The Assembly of the Y Chromosome Reveals Amplification of Genes Regulating Male Fertility in Bactrocera Dorsalis

BACKGROUND: The oriental fruit fly _Bactrocera dorsalis_ is an invasive pest causing considerable ecological and economic damage worldwide. The Y chromosome is an important target for the sterile insect technique (SIT) but its sequence and structure has been poorly explored. RESULTS: We assembled the genome of _B. dorsalis_ at the chromosome level with a total size of 562.6 Mb. The assembly includes a ∼7.6 Mb Y chromosome sequence, being the first reported Y chromosome in Tephritidae. The assembled Y chromosome is highly repetitive, and contains 61 genes, including 9 multi-copy genes. We surprisingly found that the M factor (_MoY_) in Tephritidae has multiple copies, verified by our droplet digital PCR (ddPCR) analysis. Besides, we identified 32 copies of _gyf-like on the Y chromosome_ (_gyfY_) that were highly expressed in testis. RNAi targeting the _gyfY_ resulted in depletion of live sperms, suggesting that the amplification of _gyfY_ is essential for male fertility, which facilitated the understanding of high fecundity of this invasive insect. CONCLUSION: We reported firstly the Y chromosome of _Bactrocera dorsalis_. Our results will also provide target genes for CRISPR/Cas9 based SIT, leading to the development of novel control strategies against tephritid flies.