A comparative genomic analysis of ESTs from Ustilago maydis
A large-scale comparative genomic analysis of unisequence sets obtained from an Ustilago maydis EST collection was performed against publicly available EST and genomic sequence datasets from 21 species. We annotated 70% of the collection based on similarity to known sequences and recognized protein signatures. Distinct grouping of the ESTs, defined by the presence or absence of similar sequences in the species examined, allowed the identification of U. maydis sequences present only (1) in fungal species, (2) in plants but not animals, (3) in animals but not plants, or (4) in all three eukaryotic lineages assessed. We also identified 215 U. maydis genes that are found in the ascomycete but not in the basidiomycete genome sequences searched. Candidate genes were identified for further functional characterization. These include 167 basidiomycete-specific sequences, 58 fungal pathogen-specific sequences (including 37 basidiomycete pathogen-specific sequences), and 18 plant pathogen-specific sequences, as well as two sequences present only in other plant pathogen and plant species.
KeywordsFungal comparative genomics EST analysis Ustilago maydis
We would like to acknowledge the assistance of Kristen Choffe in the creation of cDNA libraries and sequencing. Funding provided by NSERC Canada to B. J. Saville.
- Agrios GN (1997) Plant pathology, 4th edn. San Diego Academic, San DiegoGoogle Scholar
- Banuett F, Herskowitz I (1989) Different a alleles of Ustilago maydis are necessary for maintenance of filamentous growth but not for meiosis. Proc Natl Acad Sci USA 86:5878–5882Google Scholar
- Kämper J, Weinzierl G, Brachmann A, Feldbrügge M, Basse C, Steinberg G, Kahmann R, Friedrich G, Vollenbroich V, Koopmann E, et al (2001) The Ustilago maydis sequencing project. Fungal Genet Newsl 48 [Suppl]:500Google Scholar
- Ma L, Galagan J, Calvo S, Nielsen C, Elkins T, Barrett R, Wong M, Lander E, Nusbaum C, Birren B (2003) The fungal genome initiative. Fungal Genet Newsl 50 [Suppl]:300Google Scholar
- Mount DW (2001) Bioinformatics: sequence and genome analysis. Cold Spring Harbor Laboratory, Cold Spring Harbor, pp 495–497Google Scholar
- Provart N, Zhu T (2003) A browser-based functional classification SuperViewer for Arabidopsis genomics. Curr Comput Mol Biol 2003:271–272Google Scholar
- Saville BJ, Leong SA (1992) The molecular biology of pathogenesis in Ustilago maydis. In: Setlow JK (ed) Genetic engineering: principles and methods, vol 14. Plenum, New YorkGoogle Scholar
- Swann EC, Taylor JW (1993) Higher taxa of basidiomycetes: an 18S rRNA gene perspective. Mycologia 85:923–936Google Scholar
- Zdobnov EM, Apweiler R (2001) InterProScan: an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17:847–848Google Scholar