Gene and repeat annotation for snowy owl (Bubo scandiacus) and selected species

Here we provide the gene and repeat annotation for snowy owl (Bubo scandiacus), in addition to gene and repeat annotation done for some species this was compared to. It is unfortunately currently not possible to upload repeat annotation tracks to an international nucleotide sequence database such as ENA. While uploading the gene annotation is possible, some of the cross references to different databases in the functional annotation are removed. Further, the names of the entries in the publicly available genome assemblies on ENA have different names than what is found in the annotation tracks here, so we also provide the FASTA files for the snowy owl assemblies (bBubSca1.1.hap1.fasta.gz and bBubSca1.1.hap2.fasta.gz). Ideally, all this should have been available via ENA.

We annotated the snowy owl genome assemblies, in addition to downy woodpecker (Dryobates pubescens; GCA_014839835.1), Northern Carmine bee-eater (Merops nubicus; GCA_009819595.1), Northern goshawk (Accipiter gentilis; GCA_929443795.2) and barn owl (Tyto alba; GCF_018691265.1), since no genome annotation was publicly available for these species. We used 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 (Consortium et al., 2022) release 2022_03 in addition to the vertebrata part of OrthoDB v11 (Kuznetsov et al., 2022) were also aligned separately to the assemblies. Red (Girgis, 2015) was run via redmask (https://github.com/nextgenusfs/redmask) on the snowy owl assemblies to mask repetitive areas (we used the soft-masked genome assemblies available at NCBI for the other species). GALBA (Brůna et al., 2023; Buchfink et al., 2015; Hoff and Stanke, 2018; Li, 2023; Stanke et al., 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, UniProtKB/Swiss-Prot proteins, vertebrata proteins 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 2022_03 using DIAMOND (Buchfink et al., 2015) blastp to find gene names and InterProScan 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. EMBLmyGFF3 (Norling et al., 2018) was used to combine the fasta files and GFF3 files into a EMBL format for submission to ENA. These files end in gff.gz (the ones ending in fa.out.gff.gz are repeat annotations), proteins.fa.gz and mrna.fa.gz. 

All species in this study downy woodpecker (Dryobates pubescens; GCA_014839835.1), Northern Carmine bee-eater (Merops nubicus; GCA_009819595.1), Northern goshawk (Accipiter gentilis; GCA_929443795.2), barn owl (Tyto alba; GCF_018691265.1), chicken (Gallus gallus; GCF_016699485.2), zebra finch (Taeniopygia guttata; GCA_003957565.4) and California condor (Gymnogyps californianus; GCF_018139145.2) in addition to hap1 of snowy owl was repeat masked with a bird-specific library from https://www.pnas.org/doi/abs/10.1073/pnas.1616702114, provided by Alexander Suh. These files are named such as MerNubi.fa.out.gff.gz, MerNubi.fa.masked.gz and MerNubi.fna.cat.gz. 

We have also included the species specific repeat library as generated by RepeatModeler running on hap1 of snowy owl. This is called bBubSca1.1.hap1.repeatlibrary.fa.gz, with the files bBubSca1.1.hap1.fasta.masked.gz, bBubSca1.1.hap1.fasta.out.gff.gz and bBubSca1.1.hap1.fasta.cat.gz resulting from running RepeatMasker one hap1 using that library.

From the Genespace analyses we have included all files including OrthoFinder results. This is found in the file genespace.tgz.