The pea aphid, Acyrthosiphon pisum, is an emerging model system in functional and comparative genomics, in part due to the availability of new genomic approaches and the different sequencing and annotation efforts that the community has dedicated to this important crop pest insect. The pea aphid is also used as a model to study fascinating biological traits of aphids, such as their extensive polyphenisms, their bacteriocyte-confined nutritional symbiosis, or their adaptation to the highly unbalanced diet represented by phloem sap. To get insights into the molecular basis of all these processes, it is important to have an appropriate annotation of transcription factors (TFs), which would enable the reconstruction/inference of gene regulatory networks in aphids. All available annotations of pea aphid TFs are based on the first versions of the genome assembly and annotation, that are now replaced by a new reference assembly.

We took advantage of this new resource, which represents the first chromosome-level A. pisum genome, to annotate the complete repertoire of A. pisum TFs, and to complement this information by annotating genes encoding chromatin-associated and basal transcription machinery proteins. These annotations were done using information from the model Drosophila melanogaster, for which we also provide a revisited list of these proteins. The comparison between the two model systems allowed the identification of major losses or expansions in each genome, while a deeper analysis was made of ZNF TFs (with certain families expanded in the pea aphid), and the Hox gene cluster (showing reorganization in gene position in the pea aphid compared to D. melanogaster). All annotations are made available to the community the different annotations we produced storing all this information in the Aphid Transcription Factors database (ATFdb), a resource for gene regulation studies in aphids.