Joly et al. BMC Genomics 2010, 11:422 http://www.biomedcentral.com/1471-2164/11/422 Additional file 3: Mean number of SAGE tags associated with Melampsora unisequences. Additional file 4: Proportion of contigs and clones included in the putative secretome of Melampsora. Additional file 5: Characteristics of the Melampsora homologous gene groups (HGGs) predicted to be under positive selection (site- based analysis with codeml). BLASTX and PFAM hits were considered significant when E-value ≤ 1e-4 and 1e-5, respectively. Additional file 6: Significant likelihood ratio tests and sites under positive selection as inferred under the site class models M1A, M2A, M7, M8 and M8A of codeml applied to each of the Melampsora homologous gene groups (HGGs). Acknowledgements This work was supported by the Genomics Research Initiative of Natural Resources Canada to RCH. The authors would like to thank the Broad Institute and the DOE-JGI for releasing the data of the fungal genome sequencing projects. Furthermore, the authors thank Brian Boyle for technical assistance and Josyanne Lamarche, Sébastien Duplessis and Francis Martin for helpful comments on the manuscript. Author details 1Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 du PEPS, P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada. 2Department of Forest Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. 3Unité Mixte de Recherche 1202, Institut National de la Recherche Agronomique-Université Bordeaux I, Biodiversité, Génes et Communautés (BioGeCo), INRA Bordeaux- Aquitaine, 33612 Cestas Cedex, France. Authors’ contributions DLJ contributed to the conception and design of the project, conducted laboratory experiments (EST libraries), designed bioinformatics scripts, performed analysis and interpretation of the data and drafted the manuscript. NF and RCH helped conceive the project and participated in its coordination. 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