DOI: 10.5061/dryad.s1rn8pknd
title: Comprehensive annotations of genes, transcripts, and proteins of three pea aphid genome assemblies

description: 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.
description: # 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.  ### Files and variables #### File: Ap_gene_annotations.zip
 **Description:** Contains folders for each assembly
 (Ap_modified_reference, Ap_WD_male, Ap_WL_male) as well as the
 All_Proteins_Orthogroups.tsv and Naming_conventions.txt file. Each
 assembly's folder contains the .fasta genome sequence, as well as
 subfolders for AUGUSTUS (Braker [bk]), Trinity *de novo* (tdn), Trinity
 genome-guided (tgg), Stringtie (st), and PASA transcripts (.fasta),
 proteins (.faa), and genomic coordinates (.gtf). An additional annotated
 version of the PASA genomic coordinates (_annot.gtf) is provided in each
 assembly's PASA subfolder for viewing functional annotations within
 IGV. ## Code/software The assemblies were annotated with the *ab
 initio* and RNA-Seq based methods AUGUSTUS (within Braker3), Trinity (*de
 novo* and genome-guided) and Stringtie. RNA-Seq data was used from
 embryonic, nymphal, and adult stages of males and females, for both winged
 and wingless morphs when available. These programs output different
 combinations of three file types: transcript sequences (.fasta), protein
 sequences (.faa) and genomic coordinates (.gtf). Not all programs produced
 all filetypes. In cases where a particular filetype was not directly
 output by the aforementioned software, protein coding sequences were
 predicted with Transdecoder, transcripts were mapped to genomes using
 gmap, and transcript sequences extracted from genomic coordinates using
 gff-read. These various protein-coding transcript predictions were
 clustered into integrated gene models using the software PASA. All
 transcripts, proteins, and genomic coordinates are provided in this
 dataset for each method and integrated PASA gene models, as well genome
 sequence files. All ORFs (&gt; 100aa's) produced by all transcripts
 for each method, as well as those in integrated gene models produced by
 PASA, were clustered with RefSeq proteins from 20 other animal species
 (mostly insects) using OrthoFinder. The clustering of these protein
 sequences can be found in the provided .tsv file, with naming conventions
 described in a provided .txt file. Additionally, an annotated version of
 the genomic coordinates (_annot.gtf) for the PASA gene models was produced
 for each assembly for viewing in IGV. When viewed in IGV, clicking on a
 transcript within a PASA cluster displays the first orthogroup member from
 each species for each ORF in that transcript. ## Access information Data
 was derived from the following sources: Genomic sequence data * Unmodified
 reference assembly : GCF_005508785.2 * WL allele assembly long read data
 : SRR8306868 * WD allele assembly long read data : SRR10028116
 Transcriptomic sequence data * Asexual Female Ovary Stage 0-17 Embryo
 SRR073574, SRR073575 * F1 Sexual Female adult SRR1239441 * F1 WL Asexual
 Female adult SRR1239440 * F1 WD Asexual Female adult SRR1239439 * F1 WL
 Male adult SRR1239447 * F1 WD Male adult SRR1239446 * Roc1 WL Asexual
 Female Stage 18 Embryo SRR9877495, SRR9877496, SRR9877497, SRR9877498 *
 Roc1 WL Asexual Female Stage 20 Embryo SRR9877642, SRR9877643, SRR9877648,
 SRR9877649 * F1 WL Asexual Female 1st instar nymph SRR32079974,
 SRR32080032, SRR32080031 * F1 WL Asexual Female 2nd instar nymph
 SRR32080030, SRR32080029, SRR32080028 * F1 WL Asexual Female 3rd instar
 nymph SRR32080027, SRR32080026, SRR32080025 * Roc1 WD Asexual Female Stage
 18 Embryo SRR9877491, SRR9877492, SRR9877493, SRR9877494 * Roc1 WD Asexual
 Female Stage 20 Embryo SRR9877644, SRR9877645, SRR9877646, SRR9877647 * F1
 WD Asexual Female 1st instar nymph SRR32080034, SRR32080033, SRR32080022 *
 F1 WD Asexual Female 2nd instar nymph SRR32080011, SRR32080000,
 SRR32079989 * F1 WD Asexual Female 3rd instar nymph SRR32079978,
 SRR32079976, SRR32079975 * 409 WL Male Early Embryo SRR36435213,
 SRR36435212, SRR36435211 * 409 WL Male Late Embryo SRR36435210,
 SRR36435219, SRR36435218 * 409 WL Male 1st instar nymph SRR32080024,
 SRR32080023, SRR32080021 * 409 WL Male 2nd instar nymph SRR32080020,
 SRR32080019, SRR32080018 * 409 WL Male 3rd instar nymph SRR32080017,
 SRR32080016, SRR32080015 * 412 WD Male Early Embryo SRR36435221,
 SRR36435220, SRR36435217 * 412 WD Male Late Embryo SRR36435216,
 SRR36435215, SRR36435214 * 412 WD Male 1st instar nymph SRR32080014,
 SRR32080013, SRR32080012 * 412 WD Male 2nd instar nymph SRR32080010,
 SRR32080009, SRR32080008 * 412 WD Male 3rd instar nymph SRR32080007,
 SRR32080006, SRR32080005