A new genome sequence resource for five invasive fruit flies of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (Diptera, Tephritidae)

Abstract

Here, we present novel high quality genome assemblies for five invasive tephritid species of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (read depths between 65 and 78x). Three assemblies ( C. capitata, C. quilicii and Z. cucurbitae) were scaffolded with chromosome conformation data and annotated using RNAseq reads. For some species this is the first reference genome available ( B. zonata, C. quilicii and C. rosa), for others we have published improved annotated genomes ( C. capitata and Z. cucurbitae). Together, the new references provide an important resource to advance research on genetic techniques for population control, develop rapid species identification methods, and explore eco-evolutionary studies.

Keywords: fruit fly; genome assembly; invasive species; pest; tephritidae.

Figure 1.. Linkage and BUSCO completeness across the genomes presented here and phylogenetic analysis.

(a) Photographs of the five fruit fly pest species from a dorsal and lateral view © RMCA (Royal Museum for Central Africa. (b) Hi-C (Dovetail™ Omni-C™) contact map for three tephritid species showing which reads are in close proximity of each other, revealing the linear representation of the scaffolds/chromosomes within the genome. (c) Phylogenetic tree of the three tephritid fruit flies with annotation and five other diptera species. (d) BUSCO completeness results for each of the assembled tephritid genomes.