B. pensylvanicus genome assembly and annotation

Bombus_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fasta Bombus pensylvanicus reference genome assembly (scaffold0001-0019 represent main assembled chromosomes using PacBio long reads and HiC scaffolding). Assembly is also available on NCBI genbank. Scripts used for assembly are taken from https://doi.org/10.15482/USDA.ADC/25762431.v1; SIM, SHEINA (2024). Bombus huntii genome assembly scripts. Ag Data Commons. Workflow. https://doi.org/10.15482/USDA.ADC/25762431.v1)Bombus_pensylvanicus.curatedScaff.clean_sort_rename_nuc.fasta.fai: genome indexmtDNA_scaffold0168 subdirectory: Contains the fasta sequence and gff annotation for scaffold0168 which was identified from the MitoHiFi v2 workflow (https://github.com/marcelauliano/MitoHiFi) as the probable mitochondrial genome and removed from the main assembly above and the NCBI genome submission.non_arth_scaffolds subdirectory: Contains the FASTA sequence and a CSV of taxonomic identifiers to the family level of scaffolds removed from the final assembly during the BlobTools QC step.iyBomPens_scaff_egapx_RNA_out: directory containing EGAPx annotation information. Runs performed by Sheina Sim @ U.S. Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI using the external version of NCBI Eukaryotic Genome Annotation Pipeline (EGAPx 0.3.1-alpha).annotation_data.cmt: summary of annotation runrun_params.yaml: specific egap x run parametersresume.sh: scriptcomplete.genomic.gff: genomic features file 3 of complete annotation from EGAPxcomplete.genomic.gtf: EGAPx annotations in gtf 2.2 formatcomplete.proteins.faa: amino acid fasta of proteinscomplete.transcripts.fna: nucleic acid fasta of transcriptsstats subdirectory: contains feature count summaries of EGAPx annotationsannot_builder_output subdirectory: contains data from annotation builder