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Open Access Highly Accessed Research article

Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

Junhuan Xu110, Rob Linning1, John Fellers2, Matthew Dickinson3, Wenhan Zhu4, Ivan Antonov4, David L Joly1, Michael E Donaldson5, Tamar Eilam6, Yehoshua Anikster6, Travis Banks7, Sarah Munro8, Michael Mayo8, Brian Wynhoven8, Johar Ali8, Richard Moore8, Brent McCallum7, Mark Borodovsky4, Barry Saville9 and Guus Bakkeren1*

Author Affiliations

1 Pacific Agri-Food Research Centre, Agriculture & Agri-Food Canada, Summerland, BC, V0H 1Z0, Canada

2 USDA-ARS-HWWGRU, Manhattan, KS 66506, USA

3 School of Biosciences, University of Nottingham, Loughborough, UK

4 Dept. Biomedical Engineering and Computational Science and Engineering Division, Georgia Institute of Technology, Atlanta, GA 30332-0535, USA

5 Environmental & Life Sciences Graduate Program, Trent University, Peterborough, ON, K9J 7B8, Canada

6 Institute for Cereal Crops Improvement, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel

7 Cereal Research Centre, Agriculture & Agri-Food Canada, Winnipeg, MB, R3T 2M9, Canada

8 Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4E6, Canada

9 Forensic Science Program Trent University, Peterborough, ON, K9J 7B8, Canada

10 Bee Biology & Systematics Laboratory, USDA-ARS, N. Logan, UT 84341, USA

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BMC Genomics 2011, 12:161  doi:10.1186/1471-2164-12-161

Published: 24 March 2011

Abstract

Background

Rust fungi are biotrophic basidiomycete plant pathogens that cause major diseases on plants and trees world-wide, affecting agriculture and forestry. Their biotrophic nature precludes many established molecular genetic manipulations and lines of research. The generation of genomic resources for these microbes is leading to novel insights into biology such as interactions with the hosts and guiding directions for breakthrough research in plant pathology.

Results

To support gene discovery and gene model verification in the genome of the wheat leaf rust fungus, Puccinia triticina (Pt), we have generated Expressed Sequence Tags (ESTs) by sampling several life cycle stages. We focused on several spore stages and isolated haustorial structures from infected wheat, generating 17,684 ESTs. We produced sequences from both the sexual (pycniospores, aeciospores and teliospores) and asexual (germinated urediniospores) stages of the life cycle. From pycniospores and aeciospores, produced by infecting the alternate host, meadow rue (Thalictrum speciosissimum), 4,869 and 1,292 reads were generated, respectively. We generated 3,703 ESTs from teliospores produced on the senescent primary wheat host. Finally, we generated 6,817 reads from haustoria isolated from infected wheat as well as 1,003 sequences from germinated urediniospores. Along with 25,558 previously generated ESTs, we compiled a database of 13,328 non-redundant sequences (4,506 singlets and 8,822 contigs). Fungal genes were predicted using the EST version of the self-training GeneMarkS algorithm. To refine the EST database, we compared EST sequences by BLASTN to a set of 454 pyrosequencing-generated contigs and Sanger BAC-end sequences derived both from the Pt genome, and to ESTs and genome reads from wheat. A collection of 6,308 fungal genes was identified and compared to sequences of the cereal rusts, Puccinia graminis f. sp. tritici (Pgt) and stripe rust, P. striiformis f. sp. tritici (Pst), and poplar leaf rust Melampsora species, and the corn smut fungus, Ustilago maydis (Um). While extensive homologies were found, many genes appeared novel and species-specific; over 40% of genes did not match any known sequence in existing databases. Focusing on spore stages, direct comparison to Um identified potential functional homologs, possibly allowing heterologous functional analysis in that model fungus. Many potentially secreted protein genes were identified by similarity searches against genes and proteins of Pgt and Melampsora spp., revealing apparent orthologs.

Conclusions

The current set of Pt unigenes contributes to gene discovery in this major cereal pathogen and will be invaluable for gene model verification in the genome sequence.