magnoliaceae species. This study indicates that DNA barcoding provides an effective technique for the expedient identification of morphologically similar species, and it is a powerful aid to the conventional methods for species identification.",
keywords = "Candidate DNA region, DNA barcoding, Intra-and inter-specific divergence, Magnoliaceae species, Plant identification",
author = "Hua Yu and Kongyun Wu and Jingyuan Song and Yingjie Zhu and Hui Yao and Kun Luo and Yong Dai and Shijun Xu and Yulin Lin",
year = "2014",
month = "2",
day = "21",
language = "English (US)",
volume = "7",
pages = "47--53",
journal = "Plant OMICS",
issn = "1836-0661",
publisher = "Southern Cross Publishing and Printing Pty Ltd",
number = "1",

}

TY - JOUR

T1 - Expedient identification of Magnoliaceae species by DNA barcoding

AU - Yu, Hua

AU - Wu, Kongyun

AU - Song, Jingyuan

AU - Zhu, Yingjie

AU - Yao, Hui

AU - Luo, Kun

AU - Dai, Yong

AU - Xu, Shijun

AU - Lin, Yulin

PY - 2014/2/21

Y1 - 2014/2/21

N2 - Magnoliaceae species have high ornamental and medicinal importance, but they are morphologically similar. DNA barcoding has been regarded as a rapid and effective approach for species identification. To determine the efficiency of expedient identification in Magnoliaceae species by DNA barcoding, in this study, we collected 83 samples belonging to 68 species in 10 genera of Magnoliaceae. Candidate DNA regions (i.e.,psbA-trnH, matK, rbcL, ITS, ITS2, rpoB, and rpoC1) were amplified and sequenced for the evaluation of their PCR amplification, sequencing efficiency, intra-and inter-specific divergence and barcoding gap by sequence alignment and Kimura 2-Parameter (K2P) distance analysis, and the rate of correct identification was assessed by BLAST analysis. The results showed that psbA-trnH and matK exhibited high performance in efficiency of PCR amplification and the rate of successful sequencing, followed by rbcL. Associated with the analysis of 199 sequences for 96 species in 9 genera of Magnoliaceae retrieved from GenBank, it was discovered that psbA-trnH was highest in inter-specific divergence and rate of correct identification, indicating its efficiency in the identification of Magnoliaceae species. Besides, matK was also easy to amplify and had high rate of correct identification, suggesting its potential to distinguish Magnoliaceae species. This study indicates that DNA barcoding provides an effective technique for the expedient identification of morphologically similar species, and it is a powerful aid to the conventional methods for species identification.

AB - Magnoliaceae species have high ornamental and medicinal importance, but they are morphologically similar. DNA barcoding has been regarded as a rapid and effective approach for species identification. To determine the efficiency of expedient identification in Magnoliaceae species by DNA barcoding, in this study, we collected 83 samples belonging to 68 species in 10 genera of Magnoliaceae. Candidate DNA regions (i.e.,psbA-trnH, matK, rbcL, ITS, ITS2, rpoB, and rpoC1) were amplified and sequenced for the evaluation of their PCR amplification, sequencing efficiency, intra-and inter-specific divergence and barcoding gap by sequence alignment and Kimura 2-Parameter (K2P) distance analysis, and the rate of correct identification was assessed by BLAST analysis. The results showed that psbA-trnH and matK exhibited high performance in efficiency of PCR amplification and the rate of successful sequencing, followed by rbcL. Associated with the analysis of 199 sequences for 96 species in 9 genera of Magnoliaceae retrieved from GenBank, it was discovered that psbA-trnH was highest in inter-specific divergence and rate of correct identification, indicating its efficiency in the identification of Magnoliaceae species. Besides, matK was also easy to amplify and had high rate of correct identification, suggesting its potential to distinguish Magnoliaceae species. This study indicates that DNA barcoding provides an effective technique for the expedient identification of morphologically similar species, and it is a powerful aid to the conventional methods for species identification.

KW - Candidate DNA region

KW - DNA barcoding

KW - Intra-and inter-specific divergence

KW - Magnoliaceae species

KW - Plant identification

UR - http://www.scopus.com/inward/record.url?scp=84894086979&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84894086979&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:84894086979

VL - 7

SP - 47

EP - 53

JO - Plant OMICS

JF - Plant OMICS

SN - 1836-0661

IS - 1

ER -