Loop-mediated isothermal amplification (LAMP) for detection of the red ring nematode, Bursaphelenchus cocophilus

in Nematology
Restricted Access
Get Access to Full Text
Rent on DeepDyve

Have an Access Token?



Enter your access token to activate and access content online.

Please login and go to your personal user account to enter your access token.



Help

Have Institutional Access?



Access content through your institution. Any other coaching guidance?



Connect

As a first step in developing a quick, accurate and simple method for the diagnosis of red ring disease, the loop-mediated isothermal amplification (LAMP)-based identification procedure was applied to the causative agent, Bursaphelenchus cocophilus. Two LAMP primer sets were designed using two loci of ribosomal RNA genes, i.e., D2-D3 expansion segments of the large subunit (D2-D3 LSU), and internal transcribed spacers (ITS). Within those two sets of primers, the D2-D3 LSU primer set successfully yielded amplicons from B. cocophilus nematode lysate prepared from 3-year-old DESS-fixed specimens. The specificity of the primers was examined using 18 species of confamilial Aphelenchoididae nematodes and primer sensitivity was tested using a diluted series of B. cocophilus lysate. The primer set did not amplify the DNA from other aphelenchoidids, and sensitivity was achieved by ‘1:100 diluted’ B. cocophilus DNA (roughly 1/1500 of total DNA from a single third-stage juvenile).

Loop-mediated isothermal amplification (LAMP) for detection of the red ring nematode, Bursaphelenchus cocophilus

in Nematology

Sections

References

BaujardP. (1989). Remarques sur les genres des sous-familles Bursaphelenchina Paramonov, 1964 et Rhadinaphelenchinae Paramonov, 1964 (Nematoda: Aphelenchoididae). Revue de Nématologie 12323-324. Available online at http://horizon.documentation.ird.fr/exl-doc/pleins_textes/pleins_textes_5/pt5/nemato/27859.pdf.

CobbN.A. (1919). A newly discovered nematode (Aphelenchus cocophilus sp. n.) connected with a serious disease of the coconut palm. West Indian Bulletin 17203-210.

de OliveiraG.M.G.EulálioJ.BessiR.HarakawaR. (2011). Morphological and molecular characterization of Bursaphelenchus fungivorus (Nematoda: Aphelenchida) detected for the first time in Brazil. Nematologia Brasileira 3563-70.

EPPO (2005). Rhynchophorus palmarum. EPPO Bulletin 35468-471. DOI: 10.1111/j.1365-2338.2005.00883.x

EPPO (2008). Rhynchophorus ferrugineus. EPPO Bulletin 3855-59. DOI: 10.1111/j.1365-2338.2008.01195.x

FischbachJ.XanderN.C.FrohmaM.GlöklerJ.F. (2015). Shining a light on LAMP assays – a comparison of LAMP visualization methods including the novel use of berberine. BioTechniques 58189-194. DOI: 10.2144/000114275

FukutaS.KatoS.YoshidaK.MizukamiY.IshidaA.UedaJ.KanbeM.IshimotoY. (2003). Detection of tomato yellow leaf curl virus by loop-mediated isothermal amplification reaction. Journal of Virological Methods 11235-40. DOI: 10.1016/S0166-0934(03)00187-3

FutaiK. (2013). Pine wood nematode, Bursaphelenchus xylophilus. Annual Review of Phytopathology 5161-83. DOI: 10.1146/annurev-phyto-081211-172910

GerberK.Giblin-DavisR.M. (1990a). Teratorhabditis palmarum n. sp. (Nemata: Rhabditidae), an associate of Rhynchophorus palmarum and R. cruentatus (Coleoptera: Curculionidae). Journal of Nematology 22337-347. Available online at http://journals.fcla.edu/jon/article/viewFile/66180/63848.

GerberK.Giblin-DavisR.M. (1990b). Association of the red ring nematode, Rhadinaphelenchus cocophilus, and other nematode species with Rhynchophorus palmarum (Coleoptera: Curculionidae). Journal of Nematology 22143-149. Available online at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2619033/pdf/143.pdf.

Giblin-DavisR.M. (1993). Interactions of nematodes with insects. In: KhanM.W. (Ed.). Nematode interactions. London, UKChapman and Hall pp.  302-344.

Giblin-DavisR.M. (2001). Borers of palms. In: HowardF.W.MooreD.Giblin-DavisR.M.AbadR. (Eds). Insects on palms. Wallingford, UKCAB International pp.  267-305. Available online at http://www.cabi.org/isc/FullTextPDF/2001/20013091640.pdf.

Giblin-DavisR.M.KanzakiN.YeW.Mundo-OcampoM.BaldwinJ.G.ThomasW.K. (2006a). Morphology and description of Bursaphelenchus platzeri n. sp. (Nematoda: Parasitaphelenchidae), an associate of nitidulid beetles. Journal of Nematology 38150-157. Available online at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2586433/pdf/150.pdf.

Giblin-DavisR.M.KanzakiN.YeW.CenterB.J.ThomasW.K. (2006b). Morphology and systematics of Bursaphelenchus gerberae n. sp. (Nematoda: Parasitaphelenchidae), a rare associate of the palm weevil, Rhynchophorus palmarum in Trinidad. Zootaxa 118939-53. DOI: 10.11646/zootaxa.1189.1.2

GoodeyJ.B. (1960). Rhadinaphelenchus cocophilus (Cobb, 1919) n. comb., the nematode associated with ‘red-ring’ disease of coconut. Nematologica 598-102. DOI: 10.1163/187529260X00460

GriffithR. (1968a). The relationship between the red ring nematode and the palm weevil. Journal of Agricultural Society of Trinidad and Tobago 68342-356.

GriffithR. (1968b). The mechanism of transmission of red ring nematode. Journal of Agricultural Society of Trinidad and Tobago 68437-457.

GriffithR.Giblin-DavisR.M.KoshyP.K.SosammaV.K. (2005). Nematode parasites of coconut and other palms. In: LucM.SikoraR.A.BridgeJ. (Eds). Plant parasitic nematodes in subtropical and tropical agriculture2nd edition. Wallingford, UKCAB International pp.  493-527.

HartJ.H. (1905). Coconut disease. Bulletin of Miscellaneous Information Royal Botanic Gardens Trinidad 6241-243.

HoshizakiK.NakabayashiY.MamiyaY.MatsushitaM. (2015). Localized within- and between-tree variation in nematode distribution during latent state of pine wilt disease makes the disease status cryptic. Forest Pathology 46200-205. DOI: 10.1111/efp.12244

IdeT.KanzakiN.OhmuraW.OkabeK. (2016a). Molecular identification of an invasive wood-boring insect Lyctus brunneus (Coleoptera: Bostrichidae: Lyctinae) using frass by loop-mediated isothermal amplification and nested PCR assays. Journal of Economic Entomology 1091410-1414. DOI: 10.1093/jee/tow030

IdeT.KanzakiN.OhmuraW.OkabeK. (2016b). Molecular identification of the western drywood termite (Isoptera: Kalotermitidae) by loop-mediated isothermal amplification of DNA from fecal pellets. Journal of Economic Entomology 1092234-2237. DOI: 10.1093/jee/tow167

ItoH.KanzakiN.KikuchiT. (2010). [ Diagnosis of the pine wilt disease using the pinewood nematode detection kit with everyday materials.] Forest Pest 5955-59.

KanetaniS.KikuchiT.AkibaM.NakamuraK.IkegameK.TetsukaK. (2010). Detection of Bursaphelenchus xylophilus from old discs of dead Pinus armandii var. amamiana trees using a new detection kit. Forest Pathology 41387-391. DOI: 10.1111/j.1439-0329.2010.00695.x

KanzakiN.FutaiK. (2002). A PCR primer set for determination of phylogenetic relationships of Bursaphelenchus species within xylophilus group. Nematology 435-41. DOI: 10.1163/156854102760082186

KanzakiN.Giblin-DavisR.M. (2016). Pine wilt and red ring, lethal plant diseases caused by insect-mediated Bursaphelenchus nematodes. In: BrownJ.K. (Ed.). Vector-mediated transmission of plant pathogens. St Paul, MN, USAAPS Press pp.  87-107. DOI: 10.1094/9780890545355.007

KanzakiN.Giblin-DavisR.M.ZengY.YeW.CenterB.J. (2008). Diplogastrellus metamasius n. sp. (Rhabditida: Diplogastridae) isolated from Metamasius hemipterus (Olivier) (Coleoptera: Dryophthoridae) in southern Florida and Costa Rica. Nematology 10853-868. DOI: 10.1163/156854108786161409

KanzakiN.Giblin-DavisR.M.ZengY.YeW.CenterB.J. (2009). Acrostichus rhynchophori n. sp. (Rhabditida: Diplogastridae): a phoretic associate of Rhynchophorus cruentatus Fabricius and R. palmarum L. (Coleoptera: Curculionidae) in the Americas. Nematology 11669-688. DOI: 10.1163/156854109X404571

KanzakiN.Giblin-DavisR.M.GonzalezR.DuncanR.CarrilloD. (2015). Description of Ruehmaphelenchus juliae n. sp. (Tylenchina: Aphelenchoididae) isolated from an ambrosia beetle, Xylosandrus crassiusculus (Motschulsky), from South Florida. Nematology 17639-653. DOI: 10.1163/15685411-00002896

KanzakiN.AikawaT.MaeharaN.ThuP.Q. (2016). Bursaphelenchus kesiyae n. sp. (Nematoda: Aphelenchoididae), isolated from dead wood of Pinus kesiya royle ex Gordon (Pinaceae) from Vietnam with proposal of new subgroups in the B. fungivorus group. Nematology 18133-146. DOI: 10.1163/15685411-00002949

KikuchiT.AikawaT.OedaY.KarimN.KanzakiN. (2009). A rapid and precise diagnostic method for detecting the pinewood nematode Bursaphelenchus xylophilus by loop-mediated isothermal amplification. Phytopathology 991365-1369. DOI: 10.1094/PHYTO-99-12-1365

MitaraiS.OkumuraM.ToyotaE.YoshiyamaT.AonoA.SejimoA.AzumaY.SugaharaK.NagasawaT.NagayamaN. (2011). Evaluation of a simple loop-mediated isothermal amplification test kit for the diagnosis of tuberculosis. International Journal of Tuberculosis and Lung Disease 151211-1217. DOI: 10.5588/ijtld.10.0629

NotomiT.MoriY.TomitaN.KandaH. (2015). Loop-mediated isothermal amplification (LAMP): principle, features, and future prospects. Journal of Microbiology 53 1-5. DOI: 10.1007/s12275-015-4656-9

NowellW. (1919). Red ring or root disease of coconut palms. West Indian Bulletin 17189-192.

OkudaM.MatsumotoM.TanakaY.SubandiyahS.IwanamiT. (2005). Characterization of the tufB-secE-nusG-rplKAJL-rpoB gene cluster of the citrus greening organism and detection by loop-mediated isothermal amplification. Plant Disease 89705-711. DOI: 10.1094/PD-89-0705

PowersT.O. (2004). Nematode molecular diagnostics: from bands to barcodes. Annual Review of Phytopathology 42367-383. DOI: 10.1146/annurev.phyto.42.040803.140348

RorerJ.B. (1911). Diseases of the coconut palm. Circular 4. Board of Agriculture Trinidad pp. 27-33.

SilvaA.P.ParraP.P.CamposV.P.CostaS.S.VicenteC.S.L.FerreiraL.G.SouzaR.M.MotaM. (2016). Genetic diversity of Bursaphelenchus cocophilus in South America. Nematology 18605-614. DOI: 10.1163/15685411-00002980

SudhausW.KiontkeK.Giblin-DavisR.M. (2011). Description of Caenorhabditis angaria n. sp. (Nematoda: Rhabditidae), an associate of sugarcane and palm weevils (Coleoptera: Curculionidae). Nematology 1361-78. DOI: 10.1163/138855410X500334

TanakaR.KikuchiT.AikawaT.KanzakiN. (2012). Simple and quick methods for nematode DNA preparation. Applied Entomology and Zoology 47291-294. DOI: 10.1007/s13355-012-0115-9

YeW.Giblin-DavisR.M.BraaschH.MorrisK.ThomasW.K. (2007). Phylogenetic relationships among Bursaphelenchus species (Nematoda: Parasitaphelenchidae) inferred from nuclear ribosomal and mitochondrial DNA sequence data. Molecular Phylogenetics and Evolution 431185-1197. DOI: 10.1016/j.ympev.2007.02.006

YoderM.De LeyI.T.KingI.W.Mundo-OcampoM.MannJ.BlaxterM.PoirasL.De LeyP. (2006). DESS: a versatile solution for preserving morphology and extractable DNA of nematodes. Nematology 8367-376. DOI: 10.1163/156854106778493448

Figures

  • View in gallery

    Visual inspection of LAMP reaction tube by fluorescence after 60 min of incubation at 63°C. Upper lane from left to right: positive reactions to Bursaphelenchus cocophilus (three individuals of ST01; two replicates for one individual of NT25; two replicates for one individual of NT26; and two individuals of NT32); negative reaction to B. platzeri; B. penai; B. tadamiensis; B. xylophilus; B. mucronatus; B. conicaudatus. Lower lane from left to right: negative reaction to B. firmae; B. luxuriosae; B. doui; B. sinensis; B. osumiana; B. parvispicularis; B. gerberae; B. niphades; B. sakishimanus; undescribed Bursaphelenchus sp. ‘Sugadaira’ (B. eggersi group); undescribed Bursaphelenchus sp. ‘Esashi’ (B. eremus group); Aphelenchoides xylocopae.

  • View in gallery

    Agarose gel electrophoresis showing the sensitivity of LAMP for the detection of Bursaphelenchus cocophilus using diluted series of the DNA lysates. Left to right: Markers, A single individual-derived lysate, 1:5, 1:10, 1:25, 1:50, 1:100, 1:250 and 1:500 distilled lysates, and negative control (distilled water).

Index Card

Content Metrics

Content Metrics

All Time Past Year Past 30 Days
Abstract Views 25 25 17
Full Text Views 14 14 14
PDF Downloads 2 2 2
EPUB Downloads 0 0 0