DNA barcoding of Mycosphaerella species of quarantine importance to Europe

W. Quaedvlieg, J.Z. Groenewald, M. de Jesús Yáñez-Morales, P.W. Crous

Research output: Contribution to journalArticleAcademicpeer-review

47 Citations (Scopus)

Abstract

The EU 7th Framework Program provided funds for Quarantine Barcoding of Life (QBOL) to develop a quick, reliable and accurate DNA barcode-based diagnostic tool for selected species on the European and Mediterranean Plant Protection Organization (EPPO) A1/A2 quarantine lists. Seven nuclear genomic loci were evaluated to determine those best suited for identifying species of Mycosphaerella and/or its associated anamorphs. These genes included ß-tubulin (Btub), internal transcribed spacer regions of the nrDNA operon (ITS), 28S nrDNA (LSU), Actin (Act), Calmodulin (Cal), Translation elongation factor 1-alpha (EF-1a) and RNA polymerase II second largest subunit (RPB2). Loci were tested on their Kimura-2-parameter-based inter- and intraspecific variation, PCR amplification success rate and ability to distinguish between quarantine species and closely related taxa. Results showed that none of these loci was solely suited as a reliable barcoding locus for the tested fungi. A combination of a primary and secondary barcoding locus was found to compensate for individual weaknesses and provide reliable identification. A combination of ITS with either EF-1a or Btub was reliable as barcoding loci for EPPO A1/A2-listed Mycosphaerella species. Furthermore, Lecanosticta acicola was shown to represent a species complex, revealing two novel species described here, namely L. brevispora sp. nov. on Pinus sp. from Mexico and L. guatemalensis sp. nov. on Pinus oocarpa from Guatemala. Epitypes were also designated for L. acicola and L. longispora to resolve the genetic application of these names.
Original languageEnglish
Pages (from-to)101-115
JournalPersoonia
Volume29
DOIs
Publication statusPublished - 2012

Fingerprint

Mycosphaerella
quarantine
DNA barcoding
barcoding
DNA
loci
Lecanosticta
Pinus oocarpa
interspecific variation
intraspecific variation
species complex
new species
Guatemala
anamorphs
calmodulin
operon
DNA-directed RNA polymerase
RNA
tubulin
amplification

Keywords

  • eucalyptus leaves
  • ribosomal dna
  • leaf-spot
  • phylogeny
  • nuclear
  • fungus
  • genus
  • anamorphs
  • taxonomy
  • sequence

Cite this

Quaedvlieg, W. ; Groenewald, J.Z. ; de Jesús Yáñez-Morales, M. ; Crous, P.W. / DNA barcoding of Mycosphaerella species of quarantine importance to Europe. In: Persoonia. 2012 ; Vol. 29. pp. 101-115.
@article{1402d8717abe445b859ee0a57a07ddaa,
title = "DNA barcoding of Mycosphaerella species of quarantine importance to Europe",
abstract = "The EU 7th Framework Program provided funds for Quarantine Barcoding of Life (QBOL) to develop a quick, reliable and accurate DNA barcode-based diagnostic tool for selected species on the European and Mediterranean Plant Protection Organization (EPPO) A1/A2 quarantine lists. Seven nuclear genomic loci were evaluated to determine those best suited for identifying species of Mycosphaerella and/or its associated anamorphs. These genes included {\ss}-tubulin (Btub), internal transcribed spacer regions of the nrDNA operon (ITS), 28S nrDNA (LSU), Actin (Act), Calmodulin (Cal), Translation elongation factor 1-alpha (EF-1a) and RNA polymerase II second largest subunit (RPB2). Loci were tested on their Kimura-2-parameter-based inter- and intraspecific variation, PCR amplification success rate and ability to distinguish between quarantine species and closely related taxa. Results showed that none of these loci was solely suited as a reliable barcoding locus for the tested fungi. A combination of a primary and secondary barcoding locus was found to compensate for individual weaknesses and provide reliable identification. A combination of ITS with either EF-1a or Btub was reliable as barcoding loci for EPPO A1/A2-listed Mycosphaerella species. Furthermore, Lecanosticta acicola was shown to represent a species complex, revealing two novel species described here, namely L. brevispora sp. nov. on Pinus sp. from Mexico and L. guatemalensis sp. nov. on Pinus oocarpa from Guatemala. Epitypes were also designated for L. acicola and L. longispora to resolve the genetic application of these names.",
keywords = "eucalyptus leaves, ribosomal dna, leaf-spot, phylogeny, nuclear, fungus, genus, anamorphs, taxonomy, sequence",
author = "W. Quaedvlieg and J.Z. Groenewald and {de Jes{\'u}s Y{\'a}{\~n}ez-Morales}, M. and P.W. Crous",
year = "2012",
doi = "10.3767/003158512X661282",
language = "English",
volume = "29",
pages = "101--115",
journal = "Persoonia",
issn = "0031-5850",
publisher = "National Herbarium Nederland",

}

Quaedvlieg, W, Groenewald, JZ, de Jesús Yáñez-Morales, M & Crous, PW 2012, 'DNA barcoding of Mycosphaerella species of quarantine importance to Europe' Persoonia, vol. 29, pp. 101-115. https://doi.org/10.3767/003158512X661282

DNA barcoding of Mycosphaerella species of quarantine importance to Europe. / Quaedvlieg, W.; Groenewald, J.Z.; de Jesús Yáñez-Morales, M.; Crous, P.W.

In: Persoonia, Vol. 29, 2012, p. 101-115.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - DNA barcoding of Mycosphaerella species of quarantine importance to Europe

AU - Quaedvlieg, W.

AU - Groenewald, J.Z.

AU - de Jesús Yáñez-Morales, M.

AU - Crous, P.W.

PY - 2012

Y1 - 2012

N2 - The EU 7th Framework Program provided funds for Quarantine Barcoding of Life (QBOL) to develop a quick, reliable and accurate DNA barcode-based diagnostic tool for selected species on the European and Mediterranean Plant Protection Organization (EPPO) A1/A2 quarantine lists. Seven nuclear genomic loci were evaluated to determine those best suited for identifying species of Mycosphaerella and/or its associated anamorphs. These genes included ß-tubulin (Btub), internal transcribed spacer regions of the nrDNA operon (ITS), 28S nrDNA (LSU), Actin (Act), Calmodulin (Cal), Translation elongation factor 1-alpha (EF-1a) and RNA polymerase II second largest subunit (RPB2). Loci were tested on their Kimura-2-parameter-based inter- and intraspecific variation, PCR amplification success rate and ability to distinguish between quarantine species and closely related taxa. Results showed that none of these loci was solely suited as a reliable barcoding locus for the tested fungi. A combination of a primary and secondary barcoding locus was found to compensate for individual weaknesses and provide reliable identification. A combination of ITS with either EF-1a or Btub was reliable as barcoding loci for EPPO A1/A2-listed Mycosphaerella species. Furthermore, Lecanosticta acicola was shown to represent a species complex, revealing two novel species described here, namely L. brevispora sp. nov. on Pinus sp. from Mexico and L. guatemalensis sp. nov. on Pinus oocarpa from Guatemala. Epitypes were also designated for L. acicola and L. longispora to resolve the genetic application of these names.

AB - The EU 7th Framework Program provided funds for Quarantine Barcoding of Life (QBOL) to develop a quick, reliable and accurate DNA barcode-based diagnostic tool for selected species on the European and Mediterranean Plant Protection Organization (EPPO) A1/A2 quarantine lists. Seven nuclear genomic loci were evaluated to determine those best suited for identifying species of Mycosphaerella and/or its associated anamorphs. These genes included ß-tubulin (Btub), internal transcribed spacer regions of the nrDNA operon (ITS), 28S nrDNA (LSU), Actin (Act), Calmodulin (Cal), Translation elongation factor 1-alpha (EF-1a) and RNA polymerase II second largest subunit (RPB2). Loci were tested on their Kimura-2-parameter-based inter- and intraspecific variation, PCR amplification success rate and ability to distinguish between quarantine species and closely related taxa. Results showed that none of these loci was solely suited as a reliable barcoding locus for the tested fungi. A combination of a primary and secondary barcoding locus was found to compensate for individual weaknesses and provide reliable identification. A combination of ITS with either EF-1a or Btub was reliable as barcoding loci for EPPO A1/A2-listed Mycosphaerella species. Furthermore, Lecanosticta acicola was shown to represent a species complex, revealing two novel species described here, namely L. brevispora sp. nov. on Pinus sp. from Mexico and L. guatemalensis sp. nov. on Pinus oocarpa from Guatemala. Epitypes were also designated for L. acicola and L. longispora to resolve the genetic application of these names.

KW - eucalyptus leaves

KW - ribosomal dna

KW - leaf-spot

KW - phylogeny

KW - nuclear

KW - fungus

KW - genus

KW - anamorphs

KW - taxonomy

KW - sequence

U2 - 10.3767/003158512X661282

DO - 10.3767/003158512X661282

M3 - Article

VL - 29

SP - 101

EP - 115

JO - Persoonia

JF - Persoonia

SN - 0031-5850

ER -