Molecular phylogeny of Francolinus francolinus in Iraq based on mitochondrial cytochrome c oxidase I gene diversity

The Iraqi avifauna, such as the black francolin, faces habitat loss and illegal hunting, necessitating their protection to conserve genetic diversity. The cytochrome c oxidase I gene is a precise and widely used genetic marker for identifying bird diversity and protecting native species. This study used the cytochrome c oxidase I (COI) gene as a barcode, isolating genomic DNA from the skin and feathers of 14 samples. In addition, a specific primer set was designed for amplification of the cytochrome c oxidase I gene by polymerase chain reaction (PCR), and the resulting cytochrome c oxidase I sequences were aligned with sequences in the NCBI GenBank. The black francolin COI sequence divergence varies significantly among individuals from Iraq and different regions. The evolutionary tree was constructed within Francolinus francolinus to determine closely related species and diversification. The Iraqi black francolin falls within the first and second clades in the tree, with 62%-100% affinity to the original species. The outcome emphasizes that the cytochrome c oxidase I gene selected offers a reliable indicator for the classification of F. francolinus and for determining this species' viability in the Iraqi environment. The newly sequenced F. francolinus sequences are recorded in GenBank under accession numbers PV199482.1, PV199483.1, PV199484.1, PV199485.1, PV199486.1, PV199487.1, and PV199488.1. Finally, the present study may contribute to the development of a reference DNA barcoding database of Iraqi birds and confirmed the important role of genetic diversity in assessing the black francolin's ability to survive.