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Choosing and using a plant DNA barcode.

Hollingsworth PM, Graham SW, Little DP - PLoS ONE (2011)

Bottom Line: This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene.In plants, establishing a standardized DNA barcoding system has been more challenging.In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.

View Article: PubMed Central - PubMed

Affiliation: Genetics and Conservation Section, Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom. P.Hollingsworth@rbge.org.uk

ABSTRACT
The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.

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Schematic timeline of the consideration of different markers as plant barcodes.Colours (red = warm; blue = cool) represent an informal measure of enthusiasm among DNA barcoding researchers in the systematics community for CBOL and iBOL adoption of different markers. The different shading of trnL (P6) reflects the parallel use of the P6 loop for DNA profiling of degraded DNAs in ecological studies (see text). * = the two markers that form the core-barcode for land plants. rbcLa is used in this figure to distinguish this shorter barcode region of the gene proposed by Kress and Erikson [7] and the full length (ca. 1400 bp) gene sequence of rbcL. Elsewhere in the text, when we refer to rbcL we are referring to the short barcode region. The dashed lines indicate the timing of three international barcoding conferences in London (2005), Taipei (2007) and Mexico City (2009). The consideration of the different markers as barcodes are from the following sources: Kress et al. [5], Chase et al. [102], Chen et al. [54], Kew consortium [4], [6], Kim et al. see [103], Lahaye et al. [8], Newmaster et al. [104], Kress and Erickson [7], Taberlet et al. [44], Presting et al. [105].
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pone-0019254-g001: Schematic timeline of the consideration of different markers as plant barcodes.Colours (red = warm; blue = cool) represent an informal measure of enthusiasm among DNA barcoding researchers in the systematics community for CBOL and iBOL adoption of different markers. The different shading of trnL (P6) reflects the parallel use of the P6 loop for DNA profiling of degraded DNAs in ecological studies (see text). * = the two markers that form the core-barcode for land plants. rbcLa is used in this figure to distinguish this shorter barcode region of the gene proposed by Kress and Erikson [7] and the full length (ca. 1400 bp) gene sequence of rbcL. Elsewhere in the text, when we refer to rbcL we are referring to the short barcode region. The dashed lines indicate the timing of three international barcoding conferences in London (2005), Taipei (2007) and Mexico City (2009). The consideration of the different markers as barcodes are from the following sources: Kress et al. [5], Chase et al. [102], Chen et al. [54], Kew consortium [4], [6], Kim et al. see [103], Lahaye et al. [8], Newmaster et al. [104], Kress and Erickson [7], Taberlet et al. [44], Presting et al. [105].

Mentions: An historical overview of the search for a plant barcode is summarized in Figure 1, and discussed briefly below. Following initial in silico and laboratory-based assessments of the suitability of various coding and non-coding plastid markers (e.g. [4], [5]; Table 1), four main suggestions for a plant barcode were proposed by three different research groups/research consortia from the systematic community. These proposed barcodes involved various combinations of seven plastid markers. These were rpoC1+rpoB+matK or rpoC1+matK+trnH-psbA [6]; rbcL+trnH-psbA [7] and atpF-H+psbK-I+matK (K. J. Kim et al., unpublished). Various combinations of these markers were discussed at the 2nd International Barcode of Life conference in Taipei, but no agreement was reached. The following year, Lahaye et al. [8] proposed that matK alone should constitute the plant barcode.


Choosing and using a plant DNA barcode.

Hollingsworth PM, Graham SW, Little DP - PLoS ONE (2011)

Schematic timeline of the consideration of different markers as plant barcodes.Colours (red = warm; blue = cool) represent an informal measure of enthusiasm among DNA barcoding researchers in the systematics community for CBOL and iBOL adoption of different markers. The different shading of trnL (P6) reflects the parallel use of the P6 loop for DNA profiling of degraded DNAs in ecological studies (see text). * = the two markers that form the core-barcode for land plants. rbcLa is used in this figure to distinguish this shorter barcode region of the gene proposed by Kress and Erikson [7] and the full length (ca. 1400 bp) gene sequence of rbcL. Elsewhere in the text, when we refer to rbcL we are referring to the short barcode region. The dashed lines indicate the timing of three international barcoding conferences in London (2005), Taipei (2007) and Mexico City (2009). The consideration of the different markers as barcodes are from the following sources: Kress et al. [5], Chase et al. [102], Chen et al. [54], Kew consortium [4], [6], Kim et al. see [103], Lahaye et al. [8], Newmaster et al. [104], Kress and Erickson [7], Taberlet et al. [44], Presting et al. [105].
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Related In: Results  -  Collection

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pone-0019254-g001: Schematic timeline of the consideration of different markers as plant barcodes.Colours (red = warm; blue = cool) represent an informal measure of enthusiasm among DNA barcoding researchers in the systematics community for CBOL and iBOL adoption of different markers. The different shading of trnL (P6) reflects the parallel use of the P6 loop for DNA profiling of degraded DNAs in ecological studies (see text). * = the two markers that form the core-barcode for land plants. rbcLa is used in this figure to distinguish this shorter barcode region of the gene proposed by Kress and Erikson [7] and the full length (ca. 1400 bp) gene sequence of rbcL. Elsewhere in the text, when we refer to rbcL we are referring to the short barcode region. The dashed lines indicate the timing of three international barcoding conferences in London (2005), Taipei (2007) and Mexico City (2009). The consideration of the different markers as barcodes are from the following sources: Kress et al. [5], Chase et al. [102], Chen et al. [54], Kew consortium [4], [6], Kim et al. see [103], Lahaye et al. [8], Newmaster et al. [104], Kress and Erickson [7], Taberlet et al. [44], Presting et al. [105].
Mentions: An historical overview of the search for a plant barcode is summarized in Figure 1, and discussed briefly below. Following initial in silico and laboratory-based assessments of the suitability of various coding and non-coding plastid markers (e.g. [4], [5]; Table 1), four main suggestions for a plant barcode were proposed by three different research groups/research consortia from the systematic community. These proposed barcodes involved various combinations of seven plastid markers. These were rpoC1+rpoB+matK or rpoC1+matK+trnH-psbA [6]; rbcL+trnH-psbA [7] and atpF-H+psbK-I+matK (K. J. Kim et al., unpublished). Various combinations of these markers were discussed at the 2nd International Barcode of Life conference in Taipei, but no agreement was reached. The following year, Lahaye et al. [8] proposed that matK alone should constitute the plant barcode.

Bottom Line: This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene.In plants, establishing a standardized DNA barcoding system has been more challenging.In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.

View Article: PubMed Central - PubMed

Affiliation: Genetics and Conservation Section, Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom. P.Hollingsworth@rbge.org.uk

ABSTRACT
The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully pioneered in animals using a portion of the cytochrome oxidase 1 (CO1) mitochondrial gene. In plants, establishing a standardized DNA barcoding system has been more challenging. In this paper, we review the process of selecting and refining a plant barcode; evaluate the factors which influence the discriminatory power of the approach; describe some early applications of plant barcoding and summarise major emerging projects; and outline tool development that will be necessary for plant DNA barcoding to advance.

Show MeSH