Sadd et al. BMC Genomics 2010, 11:110 http://www.biomedcentral.com/1471-2164/11/110 in the pollination of a variety of standard glasshouse crops [23]. Many have considered their economic importance to be on the rise given the recent declines in honeybee numbers [25]. Bumblebees not only provide valuable pollination services in the agricultural sector, but the pollination they carry out is an integral part of many natural ecosystems [26-28]. The importance of bumblebees comes sharply into focus when we consider the threat that pollinators currently face worldwide. This pollinator crisis has been epitomised by the recent honeybee colony collapse disorder [25], but the bumble- bee has also suffered population declines in many areas over a number of decades [29-31]. Given their importance, a good knowledge of bumble- bees from the genomic level up is of great interest. An improved set of genomic resources for bumblebees would facilitate further studies in the bumblebee, and compari- sons with other bees such as the honeybee, Apis melli- fera, where the genome is already sequenced [32]. There is currently a limited set of resources available for genetic investigation, and at the time of writing, for B. terrestris, there were 61 cDNA sequences and 288 nucleotide sequences (172 of which represent microsatellite markers) in NCBI Genbank (http://www.ncbi.nlm.nih.gov, Novem- ber 2009). Further tools available include a linkage map for B. terrestris [33] and a BAC library [34]. In order to greatly expand the genomic resources available for B. terrestris we constructed a normalised expressed sequence tag (EST) library from thorax and abdomen tissue of workers. ESTs are short, unedited, randomly selected, single pass reads from cDNA libraries [35]. They provide evidence of transcriptionally active regions in an organism and are an excellent resource for upstream work including gene discovery, functional genomics and marker discovery [35,36]. Stan- dard cDNA libraries can have problems with redun- dancy, and rare transcripts are often under-represented. Therefore, we employed normalisation in order to increase the number of unique transcripts discovered [37]. Here we describe a collection of 29,428 ESTs, which represent a valuable resource for further ecological and evolutionary studies in Bombus spp. and for comparative studies with other Hymenoptera and insects. Sequences have been deposited in the GenBank, EMBL, and DDBJ nucleotide sequence databases under the Accession numbers FN611035 through to FN640462. For further material, including consensus sequences of assembled contigs, please contact the authors. Results and Discussion Sequence assembly and features A total of 29,428 quality controlled EST sequences were assembled using TGI clustering tools (TGICL). The Page 2 of 9 assembly generated 4,682 contigs and 8,651 singletons. The average number of sequences per contig was 4.43 with the maximum being 35. Contigs averaged 960 bases in length with the longest contig being 3,542 bases. In total 13,333 unique sequences were produced. A table showing all EST and contig statistics can be found as an additional file (Additional file 1). Sequence annotation The 13,333 unique sequences were used in a BLASTX search against the non-redundant (nr) database in Gen- bank (version dated 19th October 2009). A total of 7,844 (58.8%) ESTs had significant “hits” (cutoff = 1e- 05) (Table 1 and Additional File 2). Of these, the major- ity (7,260 sequences) had “best-hits” to known sequences within the Hymenoptera, with a large propor- tion (6,296 sequences) of these belonging to Apis spp A total of 5,489 sequences (41.2%) had no significant simi- larity to any sequences contained in the nr database (Additional file 3). It is possible that many of these sequences without “hits” are cDNAs of known proteins, but consist mainly of untranslated regions (UTRs), therefore reducing the likelihood that matches are found through BLASTX. However, we cannot discount the possibility that some of the proteins are novel. Gene ontology (GO) terms The assembled B. terrestris ESTs were characterised for gene ontology terms in molecular function, biological process and cellular component by comparison against annotated proteins in the SwissProt and Trembl data- bases (UniProt Knowledgebase Release 15.9) using annot8r [38]. In order to increase the accuracy of any annotations, only GO terms that had been allocated by manual curation, and not those electronically inferred, were used. The distribution of the terms in each of the Table 1 Taxonomic distribution of the “best-hits” for the 13,333 post-assembly Bombus terrestris EST sequences (BLASTX, cutoff = 1e-05) Taxonomic classification Apis spp. Nasonia vitripennis Existing Bombus terrestris sequences Other Bombus spp. Other Hymenoptera Diptera Coleoptera Other Insecta Other No hits Number of assembled ESTs 6,296 886 8 49 21 179 110 146 149 5,489 Relevant groupings have been performed, but original counts on an individual taxon identifier level can be found as an additional file (Additional file 2).