De novo chromosome-level genome assembly and annotation of the Muscovy duck (Cairina moschata)

The Muscovy duck (Cairina moschata) is an excellent lean-type poultry species characterized by large body weight, rapid growth, high lean meat yield, good liver production performance, and high feed conversion efficiency. It plays an important role in modern poultry industry. However, the quality of the currently available Muscovy duck genome remains limited. Here, we report the de novo sequencing and assembly of the Muscovy duck genome using PacBio and Hi-C technologies. The total length of the genome assembly was 1270.04 Mb, the contig N50 was 6.56 Mb, and the scaffold N50 was 77.04 Mb and it was composed of 39 chromosomes. BUSCO evaluation showed that 95.2% of conserved genes were completely assembled in the Muscovy duck genome, indicating high completeness of the assembly results. The genome annotation results showed that the proportion of repetitive sequences was 22.14%, 16,901 coding genes were predicted, and 93.4% of the genes were functionally annotated. Comparative genomic analysis revealed that expanded gene families were associated with immune-related pathways in Cairina moschata. Cairina moschata was closely related to Anas platyrhynchos and Aythya fuligula, both of which belong to the family Anatidae. These results provide valuable resources for poultry genomic breeding programs.