Sadd et al. BMC Genomics 2010, 11:110 http://www.biomedcentral.com/1471-2164/11/110 simple sequence repeats and single nucleotide poly- morphisms, respectively. With MISA the configuration file was adjusted to identify motifs of two, three, four, five or six nucleo- tides, that repeat at least six times for di-nucleotide repeats and five times for all others. MISA was then run on all the post-assembly unique sequences. With SNP identifier we adjusted the minimum minor allele frequency to 0.1 and occurrence to 2. This meant that post-assembly sequences needed to be made up of at least four ESTs to be considered. SNPi- dentifier was run on the alignments of the EST sequences. Additional file 1: Assembly statistics of the Bombus terrestris ESTs. Click here for file [ http://www.biomedcentral.com/content/supplementary/1471-2164-11- 110-S1.PDF ] Additional file 2: Counts of the “best-hits” at the individual taxonomic identifier level for the 13,333 post-assembly Bombus terrestris EST sequences (BLASTX, cutoff = 1e-05). Click here for file [ http://www.biomedcentral.com/content/supplementary/1471-2164-11- 110-S2.XLS ] Additional file 3: Presence and identity of “best-hits” for the 13,333 unique Bombus terrestris sequences in the non-redundant (nr) database of Genbank (version dated 19th October 2009) (BLASTX cutoff = 1e-05). Click here for file [ http://www.biomedcentral.com/content/supplementary/1471-2164-11- 110-S3.XLS ] Additional file 4: Gene Ontology assignments for the unique Bombus terrestris sequences. Click here for file [ http://www.biomedcentral.com/content/supplementary/1471-2164-11- 110-S4.XLS ] Additional file 5: Presence and identity of “best-hits” in paired BLASTX comparisons (cutoff = 1e-05) of the unique Bombus terrestris sequences against proteins from each of Apis mellifera, Nasonia vitripennis, Tribolium castaneum and Drosophila melanogaster. Click here for file [ http://www.biomedcentral.com/content/supplementary/1471-2164-11- 110-S5.XLS ] Additional file 6: Bombus terrestris unique sequences with “hits” to proteins from genes characterised as immune related in Apis mellifera and Drosophila melanogaster. Click here for file [ http://www.biomedcentral.com/content/supplementary/1471-2164-11- 110-S6.XLS ] Acknowledgements We acknowledge Monique Roenick and Janina Thiel (Berlin) for technical assistance, and Alfred Beck (Berlin) for computational support. This study was supported by the Max Planck Society, the Swiss National Science Foundation, CCES (GEDIHAP) and the Genetic Diversity Centre of ETH Zurich. Author details 1Institute of Integrative Biology (IBZ), ETH Zürich, Universitätsstrasse 16, 8092 Zürich, Switzerland. 2Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany. Page 8 of 9 Authors’ contributions BMS prepared the animals for the EST library, carried out bioinformatics analyses of the sequences. MK, SK and RR contributed to RNA isolation, library construction, template preparation, sequence determination and assembly. BMS, MK, SK, RR and PSH drafted the manuscript. PSH was the initiator of this project. All authors read and approved the final manuscript. Received: 30 November 2009 Accepted: 15 February 2010 Published: 15 February 2010 References 1. Goulson D: Bumblebees - their behaviour and ecology. New York, USA: Oxford University Press 2003. 2. 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