Distinguishing plant and fungal sequences in ESTs from infected plant tissues

Journal of Microbiological Methods

Volumn 54, Issue 3, 2003, Pages 339-351

  Hsiang, Tom ^a   Goodwin, Paul H ^a  

^a UNIVERSITY OF GUELPH   (Canada)

Author keywords

ESTs; Fungi; Plant diseases; Standalone BLAST

Indexed keywords

FUNGAL DNA; PLANT DNA;

ACCURACY; ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; DNA DETERMINATION; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; FUNGAL PLANT DISEASE; FUNGUS; GENE LIBRARY; GENETIC ANALYSIS; GENETIC DATABASE; GENOME; INTERMETHOD COMPARISON; NUCLEOTIDE SEQUENCE; PLANT; PLANT TISSUE; PRIORITY JOURNAL; RANDOMIZATION; UNINDEXED SEQUENCE;

FUNGI;

EID: 0037783949     PISSN: 01677012     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-7012(03)00067-8     Document Type: Article

References (25)

1. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
2. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant, Arabidopsis thaliana. Nature. 408:2000;796-815.
3. Cherry J.M., Adler C., Ball C., Chervitz S.A., Dwight S.S., Hester E.T., Jia Y., Juvik G., Roe T., Schroeder M., Weng S., Botstein D. SGD: Saccharomyces Genome Database. Nucleic Acids Res. 26:1998;73-80.
4. Cummings L., Riley L., Black L., Souvorov A., Resenchuk S., Dondoshansky I., Tatusova T. Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes. FEMS Microbiol. Lett. 216:2002;133-138.
5. Fristensky B., Balcerzak M., He D., Zhang P. Expressed sequence tags from the defense response of Brassica napus to Leptosphaeria maculans. Mol. Plant Pathol. 1999;. (On-Line. Ref. No. 1412).
6. Kendrew J. The Encyclopedia of Molecular Biology. 1994;Blackwell, Cambridge, MA.
7. Keon J., Bailey A., Hargreaves J. A group of expressed cDNA sequences from the wheat fungal leaf blotch pathogen, Mycosphaerella graminicola (Septoria tritici). Fungal Genet. Biol. 29:2000;118-133.
8. Koski L.B., Golding G.B. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52:2001;540-542.
9. Kruger W.M., Pritsch C., Chao S., Muehlbauer G.J. Functional and comparative bioinformatic analysis of expressed genes from wheat spikes infected with Fusarium graminearum. Mol. Plant-Microb. Interact. 15:2002;445-455.
10. Lewin B. Genes VI. 1997;Oxford Univ. Press, New York, NY.
11. Lin K., Kuang Y., Joseph J.S., Kolatkar P.R. Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis, and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics. Nucleic Acids Res. 30:2002;2599-2607.
12. McInerney J.O. Prokaryotic genome evolution as assessed by multivariate analysis of codon usage patterns. Microb. Comp. Genomics. 2:1997;1-10.
13. McInerney J.O. GCUA: general codon usage analysis. Bioinform. Appl. Note. 14:1998;372-373.
14. Nelson M.A., Kang S., Braun E.L.et al. Expressed sequences from conidial, mycelial and sexual stages of Neurospora crassa. Fungal Genet. Biol. 21:1997;348-363.
15. Nesti C., Poli G., Chicca M., Ambrosino P., Scapoli C., Barrai I. Phylogeny inferred from codon usage patterns in 31 organisms. CABIOS. 11:1995;167-171.
16. Ohlrogge J., Benning C. Unraveling plant metabolism by EST analysis. Curr. Opin. Plant Biol. 3:2000;224-228.
17. Patterson C. Evolution. 2nd ed. 1999;Cornell Univ. Press, Ithaca, NY.
18. Pearson W.R. Empirical statistical estimates for sequence similarity searches. J. Mol. Evol. 276:1998;71-84.
19. Pertsemlidis A., Fondon J.W. Having a BLAST with bioinformatics (and avoiding BLASTphemy). Genome Biol. 2(10):2002;1-10.
20. Quotob D., Hraber P.T., Sobral B.W.S., Gijzen M. Comparative analysis of expressed sequences in Phytophthora sojae. Plant Physiol. 123:2000;243-253.
21. Soanes D.M., Skinner W., Keon J., Hargreaves J., Talbot N.J. Genomes of phytopathogenic fungi and the development of bioinformatic resources. Mol. Plant-Microb. Interact. 15:2002;421-427.
22. Thomas S.W., Rasmussen S.W., Glaring M.A., Rouster J.A., Christiansen S.K., Oliver R.P. Gene identification in the obligate fungal pathogen Blumeria graminis by expressed sequence tag analysis. Fungal Genet. Biol. 33:2001;195-211.
23. Thomas S.W., Glaring M.A., Rasmussen S.W., Kinane J.T., Oliver R.P. Transcript profiling in the barley mildew pathogen Blumeria graminis by serial analysis of gene expression (SAGE). Mol. Plant-Microb. Interact. 15:2002;847-856.
24. Wood V., Gwilliam R., Rajadream M.-A.et al. The genome sequence of Schizosaccharomyces pombe. Nature. 415:2002;871-880.
25. Yu J., Hu S., Wang J., Wong G.K., Li S., Liu B., Deng Y., Dai L., Zhou Y., Zhang X.et al. A draft sequence of the rice genome (Oryza sativa L. spp. indica). Science. 296:2002;79-92.