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

Additional files

Additional file 1:

Number of gene predictions on each Pt EST/unigene sequence in the set not previously called by the Pgt-trained 4th order model.

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Additional file 2:

BLASTP analysis of predictions in "zero" set, against proteins predicted from the Pgt genome and the NCBI non-redundant database.

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Additional file 3:

Statistics of frameshifts predicted by GeneTack in Pt ESTs with genes called in the same strand by GeneMarkS with the 4th order model (supporting Figure 2).

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Additional file 4:

Similarity searches of Pt unigene sequences to various databases. This table shows the number of unigenes matching the various databases within certain ranges of e-values.

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Additional file 5:

Annotation results. This table holds the most-likely annotation of 2,551 unigenes based on searches against several databases. Source of the EST and number of independent sequences from various stages is indicated as are the unigene sequence match to the preliminary Pt genome 454 reads, the prediction by GeneMark and the closest homolog found among the predicted Pgt proteins. GO-annotations are also given according to cellular location, function or process, as well as EC and KEGG annotations (as produced by annot8r).

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Additional file 6:

Pt unigene sequences matching U. maydis ESTs. The file shows possible homologs between the two species and their representation over the various cDNA libraries (life cycle stages).

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Additional file 7:

Pt non-redundant unigene sequences specific for and shared between spore stages as presented in the Venn diagram (supporting Figure 3) with annotation results.

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Additional file 8:

Pt unigenes whose EST counts in the various spore stages correlate with EST counts of U. maydis homologs in equivalent cell types/spore stages.

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Additional file 9:

Pt unigenes were compared to sets of known or predicted (small) secreted proteins (SSPs). This file reveals families of likely paralogous proteins and their matches to orthologous and homeologous predicted SSPs in various in rust fungi and U. maydis. It includes representation of ESTs over the sampled stages.

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Additional file 10:

ClustalW alignment of two families of predicted (small) secreted proteins (SSPs). The alignment was used for the construction of the phylograms in Figure 4.

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