Abstract
Identification of Meloidogyne spp. is challenging when using only the classical techniques since some species share similar characteristics. In this study, 37 Meloidogyne populations were obtained from four provinces in South Africa during 2015 and 2016 and molecularly characterised. We used SCAR-PCR markers and sequencing of four DNA fragments, viz. the D2-D3 segment (28S rDNA), COI, viable region between COII and 16S rDNA and NADH5 (mtDNA) genes. Using SCAR-PCR, M. enterolobii, M. javanica, M. incognita and M. hapla (in descending order of prevalence) were identified. According to D2-D3, COI, COII/16S and NADH5 sequence analyses, the 23 M. enterolobii populations identified clustered together in a well-supported clade, while M. javanica (9 populations) and M. incognita (5 populations) grouped in another. Results showed that D2-D3 and COI genes were appropriate for accurate identification of M. enterolobii, but not to differentiate among M. arenaria, M. incognita and M. javanica. Conversely, SCAR-PCR and NADH5 were more accurate in distinguishing among different Meloidogyne spp. In conclusion, SCAR-PCR was best for the situation of mixed populations.
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References
Adam MAM, Phillips MS, Blok VC (2005) Identification of Meloidogyne spp. from north East Libya and comparison of their inter- and intra-specific genetic variation using RAPDs. Nematology 7:599–609
Adam MAM, Phillips MS, Blok VC (2007) Molecular diagnostic key for identification of single juveniles of seven common and economically important species of root-knot nematode (Meloidogyne spp.). Plant Pathology 56:190–197
Akyazi F, Felek AF (2013) Molecular identification of root-knot nematode Meloidogyne incognita from kiwi fruit orchards in Ordu province, Turkey. Turkish Journal of Entomology 37:449–456
Anonymous (2014) Meloidogyne enterolobii. EPPO Bulletin 44:159–163
Blok VC (2005) Achievements in and future prospects for molecular diagnostics of plant-parasitic nematodes. Canadian Journal of Plant Pathology 27:176–185
Blok VC, Powers TO (2009) Biochemical and molecular identification. In: Perry RN, Moens M, Starr JL (eds) Root-knot nematodes. CAB International, Wallingford, UK, pp 98–118
Blok VC, Wishart J, Fargette M, Berthier K, Phillips MS (2002) Mitochondrial DNA differences distinguishing Meloidogyne mayaguensis from the major species of tropical root-knot nematodes. Nematology 4:773–781
Bowles J, Blair D, McManus DP (1992) Geneic variants within the genus Echinococcus identified by mitochondrial DNA sequencing. Molecular and Biochemical Parasitology 54:165–173
Brito J, Powers TO, Mullin PG, Inserra RN, Dickson DW (2004) Morphological and molecular characterization of Meloidogyne mayaguensis isolates from Florida. Journal of Nematology 36:232–240
Castagnone-Sereno P (2012) Meloidogyne enterolobii (= M. Mayaguensis): profile of an emerging, highly pathogenic, root-knot nematode species. Nematology 14:133–138
Cenis JL, Opperman CH, Triantaphyllou AC (1992) Cytogenetic, enzymatic, and restriction fragment length polymorphism variation of Meloidogyne spp. from Spain. Phytopathology 82:527–531
Daneel MS (2017) Nematode pests of minor tropical and subtropical crops. In: Fourie H, Spaull VW, Jones RK, Daneel MS, De Waele D (eds) Nematology in South Africa: a view from the 21st century. Springer, Cham, Switzerland, pp 373–393
Daneel MS, De Waele D (2017) Nematode pests of banana. In: Fourie H, Spaull VW, Jones RK, Daneel MS, De Waele D (eds) Nematology in South Africa: a view from the 21st century. Springer, Cham, Switzerland, pp 359–371
Darriba D, Taboada GL, Doallo R, Posada D (2012) jModelTest 2: more models, new heuristics and parallel computing. Nature Methods 9:772
Devran Z, Söğut M (2009) Distribution and identification of root-knot nematodes from Turkey. Journal of Nematology 41:128–133
Dickson DW, De Waele D (2005) Nematode parasites of peanut. In: Luc M, Sikora RA, Bridge J (eds) Plant parasitic nematodes in subtropical and tropical agriculture. CAB International, Wallingford, UK, pp 393–436
Fourie H, van Aardt WJ, Tiedt L (2014) The effects of cropguard on the motility, ultrastructure, and respiration of two Meloidogyne species. Nematropica 44:85–92
Fourie H, Mc Donald AH, Steenkamp S, De Waele D (2017) Nematode pests of leguminous and oilseed crops. In: Fourie H, Spaull VW, Jones RK, Daneel MS, De Waele D (eds) Nematology in South Africa: a view from the 21st century. Springer, Cham, Switzerland, pp 201–230
Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755
Hugo HJ, Storey SG (2017) Nematode pests of deciduous fruit. In: Fourie H, Spaull VW, Jones RK, Daneel MS, De Waele D (eds) Nematology in South Africa: a view from the 21st century. Springer, Cham, Switzerland, pp 245–257
Janssen T, Karssen G, Verhaeven M, Coyne D, Bert W (2016) Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution. Scientific Reports 6:1–13
Jepson SB (1987) Identification of root-knot nematodes (Meloidogyne species). CAB International, Wallingford, UK
Jones JT, Haegeman A, Danchin EGJ, Gaur HS, Helder J, Jones MGK, Kikuchi T, Manzanilla-López R, Palomares-Rius JE, Wesemael WML, Perry RN (2013) Top 10 plant-parasitic nematodes in molecular plant pathology. Molecular Plant Pathology 14:946–961
Jones RK, Storey SG, Knoetze R, Fourie H (2017) Nematode pests of potato and other vegetable crops. In: Fourie H, Spaull VW, Jones RK, Daneel MS, De Waele D (eds) Nematology in South Africa: a view from the 21st century. Springer, Cham, Switzerland, pp 231–260
Karssen G, Van der Gaag DJ, Lammers W (2008) Meloidogyne enterolobii: Pest risk assessment. http://edepot.wur.nl/118623
Karssen G, Wesemae WML, Moens M (2013) Root-knot nematodes. In: Perry RN, Moens M (eds) Plant nematology. CAB International, Wallingford, UK, pp 73–108
Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Meintjes P, Drummond A (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649
Keetch DP, Buckley NH (1984) A check-list of the plant-parasitic nematodes of Southern Africa. Technical Communication 195. Pretoria, South Africa. Department of Agricultural development
Kiewnick S, Dessimoz M, Franck L (2009) Effects of the Mi-1 and the N root-knot nematode-resistance gene on infection and reproduction of Meloidogyne enterolobii on tomato and pepper cultivars. Journal of Nematology 41:134–139
Kleynhans KPN (1991) The root-knot nematodes of South Africa. Technical Communication 231. Pretoria, South Africa. Department of Agricultural Development
Landa BB, Rius JEP, Vovlas N, Carneiro RMDG, Maleita CMN, Abrantes d O, IM CP (2008) Molecular characterization of Meloidogyne hispanica (Nematoda, Meloidogynidae) by phylogenetic analysis of genes within the rDNA in Meloidogyne spp. Plant Disease 92:1104–1110
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948
Long H, Liu H, Xu JH (2006) Development of a PCR diagnostic for the root-knot nematode Meloidogyne enterolobii. Acta Phytopathologica Sinica 2:109–115
Marais M (1990) Plant-parasitic nematodes in lucerne fields in South Africa. Phytophylactica 22:449–452
Marais M, Swart A (1996) Plant-parasitic nematodes of the lower Orange River irrigation area, South Africa. African Plant Protection 2:25–30
Mc Donald AH, De Waele D, Fourie H (2017) Nematode pests of maize and other cereal crops. In: Fourie H, Spaull VW, Jones RK, Daneel MS, De Waele D (eds) Nematology in South Africa: a view from the 21st century. Springer, Cham, Switzerland, pp 183–199
McCarthy C (1997) Chromas version 1.45. Queensland: Griffifth University Gold Coast Campus. School of Health Science
Moens M, Perry RN, Starr JL (2009) Meloidogyne species a diverse group of novel and important plant parasites. In: Perry RN, Moens M, Starr JL (eds) Root-knot nematodes. CAB International, Wallingford, UK, pp 1–13
Musapa M, Kumwenda T, Mkulama M, Chishimba S, Norris DE, Thuma PE, Mharakurwa S (2013) A simple Chelex protocol for DNA extraction from Anopheles spp. Journal of Visualized Experiments 71:e3281
Mwesige R (2013) Identification and pathogenicity of root-knot nematodes from tomatoes grown in Kyenjojo and Masaka districts in Uganda. Master Thesis. University of Gent, Netherlands
Ntidi KN, Bekker S, Fourie H (2017) Nematodes of grasses and weeds. In: Fourie H, Spaull VW, Jones RK, Daneel MS, De Waele D (eds) Nematology in South Africa: a view from the 21st century. Springer, Cham, Switzerland, pp 409–418
Onkendi EM, Moleleki LN (2013a) Distribution and genetic diversity of root-knot nematodes (Meloidogyne spp.) in potatoes from South Africa. Plant Pathology 62:1184–1192
Onkendi EM, Moleleki LN (2013b) Detection of Meloidogyne enterolobii in potatoes in South Africa and phylogenetic analysis based on intergenic region and the mitochondrial DNA sequences. European Journal of Plant Pathology 136:1–5
Onkendi EM, Kariuki GM, Marais M, Moleleki LN (2014) The threat of root-knot nematodes (Meloidogyne spp.) in Africa: a review. Plant Pathology 63:727–737
Pereira F, Moreira C, Fonseca L, van Asch B, Mota M, Abrantes I, Amorim A (2013) New insights into the phylogeny and worldwide dispersion of two closely related nematode species, Bursaphelenchus xylophilus and Bursaphelenchus mucronatus. PLoS One 8:e56288
Powers TO, Harris TS (1993) A polymerase chain reaction method for identification of five major Meloidogyne species. Journal of Nematology 25:1–6
Powers TO, Mullin PG, Harris TS, Sutton LA, Higgins RS (2005) Incorporating molecular identification of Meloidogyne spp. into a large-scale regional nematode survey. Journal of Nematology 37:226–235
Rahidifard M, Fourie H, Véronneau PY, Marais M, Daneel MS, Mimee B (2018) Genetic diversity and phylogeny of south African Meloidogyne populations using genotyping by sequencing. Scientific Reports 8:13816
Rashidifard M, Shokoohi E, Hoseinipour A, Jamali S (2015) Distribution, morphology, seasonal dynamics, and molecular characterization of Tylenchulus semipenetrans from citrus orchards in southern Iran. Biologia 70:771–781
Stanton J, Jugall A, Moritz C (1997) Nucleotide polymorphisms and an improved PCR-based mtDNA diagnostic for parthenogenetic root-knot nematodes (Meloidogyne spp.). Fundamental and Applied Nematology 20:261–268
Storey SG, Malan AP, Hugo HJ (2017) Nematode pests of grapevine. In: Fourie H, Spaull VW, Jones RK, Daneel MS, De Waele D (eds) Nematology in South Africa: a view from the 21st century. Springer, Cham, Switzerland, pp 235–343
Subbotin SA (2015) Heterodera sturhani sp. n. From China, a new species of the Heterodera avenae species complex (Tylenchida: Heteroderidae). Russian Journal of Nematology 23:145–152
Subbotin SA, Sturhan D, Chizhov VN, Vovlas N, Baldwin JG (2006) Phylogenetic analysis of Tylenchida Thorne, 1949 as inferred from D2 and D3 expansion fragments of the 28S rRNA gene sequences. Nematology 8:455–474
Tigano M, De Siqueira K, Castagnone-Sereno P, Mulet K, Queiroz P, Dos Santos M, Teixeira C, Almeida M, Silva J, Carneiro R (2010) Genetic diversity of the root-knot nematode Meloidogyne enterolobii and development of a SCAR marker for this guava-damaging species. Plant Pathology 59:1054–1061
Van den Berg E, Marais M, Swart A (2017) Nematode morphology and classification. In: Fourie H, Spaull VW, Jones RK, Daneel MS, De Waele D (eds) Nematology in South Africa: a view from the 21st century. Springer, Cham, Switzerland, pp 33–71
Villar-Luna E, Goméz-Rodriguez O, Rojas-Martínez R, Zavaleta-Mejía E (2016) Presence of Meloidogyne enterolobii on Jalapeño pepper (Capsicum annuum L.) in Sinaloa, Mexico. Helminthologia 53:155–160
Visagie M, Mienie CMS, Marais M, Daneel M, Karssen G, Fourie H (2018) Identification of Meloidogyne spp. associated with Agri- and horticultural crops in South Africa. Nematology 20:397–401
Willers P (1997) First record of Meloidogyne mayaguensis Rammah and Hirschmann, 1988: Heteroderidae on commercial crops in the Mpumalanga province, South Africa. Inligtingsbulletin-Instituut vir Tropiese en Subtropiese Gewasse 294:19–20
Zijlstra C (2000) Identification of Meloidogyne chitwoodi, M. fallax and M. hapla based on SCAR-PCR: a powerful way of enabling reliable identification of populations or individuals that share common traits. European Journal of Plant Pathology 106:283–290
Zijlstra C, Uenk BJ, Van Silfhout CH (1997) A reliable, precise method to differentiate species of root-knot nematodes in mixtures on the basis of ITS-RFLPs. Fundamental and Applied Nematology 20:59–63
Zijlstra C, Donkers-Venne DTHM, Fargette M (2000) Identification of Meloidogyne incognita, M. javanica and M. arenaria using sequence characterised amplified region (SCAR) based PCR assays. Nematology 2:847–853
Acknowledgments
This research has been partially funded by the National Research Foundation under Grant CPRR160424162946. Any opinion, finding and conclusion or recommendation expressed in this material is that of the author(s) and the NRF does not accept any liability in this regard. Partial funding, by the North-West University and the Agricultural Research Council – Institute for Tropical and Subtropical Crops and use of infrastructure of these institutions, is acknowledged. The authors also convey their gratitude towards Proffs. Gerrit Karssen (NPPO, Wageningen, The Netherlands) and Wim Wesemael (ILVO, Merelbeke, Belgium) for supplying standards of cryophilic Meloidogyne spp. for SCAR-PCR analysis.
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This study was partially funded by the National Research Foundation (Grant number CPRR160424162946).
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Figure S1
Bayesian inference (BI) of Meloidogyne spp. obtained from South Africa, based on 50 sequences of partial D2-D3 28S rDNA region with length of 540 bp each under HKY + G model (those populations which are from this study are shown in bold). (PNG 634 kb)
Figure S2
Bayesian inference (BI) of Meloidogyne spp. obtained from South Africa, based on 50 sequences of COI of mtDNA with length of 250 bp each under HKY + G model (those populations which are from this study are shown in bold). (PNG 854 kb)
Figure S3
Bayesian inference (BI) of Meloidogyne spp. obtained from South Africa, based on 39 sequences of region between COII and 16S rDNA with length of 425 bp each under HKY + G model (those populations which are from this study are shown in bold). (PNG 365 kb)
Figure S4
Bayesian inference (BI) of Meloidogyne spp. obtained from South Africa, using 46 sequences of NADH5 mtDNA with length of 395 bp each under ATR model (those populations which are from this study are shown in bold). (PNG 838 kb)
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Rashidifard, M., Marais, M., Daneel, M.S. et al. Molecular characterisation of Meloidogyne enterolobii and other Meloidogyne spp. from South Africa. Trop. plant pathol. 44, 213–224 (2019). https://doi.org/10.1007/s40858-019-00281-4
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DOI: https://doi.org/10.1007/s40858-019-00281-4