Genome report: chromosome-scale genome assembly of the olive fly <i>Bactrocera oleae</i> (Diptera: Tephritidae)

The olive fruit fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae), is a specialist of Olea fruits and is a major pest of commercial olives due to their adverse impacts to fruit quality. In support of genomic and physiological research of the olive fly, we sequenced, assembled, and annotated 2 independent genomes: one from a wild-collected male and one from a wild-collected female. The resulting genomes are highly contiguous, collinear, and complete, attesting to the accuracy and quality of both assemblies. In addition to the autosomes captured as single contigs, the X and Y chromosomes were also identified as evidenced by the X chromosome showing diploid coverage in the female assembly compared to haploid coverage in the male assembly and the Y chromosome being entirely absent from the female assembly. These assemblies represent the first full chromosome-level assembly for olive fly. In addition, a complete genome assembly of a known obligate symbiont, Candidatus Erwinia dacicola, was fully sequenced. The Ca. E. dacicola genome we report here is the most contiguous to date, represented by a gapless chromosome and 2 separate gapless plasmids. These genome assemblies, along with bacterial symbiont assembly, provide foundational resources for future genetic and genomic research in support of its management as an agricultural pest.