Genome report: chromosome-scale genome assembly of the West Indian fruit fly Anastrepha obliqua(Diptera: Tephritidae)

Authors: Sim, Sheina; CONGRAINS, CARLOS - UNIVERSITY OF HAWAII; VELASCO-CUERVO, SANDRA - UNIVERSITY OF ALBERTA; Corpuz, Renee; Kauwe, Angela; Scheffler, Brian; Geib, Scott

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/11/2024
Publication Date: 2/1/2024
Citation: Sim, S.B., Congrains, C., Velasco-Cuervo, S., Corpuz, R.L., Kauwe, A.N., Scheffler, B.E., Geib, S.M. 2024. Genome report: chromosome-scale genome assembly of the West Indian fruit fly Anastrepha obliqua(Diptera: Tephritidae). G3, Genes/Genomes/Genetics. 14(4). https://doi.org/10.1093/g3journal/jkae024.
DOI: https://doi.org/10.1093/g3journal/jkae024

Interpretive Summary: Scientists from the USDA-ARS Tropical Pest Genetics and Molecular Biology Research Unit and their collaborators report the genome assembly of the West Indian fruit fly, Anastrepha obliqua, an agricultural fruit fly pest in Central and South America, and major pest of mangoes. This genome is the first Anastrepha species to be sequenced and assembled at a chromosome scale. The assembly was generated from data obtained from a single male fly, and the researches on this project report methods for obtaining high quality and high molecular weight DNA from destructively sampled insect tissue transported without the use of dry ice or other ultra-cold shipping methods. This genome assembly will serve as a foundational genomic resource for A. obliqua and closely related Anastrepha species and will support future work involving genetic pest management of this highly pestiferous taxa.

Technical Abstract: The West Indian fruit fly, Anastrepha obliqua, is a major pest of mango in Central and South America and attacks more than 60 species of host fruits. To support current genetic and genomic research on A. obliqua, we sequenced the A. obliqua genome using high-fidelity long-read sequencing and assembled it at a chromosome-scale using synteny with a closely related species, A. ludens, which, like A. obliqua, is in the A. fraterculus complex. The resulting assembly represents the five autosomes and the X chromosome which represents 95.9% of the genome, and 199 unplaced contigs representing the remaining 4.1%. Comparison between A. obliqua and six tephritid species gene sets and one non-tephritid Diptera gene set showed that 59.0% of identified orthologs are shared between all taxa included in the analysis followed by 5.4% shared within Tephritidae. This genome assembly represents the first of this species and will serve as a foundation for future genetic and genomic research in support of its management as an agricultural pest.