Use of a real-time LAMP isothermal assay for detecting 16SrII and XII phytoplasmas in fruit and weeds of the Ethiopian Rift Valley

Plant Pathology

Volumn 60, Issue 2, 2011, Pages 345-355

  Bekele, B ^a   Hodgetts, J ^b   Tomlinson, J ^b   Boonham, N ^b   Nikolic P ^c   Swarbrick, P ^d   Dickinson, M ^d  

^a ETHIOPIAN INSTITUTE OF AGRICULTURAL RESEARCH   (Ethiopia)

^b FOOD AND ENVIRONMENT RESEARCH AGENCY   (United Kingdom)

^c NATIONAL INSTITUTE OF BIOLOGY   (Slovenia)

^d UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Citrus; Diagnostics; Ethiopia; LAMP assay; Papaya; Parthenium hysterophorus

Indexed keywords

BACTERIAL DISEASE; DICOTYLEDON; DIEBACK; DISEASE SEVERITY; FRUIT; HOST-PATHOGEN INTERACTION; PHYTOPLASMA; POLYMERASE CHAIN REACTION; POPULATION DECLINE; REAL TIME; SAMPLING; SYMPTOM; WEED;

AUSTRALIA; EAST AFRICAN RIFT; ETHIOPIAN RIFT; ISRAEL;

CANDIDATUS PHYTOPLASMA; CARICA PAPAYA; CITRUS; PARTHENIUM HYSTEROPHORUS;

EID: 79952088007     PISSN: 00320862     EISSN: 13653059     Source Type: Journal    
DOI: 10.1111/j.1365-3059.2010.02384.x     Document Type: Article

References (33)

1. Altschul SF, Gush W, Miller W, Myers W, Lipman DJ, 1990. Basic local alignment search tool. Journal of Molecular Biology 215, 403-10.
2. Arocha Y, Bekele B, Tadesse D, Jones P, 2007. First report of a 16SrII group phytoplasma associated with die-back diseases of papaya and citrus in Ethiopia. Plant Pathology 56, 1039.
3. Christensen NM, Nicolaisen M, Hansen M, Schulz A, 2004. Distribution of phytoplasmas in infected plants as revealed by real-time PCR and bioimaging. Molecular Plant-Microbe Interactions 17, 1175-84.
4. Chung K-R, Khan IA, Briansky RH, 2006. Citrus Diseases Exotic to Florida: Witches' Broom Disease of Lime (WBDL). Florida, USA: University of Florida, Institute of Food and Agricultural Sciences (IFAS), Extension: Fact Sheet PP-228.
5. Deng SJ, Hiruki C, 1991. Genetic relatedness between two nonculturable mycoplasmalike organisms revealed by nucleic acid hybridization and polymerase chain reaction. Phytopathology 81, 1475-9.
6. Doyle JJ, Doyle JL, 1990. Isolation of plant DNA from fresh tissue. Focus 12, 13-5.
7. Firrao G, Gibb K, Streten C, 2005. Short taxonomic guide to the genus 'Candidatus phytoplasma'. Journal of Plant Pathology 87, 249-63.
8. Gera A, Mawassi M, Zeidan M, Spiegel S, Bar-Joseph M, 2005. An isolate of 'Candidatus Phytoplasma australiense' group associated with Nivun Haamir dieback disease of papaya in Israel. Plant Pathology 54, 560.
9. Gundersen DE, Lee I-M, 1996. Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathologia Mediterranea 35, 144-51.
10. Harrison NA, Womack M, Carpio ML, 2002. Detection and characterization of a lethal yellowing (16SrIV) group phytoplasma in Canary Island date palms affected by lethal decline in Texas. Plant Disease 86, 676-81.
11. Hodgetts J, Ball T, Boonham N, Mumford R, Dickinson M, 2007. Use of terminal restriction fragment length polymorphism (T-RFLP) for identification of phytoplasmas in plants. Plant Pathology 56, 357-65.
12. Hodgetts J, Boonham N, Mumford R, Harrison N, Dickinson M, 2008. Phytoplasma phylogenetics based on analysis of secA and 23S rRNA gene sequences for improved resolution of candidate species of 'Candidatus Phytoplasma'. International Journal of Systematic and Evolutionary Microbiology 58, 1826-37.
13. Hodgetts J, Boonham N, Mumford R, Dickinson M, 2009. Panel of 23S rRNA-gene based real-time PCR assays for improved universal and group-specific detection of phytoplasmas. Applied and Environmental Microbiology 75, 2945-50.
14. Hogenhout SA, Oshima K, Anmar ED, Kakizawa S, Kingdom HN, Namba S, 2008. Phytoplasmas: bacteria that manipulate plants and insects. Molecular Plant Pathology 9, 403-23.
15. Janke J, von Bargen S, Ulrichs C, Taye T, Bandte M, Büttner C, 2007. Studies on phyllody in Parthenium hysterophorus and detection of phytoplasmas within important crops cultivated in Ethiopia. In: Tropentag 2007 - Conference on International Research on Food Security, Natural Resource Management and Rural Development, Cuvillier Verlag Gottingen, Germany, Nov 2007, Plant Protection Session, Poster no. 11.
16. Kumar S, Tamura K, Nei M, 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Briefings in Bioinformatics 5, 150-63.
17. Lee I-M, Davis RE, 1992. Mycoplasmas which infect plants and insects. In: Maniloff J, McElhaney RN, Finch LR, Baseman JB, eds. Mycoplasmas: Molecular Biology and Pathogenesis. Washington DC, USA: American Society for Microbiology, 379-90.
18. Lee I-M, Davis RE, Gundersen DE, 2000. Phytoplasma: phytopathogenic mollicutes. Annual Review of Microbiology 54, 221-55.
19. Maktar NH, Kamis S, Mohd Yusof FZ, Hussain NH, 2008. Erwinia papaya causing papaya dieback in Malaysia. Plant Pathology 57, 774.
20. Martini M, Lee I-M, Bottner KD et al., 2007. Ribosomal protein gene-based phylogeny for finer differentiation and classification of phytoplasmas. International Journal of Systematic and Evolutionary Microbiology 57, 2037-51.
21. Nejat N, Sijam K, Abdullah SNA, Vadamalai G, Dickinson M, 2009. Phytoplasmas associated with disease of coconut in Malaysia: phylogenetic groups and host plant species. Plant Pathology 58, 1152-60.
22. Nicolaisen M, Bertaccini A, 2007. An oligonucleotide microarray-based assay for identification of phytoplasma 16S ribosomal groups. Plant Pathology 56, 332-6.
23. Pérez KA, Piñol B, Arocha Rosete Y, Wilson M, Boa E, Lucas J, 2010. Transmission of the phytoplasma associated with bunchy top symptom of papaya by Empoasca papaya Oman. Journal of Phytopathology 158, 194-6.
24. Seifu GM, 2003. Status of Commercial Fruit Production in Ethiopia. Addis Ababa, Ethiopia: Ethiopian Agricultural Research Organization (EARO).
25. Smart CD, Schneider B, Blomquist CL et al., 1996. Phytoplasma-specific PCR primers based on sequence of the 16S-23S rRNA spacer region. Applied and Environmental Microbiology 62, 2988-93.
26. Srivastava K, Singh S, 2009. Citrus decline: soil fertility and plant nutrition. Journal of Plant Nutrition 32, 197-245.
27. Taye T, Obermeier C, Einhorn G, Seemuller E, Buttner C, 2004. Phyllody disease of parthenium weed in Ethiopia. Pest Management Journal of Ethiopia 8, 39-50.
28. Thompson JD, Higgins DG, Gibson TJ, 1994. clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-80.
29. Tomlinson JA, Boonham N, Dickinson M, 2010a. Development and evaluation of a one-hour DNA extraction and loop-mediated isothermal amplification assay for rapid detection of phytoplasmas. Plant Pathology 59, 465-71.
30. Tomlinson JA, Dickinson M, Boonham N, 2010b. Rapid detection of Phytophthora ramorum and P. kernoviae by two-minute DNA extraction followed by isothermal amplification and amplicon detection by generic lateral flow device. Phytopathology 100, 143-9.
31. Tran-Nguyen LTT, Kube M, Schneider B, Reinhardt R, Gibb KS, 2008. Comparative genome analysis of 'Candidatus Phytoplasma australiense' (subgroup tuf-Australia 1: rp-A) and 'Ca. P. asteris' strains OY-M and AY-WB. Journal of Bacteriology 190, 3979-91.
32. White DT, Blackall LL, Scott PT, Walsh KB, 1998. Phylogenetic positions of phytoplasmas associated with dieback, yellow crinkle and mosaic diseases of papaya, and their proposed inclusion in 'Candidatus Phytoplasma australiense' and a new taxon, 'Candidatus Phytoplasma australasia'. International Journal of Systematic Bacteriology 48, 941-51.
33. Zhang Z, Schwartz S, Wagner L, Miller W, 2000. A greedy algorithm for aligning DNA sequences. Journal of Computational Biology 7, 203-14.