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A comparative genomic analysis of ESTs from Ustilago maydis

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Abstract

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.

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Acknowledgements

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.

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Authors and Affiliations

  1. Department of Botany, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada

    Ryan Austin & Nicholas J. Provart

  2. Department of Botany, University of Toronto at Mississauga, Mississauga, ON, L5L 1C6, Canada

    Nuno T. Sacadura, Kimberly G. Nugent, Mohan Babu & Barry J. Saville

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  1. Ryan Austin
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  2. Nicholas J. Provart
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  3. Nuno T. Sacadura
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  4. Kimberly G. Nugent
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  6. Barry J. Saville
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Corresponding author

Correspondence to Barry J. Saville.

Additional information

Supplemental Excel Table 1 used for analysis and the derivation of Fig. 3 as well as supplemental Tables 2 and 3 are available at http://www.botany.utoronto.ca/ResearchLabs/ProvartLab/ustilago/

All ESTs used in this analysis have been submitted to GenBank. The accession numbers are CF638289–CF645747, CF663122–CF663127, and CD487847–CD490309 (Supplemental Table 3)

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Austin, R., Provart, N.J., Sacadura, N.T. et al. A comparative genomic analysis of ESTs from Ustilago maydis. Funct Integr Genomics 4, 207–218 (2004). https://doi.org/10.1007/s10142-004-0118-x

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  • DOI: https://doi.org/10.1007/s10142-004-0118-x

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