Investigating Genome Compositional Features of Apis and other Hymenopteran Species

Initial analysis of the honey bee (Apis mellifera) genome in 2006 revealed several interesting features compared to other metazoan genome sequences available at that time: a low but heterogeneous GC content, an overabundance of CpG dinucleotides and a lack of repetitive elements. The average GC content of the honey bee genome is only 33%, but GC content is highly heterogeneous, ranging from 11% to 67%, with a bimodal distribution. Furthermore, unlike genes in most other metazoans, honey bee genes are overly abundant in regions of low GC content (<30%). It is unclear whether any of these genome features are related to the evolution of eusociality and we lack satisfactory explanations for them more generally. Since publication of the A. mellifera genome, genomes of several other hymenopteran insects, including additional Apis species, have become available. In this study, we compare Apis genome compositional characteristics with those of other hymenopteran insects. Comparing genome composition and organization among species with different levels of social complexity may lead to insight into genomic structural changes associated with the evolution of eusociality. We used a recursive segmentation procedure to partition genomic sequences into GC compositional domains, maximizing the difference in GC content between adjacent subsequences. We compared the distributions of GC contents in GC compositional domains among 21 hymenopteran genomes ranging in social complexity from solitary to complex eusocial. We also analyzed one eusocial and four solitary outgroups representing diverse insect taxa. Bimodal distribution of GC content within the GC compositional domains was a characteristic of the complex eusocial bees (Apis and Melipona), but not solitary or simple eusocial bees. The Apis genomes had larger ranges in GC content compared to the other species. Genes were biased to lower GC content regions in all bees, with the strongest bias in the complex eusocial bees, and the weakest bias in the solitary bees, while gene distribution tended to show little or no bias to low GC content regions in the ant genomes and non-hymenopteran insect outgroups. Further investigation of these preliminary data will provide insight into whether genomic compositional features unique to Apis are associated with the evolution of eusociality.