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

Dataset DOI: [10.5061/dryad.s1rn8pknd](https://doi.org/10.5061/dryad.s1rn8pknd)

## Description of the data and file structure

This dataset contains new annotations for three pea aphid genome assemblies: two newly released long-read assemblies for lines homozygous for the WL or WD allele at the api locus on the X-chromosome, as well as a modified reference assembly with this region corrected for the WL allele. Annotations were produced by integrating *ab initio* gene predictions with RNA-Seq-based transcript detection. RNA-Seq data were used from embryonic, nymphal, and adult male and female pea aphids, for both winged and wingless morphs when available. Additionally, protein clustering data for the gene models in both the long-read assemblies and the corrected chromosome-level reference assembly allows for the detection of missing or mis-assembled genes and their duplicates. 

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