Comparison of ribosomal DNA ITS regions among geographic isolates of Cenococcum geophilum

Current Genetics

Volumn 35, Issue 5, 1999, Pages 527-535

  Shinohara, Mari L ^a,b   LoBuglio, Katherine F ^a,c   Rogers, Scott O ^a  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b Novo Nordisk Pharma Ltd   (Japan)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Cenococcum geophilum; Group I intron; Internal transcribed spacer (ITS); Mycorrhizae; Ribosomal DNA (rDNA); RNA secondary structure

Indexed keywords

FUNGAL DNA; RIBOSOME DNA; SPACER DNA;

ADAPTATION; ARTICLE; COMPARATIVE STUDY; DNA SEQUENCE; GENETIC VARIABILITY; MYCORRHIZA; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; TAXONOMY;

BASE SEQUENCE; DNA, RIBOSOMAL; EVOLUTION, MOLECULAR; GENETICS, POPULATION; INTRONS; MITOSPORIC FUNGI; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RESTRICTION MAPPING; RNA, FUNGAL; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; VARIATION (GENETICS);

CENOCOCCUM GEOPHILUM; FUNGI; MYCORRHIZAE;

EID: 0033062206     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s002940050449     Document Type: Article

References (36)

1. Berbee ML, Yoshimura A, Sugiyama J (1995) Is Penicillium monophyletic? An evaluation of phylogeny in the family Trichocomaceae from 18 S, 5.8 S and ITS ribosomal DNA sequence data. Mycologia 87:210-222
2. Carbone I, Kohn LM (1993) Ribosomal DNA sequence divergence within internal transcribed spacer 1 of the Sclerotiniaceae. Mycologia 85:415-427
3. Chambers C, Dutta SK, Crouch RJ (1986) Neurospora crassa ribosomal DNA: sequence of internal transcribed spacer and comparison with N. intermedia and N. sitophila. Gene 44:159-164
4. Gilbert DG (1990) LoopViewer, a Macintosh program for visualizing RNA secondary structure. Published electronically on the Internet, available via anonymous ftp to iubio.bio.indiana.edu
5. Hopple JS, Vilgalys R (1994) Phylogenetic relationships among coprinoid taxa and allies based on data from restriction-site mapping of nuclear rDNA. Mycologia 86:96-107
6. Jaeger JA, Turner DH, Zuker M (1989) Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol 183:281-306
7. Liu Y, Ammirati JF, Rogers SO (1997) Phylogenetic relationships in Dermocybe and related Cortinarius taxa based on nuclear ribosomal RNA internal transcribed spacers. Can J Bot 75:519-532
8. Liu Y, Rogers SO, Ammirati JF, Keller K (1995) Dermocybe, section Sanguineae: a look at species relationships within the sanguinea complex. Sydowia X: 142-154
9. LoBuglio KF, Rogers SO, Wang CJK (1991) Variation in ribosomal DNA among isolates of the mycorrhizal fungus Cenococcum geophilum. Can J Bot 69:2331-2343
10. LoBuglio KF, Pitt JI, Taylor JW (1993) Phylogenetic analysis of two ribosomal DNA regions indicates multiple independent losses of a sexual Talaromyces state among asexual Penicillium species in subgenus Biverticillium. Mycologia 85:592-604
11. LoBuglio KF, Berbee ML, Taylor JW (1996) Phylogenetic origins of the asexual mycorrhizal symbiont Cenococcum geophilum Fr. and other mycorrhizal fungi among the ascomycetes. Mol Phylog Evol 6:287-294
12. Massicotte HB, Trappe JM, Peterson RL, Melville LH (1992) Studies on Cenococcum geophilum. II. Sclerotium morphology, germination and formation in pure culture and growth pouches. Can J Bot 70:125-132
13. McCabe PC (1990) Production of single-stranded DNA by asymmetric PCR. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, Inc., Harcourt Brace Jovanovich, Publishers, New York, pp 76-83
14. Nues RW van, Rientjes JMJ, van der Sande CAFM, Zerp SF, Sluiter C, Venema J, Planta RJ, Raue HA (1994) Separate structural elements within internal transcribed spacer 1 of Saccharomyces cerevisiae precursor ribosome RNA direct the formation of 17S and 26S rRNA. Nucleic Acids Res 22:912-919
15. Rehner SA, Uecker FA (1994) Nuclear ribosomal internal transcribed spacer phylogeny and host diversity in the coelomycete Phomopsis. Can J Bot 74:1666-1674
16. Rogers SO, Bendich AJ (1985) Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol Biol 5:69-76
17. Rogers SO, Bendich AJ (1994) Extraction of total cellular DNA from plants, algae and fungi. In: Gelvin SB, Schilperoort RA (eds) Plant Molecular Biology Manual, 2nd edn. Kluwer Academic Press, Dordrecht, The Netherlands, pp D1:1-8
18. Rogers SO, Rehner S, Bledsoe C, Mueller GJ, Ammirati JF (1989) Extraction of DNA from Basidiomycetes for ribosomal DNA hybridizations. Can J Bot 67:1235-1243.
19. Rogers SO, Yan ZH, Shinohara M, LoBuglio KF, Wang CJK (1993) Messenger RNA intron on the nuclear 18S ribosomal RNA gene of deuteromycetes. Curr Genet 23:338-342
20. Sande CAFM van der, Kwa M, van Nues RW, van Heerikhuizen H, Raue HA, Planta RJ (1992) Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA. J Mol Biol 223:899-910
21. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467
22. Schaak J, Mao J, Soll D (1982) The 5.8S RNA gene sequence and the ribosomal repeat of Schizosaccharomyces pombe. Nucleic Acids Res 10:2851-2864
23. Schlick A, Kuhls K, Meyer W, Lieckfeldt E, Borner T, Messner K (1994) Fingerprinting reveals gamma-ray induced mutations in fungal DNA: implications for identification of parent strains of Trichoderma harzianum. Curr Genet 26:74-78
24. Schlotterer C, Hauser M, von Haeseler A, Tautz D (1994) Comparative evolutionary analysis of rDNA ITS regions in Drosophila. Mol Biol Evol 11:513-522
25. Shinohara ML, LoBuglio KF, Rogers SO (1996) Group-I intron family in the nuclear ribosomal RNA small subunit genes of Cenococcum geophilum isolates. Curr Genet 29:377-387.
26. Swofford DL (1993) PAUP: phylogenetic analysis using parsimony, version 3.1.1. Illinois Natural History Survey, Champaign, Illinois
27. Swofford DL (1998) PAUP*: phylogenetic analysis using parsimony, version 4.0b1. Sinauer and Associates, Inc., Sunderland, Massachusetts
28. Tautz D, Renz M (1983) An optimized freeze-squeeze method for the recovery of DNA fragments from agarose gels. Anal Biochem 132:14-19
29. Thuring RWJ, Sanders J, Borst P (1975) A freeze-squeeze method for recovering long DNA from agarose gels. Anal Biochem 66:213-220
30. Trappe JM (1964) Mycorrhizal host and distribution of Cenococcum graniforme. Lloydia 27:100-106
31. Trappe JM (1977) Selection of fungi for ectomycorrhizal inoculation in nurseries. Annu Rev Phytopathol 15:203-222
32. Veldman GM, Klootwijk J, van Heerikhuizen H, Planta RJ (1981) The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript. Nucleic Acids Res 9:4847-4862
33. Vilgalys R, Sun BL (1994) Ancient and recent patterns of geographic speciation in the oyster mushroom Pleurotus revealed by phylogenetic analysis of ribosomal DNA sequences. Proc Natl Acad Sci USA 91:4599-4603
34. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis MA, Gelfand DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic Press, Inc., Harcourt Brace Jovanovich, Publishers, New York, pp 315-322
35. Yan ZH, Rogers SO, Wang CJK (1995) Assesment of Phialophora species based on ribosomal DNA internal transcribed spacers and morphology. Mycologia 87:72-83
36. Yeh L-CC, Lee JC (1990) Structural analysis of the internal transcribed spacer 2 of the precursor ribosomal RNA from Saccharomyces cerevisiae. J Mol Evol 211:699-712