DNA barcoding and phylogenetic analysis of major fruit fly pests occurring in New Delhi

Abstract

Accurate and rapid species identification of tephritid fruit flies is critical for effective pest management, particularly where morphologically similar species coexist. The present study aimed to document economically important fruit fly pests in Delhi and to establish DNA barcode-based identification using mitochondrial cytochrome c oxidase subunit I (mtCOI) gene. Adult flies were collected using cue lure and methyl eugenol traps and also through laboratory rearing of infested fruit and vegetables. All samples were morphologically identified and representative samples were subjected to COI gene amplification and Sanger sequencing. A total of 264 specimens representing five species, Zeugodacus cucurbitae (Coquillett, 1899); Z. tau Walker, 1849; Bactrocera dorsalis (Hendel, 1912); B. zonata (Saunders, 1842) and B. divenderi Maneesh, Hancock & Prabhakar, 2022 were recorded from cucurbitaceous vegetables and fruit crops including mango, guava and pomegranate. Twelve barcodes, showing high sequence similarity (98.06-100%) were generated using the universal primer pair (LCO1490 and HCO2198) and deposited in GenBank. Phylogenetic analyses using the Neighbor-Joining (NJ) method recovered distinct clusters corresponding to the morphologically identified species and clearly separated the genera Zeugodacus and Bactrocera. The generated DNA barcodes provide a valuable molecular reference for fruit fly identification in Delhi and demonstrate the usefulness of COI barcoding as a tool for surveillance, diagnostics and integrated management.