Domain II hairpin structure in ITS1 sequences as an aid in differentiating recently evolved animal and plant pathogenic fungi

Mycopathologia

Volumn 166, Issue 1, 2008, Pages 1-16

  Bridge, P D ^a   Schlitt, T ^a   Cannon, P F ^b   Buddie, A G ^b   Baker, M ^c   Borman, A M ^d  

^a BRITISH ANTARCTIC SURVEY   (United Kingdom)

^b CABI   (United Kingdom)

^c WILLIAM HARVEY HOSPITAL   (United Kingdom)

^d PUBLIC HEALTH ENGLAND   (United Kingdom)

Author keywords

Arthroderma; Colletotrichum; ITS; Sequence analysis; Structural models; Trichophyton

Indexed keywords

FUNGAL DNA; FUNGAL RNA; RIBOSOMAL SPACER DNA; RIBOSOME RNA;

ANIMAL; ARTHRODERMA; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; COLLETOTRICHUM; COMPARATIVE STUDY; CONFORMATION; FUNGUS; GENETICS; MICROBIOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PATHOGENICITY; PHYLOGENY; PLANT DISEASE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; TRICHOPHYTON; VIRULENCE;

ANIMALS; ARTHRODERMATACEAE; BASE SEQUENCE; COLLETOTRICHUM; DNA, FUNGAL; DNA, RIBOSOMAL SPACER; EVOLUTION, MOLECULAR; FUNGI; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; PLANT DISEASES; REPETITIVE SEQUENCES, NUCLEIC ACID; RNA, FUNGAL; RNA, RIBOSOMAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY; TRICHOPHYTON; VIRULENCE;

ANIMALIA; ARTHRODERMA; COLLETOTRICHUM; FUNGI; TRICHOPHYTON;

EID: 40449137040     PISSN: 0301486X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11046-008-9094-3     Document Type: Article

References (37)

1. Bridge PD, Spooner BM, Roberts PJ. The impact of molecular data in fungal systematics. Adv Bot Res 2005;42:33-67.
2. Edel V, Steinberg C, Gautheron N, Alabouvette C. Evaluation of restriction analysis of polymerase chain reaction (PCR)-amplified ribosomal DNA for the identification of Fusarium species. Mycol Res 1996;101:179-87.
3. Bridge PD, Waller JM, Davies D, Buddie AG. Variability of Colletotrichum kahawae in relation to other Colletotrichum species from tropical perennial crops and the development of diagnostic techniques. J Phytopathol 2008. doi:10.1111/j.1439-0434.2007.01354.x.
4. Tymon AM, Shah PA, Pell JK. PCR-based molecular discrimination of Pandora neoaphidis isolates from related entomopathogenic fungi and development of species-specific diagnostic primers. Mycol Res 2004;108:419-33.
5. Xue B, Goodwin PH, Annis SL. Pathotype identification of Leptosphaeria maculans with PCR and oligonucleotide primers from ribosomal internal transcribed spacer sequences. Physiol Mol Plant Pathol 1992;41:179-88.
6. Brown AE, Muthumeenakshi S, Sreenivasaprasad S, Mills PR, Swinburne TR. A PCR primer-specific to Cylindrocarpon heteronema for detection of the pathogen in apple wood. FEMS Microbiol Lett 1993;108:117-20.
7. Sreenivasaprasad S, Mills PR, Meehan BM, Brown AE. Phylogeny and systematics of 18 Colletotrichum species based on ribosomal DNA spacer sequences. Genome 1996;39:499-512.
8. Makimura K, Tamura Y, Mochizuki T, Hasegawa A, Tajiri Y, Hanazawa R, Uchida K, Saito H, Yamaguchi H. Phylogenetic classification and species identification of dermatophyte strains based on DNA sequences of nuclear ribosomal internal transcribed spacer 1 regions. J Clin Microbiol 1999;37:920-4.
9. van Neus RW, Rientjes JM, van der Sande CA, Zerp SF, Sluiter C, Venema J, Planta RJ, Raue HA. Separate structural elements within the internal transcribed spacer 1 of Saccharomyces cerevisiae precursor ribosomal RNA direct the formation of 17S and 26S rRNA. Nucl Acid Res 1994;22:912-9.
10. Gottschling M, Plötner J. Secondary structure models of the nuclear internal transcribed spacer regions and 5.8S rRNA in Calciodinelloideae (Peridiniaceae) and other dinoflagellates. Nucl Acid Res 2004;32:307-15.
11. Lalev AI, Nazar RN. Structural equivalence in the transcribed spacers of pre-rRNA transcripts in Schizosaccharomyces pombe. Nucl Acid Res 1999;27:3071-8.
12. Campbell CS, Wright WA, Cox M, Vining TF, Major CS, Arsenault MP. Nuclear ribosomal DNA internal transcribed spacer 1 (ITS1) in Picea (Pinaceae): sequence divergence and structure. Mol Phylogen Evol 2005;35:165-85.
13. Won H, Renner SS. The internal transcribed spacer on nuclear ribosomal DNA in the gymnosprem Gnetum. Mol Phylogenet Evol 2005;36:581-97.
14. Gonzalez P, Labarère J. Sequence and secondary structure of the mitochondrial small-subunit rRNA V4, V6 and V9 domains reveal highly species-specific variations within the genus Agrocybe. Appl Environ Microbiol 1998;64:4149-60.
15. Tuckwell DS, Nicholson MJ, McSweeney SS, Theodorou MK, Brookman JL. The rapid assignment of ruminal fungi to presumptive genera using ITS1 and ITS2 RNA secondary structures to produce group-specific fingerprints. Microbiology 2005;151:1557-67.
16. Landis FC, Gargas A. Using ITS2 secondary structure to create species-specific oligonucleotide probes for fungi. Mycologia 2007;99:681-92.
17. Cannon PF, Bridge PD, Monte E. Linking the past, present, and future of Colletotrichum systematics. In: Prusky D, Freeman S, Dickman M, editors. Colletotrichum: host specificity, pathology, and host-pathogen interaction. St Paul Minnesota: American Phytopathological Society, 2000. p. 1-20.
18. Sreenivasaprasad S, Brown AE, Mills PR. DNA sequence variation and interrelationships among Colletotrichum species causing strawberry anthracnose. Physiol Mol Plant Pathol 1992;41:265-81.
19. Sreenivasaprasad S, Mills PR, Brown AE. Nucleotide sequence of the rDNA spacer 1 enables identification of isolates of Colletotrichum as C. acutatum. Mycol Res 1994;98:186-8.
20. Summerbell RC, Haugland RA, Li A, Gupta AK. rRNA gene internal transcribed spacer 1 and 2 sequences of asexual, anthropophilic dermatophytes related to Trichophyton rubrum. J Clin Microbiol 1999;37:4005-11.
21. Kirk PM, Cannon PF, David JC, Stalpers JA, editors. Ainsworth & Bisby's dictionary of the fungi. 9th ed. Wallingford: CAB International; 2001.
22. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acid Res 1994;22:4673-80.
23. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucl Acid Res 2003;31:3406-15.
24. Clamp M, Cuff J, Searle SM, Barton GJ. The Jalview Java Alignment Editor. Bioinformatics 2004;20:426-7.
25. Höchsmann, M. The tree alignment model: Algorithms, implementations and applications for the analysis of RNA secondary structures. PhD Thesis Bielefeld University, 2005. (available as.pdf file at http://bibiserv.techfak. uni-bielefeld.de/rnaforester/diss_hoechsmann.pdf ).
26. Höchsmann M, Voss B, Giegerich R. Pure multiple RNA secondary structure alignments: a progressive profile approach. IEEE/ACM Trans Comput Biol Bioinform 2004;1:53-62.
27. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, 2005.
28. Page RDM. TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Appl Biosci 1996;12:357-8.
29. Freeman S, Minz D, Jurkevitch E, Maymon M, Shabi E. Molecular analyses of Colletotrichum species from almond and other fruits. Phytopathology 2000;90:608-14.
30. Afanador-Kafuri L, Minz D, Maymon M, Freeman S. Characterization of Colletotrichum isolates from Tamarillo, Passiflora, and Mango in Colombia and identification of a unique species from the genus. Phytopathology 2003;93:579-87.
31. Makimura K, Mochizuki T, Hasegawa A, Uchida K, Saito H, Yamaguchi H. Phylogenetic classification of Trichophyton mentagrophytes complex strains based on DNA spacers of nuclear ribosomal internal transcribed spacer 1 regions. J Clin Microbiol 1998;36:2629-33.
32. Gräser Y, de Hoog GS, Kuijpers AFA. Recent advances in the molecular taxonomy of dermatophytes In: Kushwaha RKS, Guarro J, editors. Biology of Dermatophytes and other Keratinophilic fungi. Bilbao Spain: Revista Iberoamericana de Micologia (suppl.), 2000, p. 17-21.
33. Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. JMol Biol 1999;288:911-40.
34. Goertzen LR, Cannone JJ, Gutell RR, Jansen RK. ITS secondary structure derived from comparative analysis: implications for sequence alignment, phylogeny of the Asteraceae. Mol Phylogenet Evol 2003;29:216-34.
35. Gardner PP, Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics 2004;5:140.
36. Mayol M, Rossello JA. Why ribosomal DNA spacers (ITS) tell different stories in Quercus. Mol Phylogenet, Evol 2001;19:167-76.
37. Liu JS, Schardl CL. A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes. Plant Mol Biol 1994;26:775-8.