Comprehensive annotations of genes, transcripts, and proteins of three pea aphid genome assemblies

Accurate genome assembly and annotation are crucial for analyses of duplication and gene family evolution. Short-read genome assemblies can mis-assemble newly duplicated genes, and gene prediction programs can break-up, merge, or miss genes, obscuring accurate gene content. Here, we leverage transcriptomic data from various life stages, morphs, and sexes of the pea aphid Acyrthosiphon pisum to produce more comprehensive gene annotations for two long-read genome assemblies, as well as a modified version of the reference assembly, corrected at a critical morph-determination locus called api. We integrated three RNA-seq-based transcript assembly methods (Trinity de novo, Trinity genome-guided, and Stringtie) and the ab initio method AUGUSTUS to produce gene models for all three assemblies using PASA. Proteins produced by these gene models were clustered with the pea aphid RefSeq proteins, as well as those from twenty other Eukaryotic species, using OrthoFinder. This dataset contains files for all PASA gene models (GTF format), transcripts, proteins, and the assemblies themselves (FASTA format). Additionally, the Orthogroup clustering information for all proteins from all methods for all assemblies is provided (TSV format). When these genome annotations are viewed in IGV, clicking on each transcript provides information on the closest orthologs from each species for each protein predicted to be coded by that transcript. The transcript and protein files can be use to search for pea aphid orthologs of proteins of interest. These data properly assemble previously mis-assembled genes and reveal a larger than expected amount of gene duplication, providing a valuable resource for studying gene family evolution in pea aphids.