Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode

Barbara A Whitlock, Amanda M. Hale, Paul A. Groff

Research output: Contribution to journalArticle

86 Citations (Scopus)

Abstract

Background: The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species. Methodology/Principal Findings: Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships. Conclusions/Significance: Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding.

Original languageEnglish
Article numbere11533
JournalPLoS One
Volume5
Issue number7
DOIs
StatePublished - Aug 13 2010

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Gentianaceae
Gentiana
Plant DNA
DNA barcoding
Substitution reactions
Angiosperms
Sequence Alignment
DNA
Chloroplasts
Genetic Markers
Sequence Analysis
barcoding
sequence alignment
Angiospermae
chloroplasts
methodology

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Intraspecific inversions pose a challenge for the trnH-psbA plant DNA barcode. / Whitlock, Barbara A; Hale, Amanda M.; Groff, Paul A.

In: PLoS One, Vol. 5, No. 7, e11533, 13.08.2010.

Research output: Contribution to journalArticle

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