Supplementary Data for Paulo and Nguyen et al. 2023 (Genetics of the black pupae phenotype in Tephritidae)

The file alud_genome_annotation_v2024.07.26.tar.gz includes all de novo genome assembly and annotations for Anastrepha ludens described in Paulo and Nguyen et al. 2023. Please note that although the genome sequences are the same, these analyses were conducted before the release of the reference genome on NCBI. Therefore, scaffolds and contigs have different names and possibly different orientations. The authors are making these data available for reproducibility purposes. We recommend any future analysis should be conducted with the updated reference genome sequences for A. ludens RefSeq assembly GCF_028408465.1 (idAnaLude1.1) and its annotations generated by the NCBI Eukaryotic Genome Annotation Pipeline.
Supplementary Data includes:
alud_HiC_Scaffold_20220524_subset.masked.fa: Masked genome.fasta (chromosome scaffolds).alud_augustus.filtered.fa: BRAKER2 peptides.fasta (filtered for longest isoforms).alud_augustus.filtered_vs_uniprot_dmel.blastp: BLASTp annotations.alud_augustus.filtered.interproScan.tsv: InterProScan annotations.alud_augustus.filtered.emapper_diptera.txt: eggNOG-mapper annotations.Decompress files:
tar -xzvf alud_genome_annotation_v2024.07.26.tar.gzgunzip ./*.gz