Genome annotations of Drosophila melanogaster and Drosophila simulans wild-type strains from long read sequencing assemblies

Genome assemblies were performed for eight wild-type strains of Drosophila melanogaster and Drosophila simulans from Oxford Nanopore long read sequencing (please refer to Mohamed et al. Cells 2020 (doi:10.3390/cells9081776)). Assemblies were deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB50024 (https://www.ebi.ac.uk/ena/browser/view/PRJEB50024).

Transposable Element annotations: we used RepeatMasker 4.1.0 (http://repeatmasker.org/) -species Drosophila, followed by OneCodeToFindThemAll (Bailly-Bechet et al. 2014) with default parameters.

Gene annotations: We retrieved gtf files from FlyBase : ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/gft/dmel-all-r6.46.gtf.gz and ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/gtf/dsim-all-r2,02.gtf.gz. The corresponding fasta files were also downloaded from FlyBase: ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r6,46_FB2022_03/fasta/dmel-all-chromosome-r6.46.fasta.gz and ftp.flybase.net/genomes/Drosophila_simulans/dsim_r2,02_FB2017_04/fasta/dsim-all-chromosome-r2,02.fasta.gz. We used Liftoff (Shumate and Salzberg, 2020) to lift over gene annotations from the references to our genome assemblies. We used -flank 0.2 and only kept the “gene” and “exon” terms.