BSF_SA_annotation.gff

This .gff file contains the annotation information for the South African black soldier fly genome.Repetitive sequences were identified and masked in the assembly using RepeatMasker v4.0.7 (Smit et al., 2015). The Dfam_Consensus_2017127 and RepBase-20170127 databases were merged to identify and soft mask repetitive regions using the RMBlastn v2.6.0 sequence search engine. The final assembled genome was then annotated using available protein data generated in a previous study (Generalovic et al., 2021), and transcriptomic data generated in by Hull et al. 2023. For the transcriptomic data, quality filtering was performed similarly as described above, and the resulting reads were mapped against the indexed draft genome using TopHat v2.2.1 (Kim et al., 2013). Only paired mapped sequences were retained for downstream analyses using the filterBam option of Augustus v3.2.3 (Stanke et al., 2006). Additionally, intron locations were determined using the bam2hints option of Augustus, with these intron hints and the mapped RNA-seq reads being utilised in the annotation of the BSF genome through Augustus.