Morphological and Molecular Characteristics of Pratylenchus coffeae from the Origin of Robusta Coffee Plantation in Malang, East Java

Aris Budiman(1), Supramana Supramana(2*), Giyanto Giyanto(3)

(1) Indonesian Coffee and Cocoa Research Institute (ICCRI) Jln. PB Sudirman No. 90, Jember, East Java 68118
(2) Department of Plant Protection, Faculty of Agriculture, IPB University Jln. Kamper, Kampus IPB Dramaga, Bogor, West Java 16680
(3) Department of Plant Protection, Faculty of Agriculture, IPB University Jln. Kamper, Kampus IPB Dramaga, Bogor, West Java 16680
(*) Corresponding Author


Pratylenchus coffeae is the most important plant-parasitic nematode in Robusta coffee plantations. Information regarding morphology, morphometric and molecular characters of P. coffeae has not been reported in Indonesia. This study is aimed to describe those characters of P. coffeae that attack Robusta coffee. Root samples were taken from Robusta coffee plantation in Malang, East Java. Nematode extractions was conducted using a mist chamber method. Morphology and morphometric characters were observed from the permanent nematode slides. Single nematode DNA extract was amplified at the D2D3 segment of 28S rRNA and ITS1-5.8S-ITS2 rRNA with universal primers. Amplicon was sequenced and analysed for phylogenetic tree relationships. Female morphological key character of P. coffeae observed are: lip with two annulations, four lateral lines, esophageal overlap with intestine ventrally, monodelphic, and truncated tail shape. Male spicules curved ventrally. Female morphometrics are: n=26, L = 556.4 μm, DGO = 2.4 μm, anterior gonad = 174.8 μm, a = 28.5, b = 6.1, b’ = 4.1, c = 20.1, c’ = 2.3, V = 81.7. A Male is smaller than a female with n=24, L = 505.9 μm,  a = 32.3, b = 5.5, b '= 3.9, c = 15.3, c' = 2.8 and T = 40.6. The molecular characters of P. coffeae were investigated for two isolates, namely SA1 and SA2.  Based on the D2D3 and ITS1-5.8S-ITS2 regions, isolate SA1 has similarity level of 99% and 97% to the P. coffeae  from NCBI. Similar result was shown by Isolate SA2 with similarity of 100% and 100% respectively. Phylogenetic tree analysis using Maximum Likelihood at the D2D3 segment of 28S rRNA and ITS1-5.8S-ITS2 regions showed that P. coffeae in this study was included in one clade with P. coffeae from several countries.


morphometric; phylogenetic tree; rRNA

Full Text:



Araya, T.Z., W.P. Padilla, A. Archidona-Yuste, C. Cantalapiedra-Navarrete, G. Liébanas, J.E. Palomares-Rius & P. Castillo. 2016. Root-lesion Nematodes of the Genus Pratylenchus (Nematoda: Pratylenchidae) from Costa Rica with Molecular Identification of P. gutierrezi and P. panamaensis Topotypes. European Journal of Plant Pathology 145: 973-998.

Bally, W. & G. Reydon. 1931. De Tegenwoordige Stand van het Vraagstuk van de Wortelaaltjes in de Koffiecultuur. Archief voor de Koffiecultuur in Nederland Indie 5: 23-216.

Blaxter, M. 2001. Molecular Analysis of Nematode Evolution. p. 1-24. In M.W. Kennedy & M.W. Hartnett (eds). Parasitic Nematodes: Molecular Biology, Biochemistry and Immunology. CABI, Wallingford.

Castillo, P. & N. Vovlas. 2007. Pratylenchus (Nematoda: Pratylenchidae): Diagnosis, Biology, Pathogenicity and Management, Brill, Leiden, NL. 529 p

De Ley, P., M.-A. Felix, L.M. Frisse, S.A. Nadler, P.W. Sternberg & W.K. Thomas. 1999. Molecular and Morphological Characterisation of Two Reproductively Isolated Species with Mirror-image Anatomy (Nematoda: Cephalobidae). Nematology 1: 591-612.

[EPPO] European and Mediterranean Plant Protection Organization. 2013. PM 7/119 (1) Nematode extraction. EPPO Bulletin 43: 471-495.

Holterman, M., A. van der Wurff, S. van den Elsen, H. van Megen, T. Bongers, O. Holovachov, J. Bakker & J. Helder. 2006. Phylum-wide Analysis of SSU rDNA Reveals Deep Phylogenetic Relationships among Nematodes and Accelerated Evolution toward Crown Clades. Molecular Biology and Evolution 23: 1792-1800.

Inserra, R., L. Duncan, A. Troccoli, D. Dunn, J. Maia Dos Santos, D. Kaplan & N. Vovlas. 2001. Pratylenchus jaehni p. n. from Citrus in Brazil and its Relationship with P. coffeae and P. loosi (Nematoda: Pratylenchidae). Nematology 3: 653-665.

Kaplan, D., W. Thomas, L. Frisse, J.L. Sarah, J.M. Stanton, P. Speijer, D. Marin & C. Opperman. 2000. Phylogenetic Analysis of Geographically Diverse Radopholus similis via rDNA Sequence Reveals a Monomorphic Motif. Journal of Nematology 32: 134-142.

Liao, L.L., S.L. Zhang, S. Xiao & S.S. Zhang. 2015. Identification and Pathogenicity of Root-lesion Nematodes Parasiting on the Peanut. Journal of Fujian Agriculture and Forestry University 44: 240-244.

Lira, V.L., M. Rosa, S.A. de Oliveira, C.M.G. de Oliveira & R.M. de Moura. 2014. Morphometric and Molecular Analysis of Pratylenchus coffeae Populations from Yam Tubers, Pernambuco State, Brazil. Nematropica 44: 152-165.

Nguyen, T.T. 2010. A Comparative Polyphasic Study of 10 Pratylenchus coffeae Populations from Vietnam [Disertasi]. Katholic University of Leuven, Belgia (BL). 141 p.

Nguyen, T.T., L. Waeyenberge, A. Elsen, H.H. Nhi & D. De. 2014. Molecular Characterisation of Pratylenchus coffeae Populations from Vietnam. Russian Journal of Nematology 22: 121-130.

Palomares-Rius, J.E., I. Guesmi, N. Horrigue-Raouani, C. Cantalapiedra-Navarrete, G. Liébanas & P. Castillo. 2014. Morphological and Molecular Characterisation of Pratylenchus oleae n. sp. (Nematoda: Pratylenchidae) Parasitizing Wild and Cultivated Olives in Spain and Tunisia. European Journal of Plant Pathology 140: 53-67.

Ryss, A.Y. 2017. A simple Express Technique to Process Nematodes for Collection Slide Mounts. Journal of Nematology 49: 27-32.

Siddiqi, M.R. 2000. Tylenchida: Parasites of Plants and Insects, 2nd Edition, CAB International, Wallingford, UK. 833 p.

Subbotin, S.A. & M. Moens. 2006. Molecular Taxonomy and Phylogeny. p. 33-58. In R. Perry & M. Moens (eds). Plant Nematology. CAB International, Wallingford.

Wiryadiputra, S. 1995. Estimation of Yield Losses Caused by Pratylenchus coffeae on Robusta Coffee, p. 980–985. In Parman, (ed.). Peran Fitopatologi dalam Pembangunan Pertanian Berkelanjutan di Kawasan Timur Indonesia. Risalah Kongres Nasional XIII dan Seminar Ilmiah Perhimpunan Fitopatologi Indonensia. Mataram, 25 - 27 September 1995


Article Metrics

Abstract views : 3445 | views : 2585


  • There are currently no refbacks.

Copyright (c) 2019 Jurnal Perlindungan Tanaman Indonesia

Creative Commons License
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.

Jurnal Perlindungan Tanaman Indonesia ISSN 1410-1637 (print), ISSN 2548-4788 (online) is published by the Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, in collaboration with Indonesian Entomological Society (Perhimpunan Entomologi Indonesia, PEI) and Indonesian Phytopathological Society (Perhimpunan Fitopatologi Indonesia, PFI). The content of this website is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.  

View website statistics