Phylogenetic relationships among ascomycetes: Evidence from an RNA polymerse II subunit

Molecular Biology and Evolution

Volumn 16, Issue 12, 1999, Pages 1799-1808

  Liu, Yajuan J ^b   Whelen, Sally ^a   Hall, Benjamin D ^c  

^a ROSETTA INPHARMATICS   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c NONE

Author keywords

Ascomycetes; Ascomycota; Evolution; Phylogeny; RNA polymerase II; RPB2

Indexed keywords

RIBOSOME DNA; RNA POLYMERASE II;

ARTICLE; ASCOMYCETES; DNA SEQUENCE; GENE AMPLIFICATION; GENETIC CONSERVATION; GENETIC VARIABILITY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RNA ANALYSIS; SEQUENCE ANALYSIS;

EID: 0032750944     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a026092     Document Type: Article

References (44)

1. ALEXOPOULOS, C. J., C. W. MIMS, and M. BLACKWELL. 1996. Introductory mycology. 4th edition. John Wiley and Sons.
2. BARR, M. E. 1983. The ascomycete connection. Mycologia 75: 1-13.
3. _. 1987. Prodromus to Class Loculoascomycetes. Newell, Amherst, Mass.
4. _. 1990. Prodromus to nonlichenized, pyrenomycetous members of Class Hymenoascomycetes. Mycotaxon 39:43-184.
5. BERBEE, M. L. 1996. Loculoascomycete origins and evolution of filamentous ascomycete morphology based on 18S rRNA gene sequence data. Mol. Biol. Evol. 13:462-470.
6. BERBEE, M. L., and J. W. TAYLOR. 1992. Two ascomycete classes based on fruiting-body characters and ribosomal DNA sequences. Mol. Biol. Evol. 9:278-284.
7. _. 1995. From 18S ribosomal sequence data to evolution of morphology among the fungi. Can. J. Bot. 73(Suppl. 1): S677-S683.
8. DENTON, A. L., B. L. MCCONAUGHY, and B. D. HALL. 1998. Usefulness of RNA polymerase II coding sequences for estimation of green plant phylogeny. Mol. Biol. Evol. 15: 1082-1085.
9. ERIKSSON, O., and D. L. HAWKSWORTH. 1993. Outline of the Ascomycetes - 1993. Syst. Ascomycet. 12:1-257.
10. FELSENSTEIN, J. 1981. A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biol. J. Linn. Soc. 16:183-196.
11. _. 1993. PHYLIP (phylogeny inference package). Version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle.
12. GARGAS, A. 1992. Phylogeny of Discomycetes and early radiation of the filamentous Ascomycetes inferred from 18s rDNA data. Ph.D. dissertation, University of California, Berkeley.
13. GARGAS, A., and J. W. TAYLOR. 1995. Phylogeny of Disco-mycetes and early radiation of the apothecial Ascomycotina inferred from SSU rDNA sequence data. Exp. Mycol. 19: 7-15.
14. HAASE, G., L. SONNTAG, Y. VON DE PEER, J. M. J. UIJTHOF, A. PODBIELSKI, and B. MELZER-KRICK. 1995. Phylogenetic analysis of ten black yeast species using nuclear small sub-unit rRNA gene sequences. Antonie Van Leeuwenhoek 68: 19-33.
15. HAWKSWORTH, W. L. 1991. The fungal dimension of biodiversity: magnitude, significance and conservation. Mycol. Res. 95:641-655.
16. HAWKSWORTH, W. L., P. M. KIRK, B. C. SUTTON, and D. N. PEGLER. 1995. Ainsworth & Bisby's dictionary of the fungi. 8th edition. CAB International.
17. HIGGINS, D. G., A. J. BLEASBY, and R. FUCHS. 1992. CLUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci. 8:189-191.
18. HONEGGER, R. 1991. Functional aspects of the lichen symbiosis. Annu. Rev. Plant Physiol. Plant Mol. Biol. 42:553-578.
19. IWABE, N., K. KUMA, H. KISHINO, M. HASEGAWA, and T. MIYATA. 1991. Evolution of RNA polymerases and branching patterns of the three major groups of archaebacteria. J. Mol. Evol. 32:70-78.
20. JAMES, P., S. WHELEN, and B. D. HALL. 1991. The RET1 gene of yeast encodes the second-largest subunit of RNA polymerase III. J. Biol. Chem. 266:5616-5624.
21. JONES, D. T., W. R. TAYLOR, and J. M. THORNTON. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl Biosci. 8:275-282.
22. KISHINO, H., and M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
23. KLENK, H.-P., W. ZILLIG, M. LANZENDÄRFER, B. BRAMPP, and P. PALM. 1995. Location of protist lineages in a phylogenetic tree inferred from sequences of DNA-dependent RNA polymerases. Arch. Protistenkd. 145:221-230.
24. KURTZMAN, C. P. 1993. Systematics of the ascomycetous yeasts assessed from ribosomal RNA sequence divergence. Antonie Van Leeuwenhoek 63:165-174.
25. KURTZMAN, C. P., and C. J. ROBNETT. 1995. Molecular relationships among hyphal ascomycetous yeasts and yeastlike taxa. Can. J. Bot. 73(Suppl. 1):S824-S830.
26. LANDVIK, S. 1996. Neolecta, a fruit-body-producing genus of the basal ascomycetes, as shown by SSU and LSU rDNA sequences. Mycol. Res. 100:199-202.
27. LOBUGLIO, K. F., M. L. BERBEE, and J. W. TAYLOR. 1996. Phylogenetic origins of the asexual mycorrhizal symbiont Cenococcum geophilum Fr. and other mycorrhizal fungi among the Ascomycetes. Mol. Phylogenet. Evol. 6:287-294.
28. LUTTRELL, E. S. 1955. The ascostromatic Ascomycetes. Mycologia 47:511-532.
29. NANNFELDT, J. A. 1932. Studien uber die Morphologie und Systematik der Nicht-Lichenisierten Inoperculaten Discomyceten. Nova Acta Regiae Soc. Sci. Upsaliensis 8(Ser. IV):1-368.
30. NISHIDA, H., and J. SUGIYAMA. 1993. Phylogenetic Relationships among Taphrina, Saitoella, and other higher fungi. Mol. Biol. Evol. 10:431-436.
31. _. 1994. Archiascomycetes: detection of a major new lineage within the Ascomycota. Mycoscience 35:361-366.
32. ROGERS, S. O., and A. J. BENDICH. 1994. Extraction of total cellular DNA from plant, algal, and fungal tissues. Pp. D1, 1-8 in S. GELVIN and R. A. SCHILPEROORT, eds. Plant molecular biology manual. 3rd edition. Kluwer Academic Publishers, Boston, Mass.
33. SAENZ, G. S., J. W. TAYLOR, and A. GARGAS. 1994. 18s rRNA gene sequences and supraordinal classification of the Erysiphales. Mycologia 86:212-216.
34. SIDOW, A., and K. THOMAS. 1993. A molecular evolutionary framework for eukaryotic model organisms. Curr. Biol. 4: 596-603.
35. SPATAFORA, J. W. 1995. Ascomal evolution of filamentous ascomycetes: evidence from molecular data. Can. J. Bot. 73(Suppl. 1):S811-S815.
36. SPATAFORA, J. W., and M. BLACKWELL. 1993. Molecular systematics of unitunicate perithecial ascomycetes: the Clavicipitales-Hypocreales connection. Mycologia 85:912-922.
37. _. 1994. Cladistic analysis of Partial ssrDNA sequences among unitunicate perithecial ascomycetes and its implications on the evolution of centrum development. Pp. 233-241 in D. L. HAWKSWORTH, ed. Ascomycete systematics. Problems and perspectives in the nineties. Plenum Press, New York.
38. STILLER, J. W., and B. D. HALL. 1997. The origin of red algae: implications for plastid evolution. Proc. Natl. Acad. Sci. USA 94:4520-4525.
39. STRIMMER, K., and A. VON HAESELER. 1997. PUZZLE, Version 4.0: maximum likelihood analysis for nucleotide, amino acid, and two-state data. Zoologisches Institut, Universitaet Muenchen, Munich, Germany.
40. SWOFFORD, D. 1993. PAUP: phylogenetic analysis using parsimony. Version 3.1.1. National Museum of Natural History, Washington, D.C.
41. TEMPLETON, A. R. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes. Evolution 37: 221-244.
42. THURIAUX, P., and A. SENTENAC. 1992. Yeast nuclear RNA polymerases. Pp. 1-48 in E. JONES, J. PRINGLE, and J. BROACH, eds. The molecular and cellular biology of the yeast Saccharomyces. Cold Spring Harbor Laboratory Press, New York.
43. WINKA, K., O. E. ERIKSSON, and A. BANG. 1998. Molecular evidence for recognizing the Chaetothyriales. Mycologia 90:822-830.
44. YANG, Z. 1995. Phylogenetic analysis by maximum likelihood (PAML). Version 1.1. Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park.