Sadd et al. BMC Genomics 2010, 11:110 http://www.biomedcentral.com/1471-2164/11/110 Page 6 of 9 Figure 2 Schematic showing the potential presence in bumblebees of components from the major described pathways in honeybee immunity that are implicated in the defence against bacterial, fungal and viral pathogens (schematic adapted from [48]). Shaded and bold outlined components indicate this component from either Apis mellifera or Drosophila melanogaster is “hit” by a sequence in the Bombus terrestris EST library. suggest that a large number of these markers will be variable [51]. These identified potential SSRs together with existing markers from B. terrestris [52-54] make up a significant resource for molecular ecology studies. While EST derived SSRs tend to show a lower level of polymorph- ism than those identified from genomic libraries, they can more often be used across related species [36,51,55]. Given the pervasive importance of species of the genus Bombus in temperate pollinator communities, this is a highly advantageous feature. In addition to SSRs, contigs built from a number of EST reads can be useful sources of potential SNPs. While the normalization procedure used in this work reduces such redundancy and thus the likelihood of finding SNPs, 1,973 contigs contain at least four sequences, a minimum for reliable identification of SNPs [56]. These contigs cover 2,124,958 bases. Using SNPidentifier [57] with minimum minor allele frequency of 0.1 and a minimum occurrence of 2, we were able to find 854 potential SNPs occuring in 573 contigs. These potential SNPs provide an additional set of genetic mar- kers for subsequent population studies. Conclusions The resource provided by the presented EST library will serve researchers in a diverse range of biological fields. The detected markers will facilitate further population level studies, and the sequences themselves can be used in investigations of particular genes, and also in func- tional genomic approaches. Further, as demonstrated here, the sequences allow genomic comparisons with the honeybee A. mellifera and other insects, informing on such things as potential gene loss or pseudogene evolution. This EST library will also be a practical resource in the assembly and annotation of the impend- ing B. terrestris genome http://www.hgsc.bcm.tmc.edu. These elements, coupled with the major commercial and ecosystem functions of B. terrestris and related hymenoptera, mean that this EST library is a useful resource for ongoing research. Methods Animals Colonies were set-up with field caught queens collected from Northern Switzerland in the spring of 2007