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The pitfalls of molecular species identification : a case study within the genus Pratylenchus (Nematoda: Pratylenchidae)

Toon Janssen (UGent) , Gerrit Karssen (UGent) , Marjolein Couvreur (UGent) , Lieven Waeyenberge and Wim Bert (UGent)
(2017) NEMATOLOGY. 19(10). p.1179-1199
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Abstract
Comprehensive morphological and molecular analyses revealed that published ITS sequences of the economically important plant-parasitic nematode Pratylenchus goodeyi are actually sequences from distantly free-living bacterivorous 'cephalobids'. We demonstrated that this incorrect labelling resulted in a cascade of erroneous interpretations, as shown by the reports of 'P. goodeyi' on banana in China and on cotton in India. This clearly illustrates the risk of mislabelled sequences in public databases. Other mislabelled Pratylenchus cases are discussed to illustrate that this is not an isolated case. Herein, P. lentis n. syn. is considered a junior synonym of P. pratensis while P. flakkensis was for the first time linked to DNA sequences using topotype material. As taxonomic expertise is decreasing and sequence-based identification is growing rapidly, the highlighted problem may yet increase and a strong link between morphology and DNA sequences will be of crucial importance in order to prevent, or at least minimise, sequence-based misidentifications.
Keywords
Acrobeloides cf. nanus, diagnostics, mislabelled sequences, molecular phylogeny, new synonym, Pratylenchus flakkensis, Pratylenchus goodeyi, Pratylenchus lentis n. syn., Pratylenchus pratensis, topotypes, ROOT-LESION NEMATODES, N. SP, DNA BARCODES, CEPHALOBIDAE, ACROBELOIDES, MORPHOLOGY, RDNA, VARIABILITY, CHARACTERS, FRAMEWORK

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Chicago
Janssen, Toon, Gerrit Karssen, Marjolein Couvreur, Lieven Waeyenberge, and Wim Bert. 2017. “The Pitfalls of Molecular Species Identification : a Case Study Within the Genus Pratylenchus (Nematoda: Pratylenchidae).” Nematology 19 (10): 1179–1199.
APA
Janssen, T., Karssen, G., Couvreur, M., Waeyenberge, L., & Bert, W. (2017). The pitfalls of molecular species identification : a case study within the genus Pratylenchus (Nematoda: Pratylenchidae). NEMATOLOGY, 19(10), 1179–1199.
Vancouver
1.
Janssen T, Karssen G, Couvreur M, Waeyenberge L, Bert W. The pitfalls of molecular species identification : a case study within the genus Pratylenchus (Nematoda: Pratylenchidae). NEMATOLOGY. 2017;19(10):1179–99.
MLA
Janssen, Toon, Gerrit Karssen, Marjolein Couvreur, et al. “The Pitfalls of Molecular Species Identification : a Case Study Within the Genus Pratylenchus (Nematoda: Pratylenchidae).” NEMATOLOGY 19.10 (2017): 1179–1199. Print.
@article{8536452,
  abstract     = {Comprehensive morphological and molecular analyses revealed that published ITS sequences of the economically important plant-parasitic nematode Pratylenchus goodeyi are actually sequences from distantly free-living bacterivorous 'cephalobids'. We demonstrated that this incorrect labelling resulted in a cascade of erroneous interpretations, as shown by the reports of 'P. goodeyi' on banana in China and on cotton in India. This clearly illustrates the risk of mislabelled sequences in public databases. Other mislabelled Pratylenchus cases are discussed to illustrate that this is not an isolated case. Herein, P. lentis n. syn. is considered a junior synonym of P. pratensis while P. flakkensis was for the first time linked to DNA sequences using topotype material. As taxonomic expertise is decreasing and sequence-based identification is growing rapidly, the highlighted problem may yet increase and a strong link between morphology and DNA sequences will be of crucial importance in order to prevent, or at least minimise, sequence-based misidentifications.},
  author       = {Janssen, Toon and Karssen, Gerrit and Couvreur, Marjolein and Waeyenberge, Lieven and Bert, Wim},
  issn         = {1388-5545},
  journal      = {NEMATOLOGY},
  language     = {eng},
  number       = {10},
  pages        = {1179--1199},
  title        = {The pitfalls of molecular species identification : a case study within the genus Pratylenchus (Nematoda: Pratylenchidae)},
  url          = {http://dx.doi.org/10.1163/15685411-00003117},
  volume       = {19},
  year         = {2017},
}

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