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Comparison of two short DNA barcoding loci (COI and COII) and two longer ribosomal DNA genes (SSU & LSU rRNA) for specimen identification among quarantine root-knot nematodes (Meloidogyne spp.) and their close relatives

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Abstract

Root-knot nematodes (Meloidogyne spp.) are important pests of numerous crops worldwide. Some members of this genus have a quarantine status, and accurate species identification is required to prevent further spreading. DNA barcoding is a method for organism identification in non-complex DNA backgrounds based on informative motifs in short DNA stretches (≈600 bp). As part of the EU 7th Framework project QBOL, 15 Meloidogyne species were chosen to compare the resolutions offered by two typical DNA barcoding loci, COI and COII, with the distinguishing signals produced by two ribosomal DNA genes (small and large subunit rDNA; SSU ≈ 1,700 and LSU ≈ 3,400 bp). None of the four markers distinguished between the tropical species Meloidogyne incognita, M. javanica and M. arenaria. Taking P ID (Liberal) values ≥0.93 as a measure for species delimitation, the four mtDNA and rDNA markers performed well for the tropical Meloidogyne species complex, M. enterolobii, M. hapla, and M. maritima. Within cluster III A (Holterman et al. Phytopathology, 99, 227–235, 2009), SSU rDNA did not offer resolution at species level. Both mtDNA loci COI and COII did, whereas for LSU rDNA a longer fragment (≥700 bp) is required. The high level of mitochondrial heteroplasmy recently reported for M. chitwoodi (Humphreys-Pereira and Elling Nematology, 15, 315–327, 2013) was not found in the populations under investigation, suggesting this could be a regional phenomenon. For identification of RKNs, we suggest the combined use of SSU rDNA with one of three other markers presented here.

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Acknowledgments

We would like to express our thanks to all colleagues who provided nematode material for this study. Funding was supplied by EU 7th Framework project QBOL (KBBE-2008-1-4-01). Initial work on the COI gene was funded by the Swiss State Secretariat for Education and Research (SER) as part of COST Action 872 (project nr. C07.0072). We also would like to acknowledge all colleagues from the QBOL project and our partner institutes for proving the reference material used in this study.

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  1. Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, 8820, Waedenswil, Switzerland

    Sebastian Kiewnick & Juerg Ernst Frey

  2. Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands

    Martijn Holterman, Sven van den Elsen, Hanny van Megen & Johannes Helder

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  1. Sebastian Kiewnick
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  2. Martijn Holterman
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Correspondence to Sebastian Kiewnick.

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Kiewnick, S., Holterman, M., van den Elsen, S. et al. Comparison of two short DNA barcoding loci (COI and COII) and two longer ribosomal DNA genes (SSU & LSU rRNA) for specimen identification among quarantine root-knot nematodes (Meloidogyne spp.) and their close relatives. Eur J Plant Pathol 140, 97–110 (2014). https://doi.org/10.1007/s10658-014-0446-1

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