Spurfowl High-quality hybrid de novo genome assemblies of two pheasants: Black Francolin and Double-Spurred Spurfowl.

Pheasants are an important group of birds of the Galliformes order, valued for their ornamental and economic value as poultry and game birds. They exhibit a diverse range of sexual dimorphism, reflecting varying degrees of sexual selection within a single family. However, genomic data from species with lesser dimorphism remains scarce. In this study, we present high-quality de novo hybrid genome assemblies of two such birds: Black Francolin (Francolinus francolinus) and Double-spurred spurfowl (Pternistis bicalcaratus), marking the first reference genome of their respective genera. We assembled the genomes using a hybrid approach that combined Illumina short reads, PacBio subreads, and HiFi reads. We generated 397 million Illumina reads (60x coverage) and 7.5 million PacBio subreads (80x coverage) for the Black Francolin, and 214 million Illumina reads (64x coverage) and 8.6 million PacBio subreads (99x coverage) for the Double spurred Spurfowl. We compared multiple genome assemblers, including HASLR, Flye, Masurca, WenganA, WenganD, and Hifiasm. We evaluated the results using QUAST to assess assembly quality by comparing the number of scaffolds and their N50. Masurca performed best for Black Francolin with 833 scaffolds and a 7.75 Mb N50, followed by WenganD (7.8 Mb N50, 1119 scaffolds) and WenganA (7.9 Mb N50, 2007 scaffolds) and for the Double-spurred Spurfowl Masurca outperformed other assemblers with 599 scaffolds and 16.4 Mb N50, while Flye gave 1067 scaffolds and 12.9 Mb N50. Genomic data is crucial for studying trait evolution, and these genomes will offer valuable insights into sexual selection and insights for their conservation and management.