The iphyclassifier, an interactive online tool for phytoplasma classification and taxonomic assignment

Methods in Molecular Biology

Volumn 938, Issue , 2013, Pages 329-338

  Zhao, Yan ^a   Wei, Wei ^b   Lee, Ing Ming ^a   Shao, Jonathan ^a   Suo, Xiaobing ^c   Davis, Robert E ^c  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

^c U S DEPARTMENT OF AGRICULTURE   (United States)

Author keywords

Candidatus Phytoplasma' species assignment; I PhyClassifier; Phytoplasma classification; Restriction fragment length polymorphism; Similarity coefficient

Indexed keywords

ARTICLE; ENZYME DEGRADATION; GEL ELECTROPHORESIS; IPHYCLASSIFIER; NONHUMAN; ONLINE SYSTEM; PHYTOPLASMA; PRIORITY JOURNAL; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEQUENCE ANALYSIS; TAXONOMIC IDENTIFICATION;

EID: 84934434700     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-89-2_28     Document Type: Article

References (31)

1. Kuske CR, Kirkpatrick BC (1992) Phylogenetic relationships between the western aster yellows mycoplasmalike organism and other prokaryotes established by 16S rRNA gene sequence. Int J Syst Bacteriol 42:226-233
2. Namba S et al (1993) Phylogenetic diversity of phytopathogenic mycoplasmalike organisms. Int J Syst Bacteriol 43:461-467
3. Gundersen DE et al (1994) Phylogeny of mycoplasmalike organisms (phytoplasmas): a basis for their classi fi cation. J Bacteriol 176:5244-5254
4. Schneider B et al (1995) Phylogenetic classi fi cation of plant pathogenic mycoplasma-like organisms or phytoplasmas. In: Razin R, Tully JG (eds) Molecular and diagnostic procedures in mycoplasmology. Academic, San Diego, pp 369-380
5. Seemüller E et al (1998) Current status of molecular classi fi cation of the phytoplasmas. J Plant Pathol 80:3-26
6. Lee I-M et al (1993) Universal amplification and analysis of pathogen 16S rDNA for classi fi cation and identi fi cation of mycoplasmalike organisms. Phytopathology 83:834-842
7. Lee I-M et al (1998) Revised classi fi cation scheme of phytoplasmas based on RFLP analyses of 16S rRNA and ribosomal protein gene sequences. Int J Syst Bacteriol 48:1153-1169
8. Lee I-M, Davis RE, Gundersen-Rindal DE (2000) Phytoplasma: phytopathogenic mollicutes. Annu Rev Microbiol 54:221-255
9. Schneider B et al (1993) Classi fi cation of plantpathogenic mycoplasma-like organisms using restriction-site analysis of PCR-ampli fi ed 16S rDNA. Microbiology 139:519-527
10. Lee I-M et al (2006) ' Candidatus Phytoplasma americanum', a phytoplasma associated with a potato purple top wilt disease complex. Int J Syst Evol Microbiol 56:1593-1597
11. Wei W et al (2007) Computer-simulated RFLP analysis of 16S rRNA genes: identi fi cation of ten new phytoplasma groups. Int J Syst Evol Microbiol 57:1855-1867
12. Wei W et al (2008) Automated RFLP pattern comparison and similarity coef fi cient calculation for rapid delineation of new and distinct phytoplasma 16Sr subgroup lineages. Int J Syst Evol Microbiol 58:2368-2377
13. Zhao Y et al (2009) ' Candidatus Phytoplasma tamaricis', a novel taxon discovered in witches'- broom-diseased salt cedar (Tamarix chinensis Lour.). Int J Syst Evol Microbiol 59:2496-2504
14. Zhao Y et al (2009) Construction of an interactive online phytoplasma classi fi cation tool, i PhyClassi fi er, and its application in analysis of the peach X-disease phytoplasma group (16SrIII). Int J Syst Evol Microbiol 59: 2582-2593
15. Jomantiene R et al (2010) Onion is host for two phytoplasma lineages, subgroups 16SrI-A and 16SrI-(B/L)L, in Lithuania: a Hinf I site revealed a SNP marking divergent branches of evolution. J Plant Pathol 92:461-470
16. Jomantiene R et al (2011) Phytoplasmas infecting sour cherry and lilac represent two distinct lineages having close evolutionary af fi nities with clover phyllody phytoplasma. Eur J Plant Pathol 130:97-107
17. Lee I-M et al (2011) ' Candidatus Phytoplasma costaricanum', a new phytoplasma associated with a newly emerging disease in soybean in Costa Rica. Int J Syst Evol Microbiol. doi: 10.1099/ijs.0.029041-0
18. The IRPCM Phytoplasma/Spiroplasma Working Team - Phytoplasma taxonomy group (2004) ' Candidatus Phytoplasma', a taxon for the wall-less, non-helical prokaryotes that colonize plant phloem and insects. Int J Syst Evol Microbiol 54:1243-1255
19. Pearson WR, Lipman DJ (1988) Improved tools for biological sequence comparison. PNAS USA 85:2444-2448
20. Altschul SF et al (1990) Basic local alignment search tool. J Mol Biol 215:403-410
21. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-speci fi c gap penalties and weight matrix choice. Nucl Acids Res 22:4673-4680
22. Schneider B, Seemüller E (1994) Presence of two sets of ribosomal genes in phytopathogenic mollicutes. Appl Environ Microbiol 60:3409-3412
23. Liefting LW et al (1996) Sequence heterogeneity in the two 16S rRNA genes of Phormium yellow leaf phytoplasma. Appl Environ Microbiol 62:3133-3139
24. Davis RE, Sinclair WA (1998) Phytoplasma identity and disease etiology. Phytopathology 88:1372-1376
25. Davis RE, Dally EL (2001) Nonfunctional tRNA gene in an unusual example of rRNA interoperon sequence heterogeneity in phytoplasma. Phytopathology 91:S21
26. Davis RE et al (2003) Differential amplification of sequence heterogeneous ribosomal RNA genes and classi fi cation of the ' Fragaria multicipita ' phytoplasma. Microbiol Res 158:229-236
27. Jomantiene R et al (2002) New group 16SrIII phytoplasma lineages in Lithuania exhibit interoperon sequence heterogeneity. Eur J Plant Pathol 108:507-517
28. Nei M, Li W-H (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. PNAS USA 76:5269-5273
29. Gundersen DE, Lee I-M (1996) Ultrasensitive detection of phytoplasmas by nested-PCR assays using two universal primer pairs. Phytopathol Mediterr 35:144-151
30. Murray RGE, Schleifer KH (1994) Taxonomic notes: a proposal for recording the properties of putative taxa of prokaryotes. Int J Syst Bacteriol 44:174-176
31. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species de fi nition in bacteriology. Int J Syst Bacteriol 44:846-849