Gene annotations for Ara ararauna, Ara chloropterus and Ara severus

This repository contains gene annotations for Ara ararauna (GCA_028858755.1),  Ara chloropterus (GCA_010014725.2) and Ara severus (GCA_024733695.1).

We annotated the genome assemblies using a pre-release version of the EBP-Nor genome annotation pipeline (https://github.com/ebp-nor/GenomeAnnotation). First, AGAT (https://zenodo.org/record/7255559) agat_sp_keep_longest_isoform.pl and agat_sp_extract_sequences.pl were used on the GRCg7b (GCA_016699485.1) chicken genome assembly and annotation to generate one protein (the longest isoform) per gene. Miniprot (Li, 2023) was used to align the proteins to the curated assemblies. UniProtKB/Swiss-Prot (UniProt Consortium, 2023) release 2023_02 in addition to the Vertebrata part of OrthoDB v11 (Kuznetsov et al., 2023) were also aligned separately to the assemblies. RED (Girgis, 2015) was run via redmask (https://github.com/nextgenusfs/redmask) on the assemblies to mask repetitive areas. GALBA (Brůna et al., 2023; Buchfink, Xie, & Huson, 2015; Hoff & Stanke, 2019; Li, 2023; Stanke, Schöffmann, Morgenstern, & Waack, 2006) was run with the chicken proteins using the miniprot mode on the masked assemblies. 

The funannotate-runEVM.py script from Funannotate was used to run EvidenceModeler (Haas et al., 2008) on the alignments of chicken proteins to the parrot genome assemblies, UniProtKB/Swiss-Prot proteins, Vertebrata proteins from OrthoDB, and the predicted genes from GALBA. The resulting predicted proteins were compared to the protein repeats that Funannotate distributes, using DIAMOND blastp, and the predicted genes were filtered based on this comparison using AGAT. The filtered proteins were compared to the UniProtKB/Swiss-Prot release 2023_02 using DIAMOND (Buchfink et al., 2015) blastp to find gene names and InterProScan (Jones et al., 2014) was used to discover functional domains. AGATs agat_sp_manage_functional_annotation.pl was used to attach the gene names and functional annotations to the predicted genes. 

Ara_chloropterus.gff.gz - gene annotations for Ara chloropterus.
Ara_chloropterus.proteins.fa.gz - predicted proteins for Ara chloropterus.
Ara_severus.gff.gz - gene annotations for Ara severus.
Ara_severus.proteins.fa.gz - predicted proteins for Ara severus.
bAraAra1.gff.gz - gene annotations for Ara ararauna. 
bAraAra1.proteins.fa.gz - predicted proteins for Ara ararauna.