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

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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.

Nematology

International Journal of Fundamental and Applied Nematological Research

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Figures

  • Light microscopy photomicrographs and SEM pictures of specimens of Pratylenchus goodeyi. A: Entire female body; B-D: Female anterior region; E: Female gonoduct; F, G: Spermatheca; H-I: Tail region; J: Female labial region, en face view; K: Female labial region, lateral view; L: Female lateral field at vulval region; M: Female vulval region; N: Female tail; O: Male labial region, lateral view; P: Male lateral field at mid-body; Q, R: Male tail region. (Light microscopy scale bars = 10 μm; SEM scale bars = 1 μm.)

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  • Phylogenetic position of misidentified Pratylenchus goodeyi sequences (FJ712922-FJ712926, KF275665, KF700243, KF840454, KF840455, KF840456, KF856291 and KM874803 indicated by ) within the Cephalobidae as inferred from Bayesian analysis of the ITS of RNA gene sequences using GTR + I + G model. Posterior probabilities are given for appropriate clades. Newly obtained sequences are indicated in bold.

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  • Light microscopy photomicrographs of specimens of Acrobeloides cf. nanus. A, B: Female anterior region, showing morphological variation of labial probolae between different specimens; C: Lateral field at mid-body; D, E: Female tail region, showing morphological variation of tail tip between different specimens. (Scale bars = 10 μm.)

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  • Phylogenetic relationships within the genus Pratylenchus as inferred from Bayesian analysis of D2-D3 of 28S rRNA gene sequences using GTR + I + G model. Posterior probabilities are given for appropriate clades. Newly obtained sequences are indicated in bold. 18S rRNA gene sequence obtained from topotype specimen of P. lentis. ITS of RNA gene sequences from the same specimen matched with ITS sequences from Troccoli et al. (2008). ∗∗Previously misidentified as P. pratensis (de la Peña et al., 2007).

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  • Phylogenetic relationships within the genus Pratylenchus as inferred from Bayesian analysis of 18S rRNA gene sequences using GTR + I + G model. Posterior probabilities are given for appropriate clades. Newly obtained sequences are indicated in bold.

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  • Light microscopy photomicrographs of specimens of Pratylenchus pratensis. A: Entire female; B-D: Female anterior region; E: Female gonoduct, spermatheca, uterus, vulva, and post-uterine sac; F: Lateral field at mid-body; G-J: Morphological variability in female tail region. (Scale bars: A = 100 μm; B-J = 10 μm.)

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  • Phylogenetic relationships within the genus Pratylenchus as inferred from Bayesian analysis of the COI gene sequences using GTR + I + G model. Posterior probabilities of over 70% are given for appropriate clades. Newly obtained sequences are indicated in bold.

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  • Light microscopy photomicrographs and SEM pictures of specimens of Pratylenchus flakkensis. A-T: female, U-W: male. A: Entire body; B-D: Anterior region; E: Labial region, en face view; F: Spermatheca; G: Posterior gonoduct; H: Lateral field at mid-body; I: Labial region, lateral view; J: Lateral field at vulval region; K: Lateral field at mid-body; L, M: Tail region; N-T: Morphological variation of tail tip; U: Labial region, lateral view; V: Lateral field at mid-body; W: Tail region. (Scale bars: A-D, F-H, J, K, M-S = 10 μm; E, I, L, T-W = 1 μm.)

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  • Phylogenetic position of genuine (dark grey frame) and misidentified Pratylenchus goodeyi sequences (light grey frame) as inferred from Bayesian analysis of the ITS of RNA gene sequences using GTR + I + G model. Posterior probabilities are given for appropriate clades. Newly obtained sequences are indicated in bold.

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  • Phylogenetic relationships as inferred from Bayesian analysis of the 18S rRNA gene sequences using GTR + I + G model, showing the large genetic distance between genuine Pratylenchus goodeyi sequences and sequences of Acrobeloides cf. nanus and closely related misidentified ‘P. goodeyi’ sequences. Posterior probabilities are given for appropriate clades. Newly obtained sequences are indicated in bold.

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