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Background  Despite the recent sequencing of seven ant genomes, no genomic data are available for the genus  Formica , an important group for the study of eusocial traits. We sequenced the transcriptome of the ant  Formica exsecta  with the 454 FLX Titanium technology from a pooled sample of workers from 70 Finnish colonies.    Results  About 1,000,000 reads were obtained from a normalised cDNA library. We compared the assemblers  MIRA3.0  and  Newbler2.6  and showed that the latter performed better on this dataset due to a new option which is dedicated to improve contig formation in low depth portions of the assemblies. The 29,579 contigs represent 27 Mb. 50% showed similarity with known proteins and 25% could be assigned a category of gene ontology. We found more than 13,000 high-quality single nucleotide polymorphisms. The Δ9 desaturase gene family is an important multigene family involved in chemical communication in insects. We found six Δ9 desaturases in this  Formica exsecta  transcriptome dataset that were used to reconstruct a maximum-likelihood phylogeny of insect desaturases and to test for signatures of positive selection in this multigene family in ant lineages. We found differences with previous phylogenies of this gene family in ants, and found two clades potentially under positive selection.    Conclusion  This first transcriptome reference sequence of  Formica exsecta  provided sequence and polymorphism data that will allow researchers working on  Formica  ants to develop studies to tackle the genetic basis of eusocial phenotypes. In addition, this study provided some general guidelines for  de novo  transcriptome assembly that should be useful for future transcriptome sequencing projects. Finally, we found potential signatures of positive selection in some clades of the Δ9 desaturase gene family in ants, which suggest the potential role of sequence divergence and adaptive evolution in shaping the large diversity of chemical cues in social insects.

Transcriptome Characterisation of the Ant Formica exsecta with New Insights into the Evolution of Desaturase Genes in Social Hymenoptera