Abstract Falcons (genus Falco) are a rapidly diversified bird clade, with 38 species evolving over the past ∼7.5 million years. Despite their ecological and evolutionary significance, high-quality genomic resources remain limited. Here, we present two chromosome-level genome assemblies for Falco peregrinus and Falco biarmicus, enabling detailed analyses of genome architecture, gene content, transposable elements (TEs), and structural variation. Using PacBio HiFi sequencing, we generated highly contiguous assemblies (N50: 60.76-77.83 Mb) with 97% BUSCO completeness. Comparative analyses with Gallus gallus and Falco rusticolus revealed strong synteny among Falco species, whereas extensive chromosomal rearrangements were observed in comparison with the more distantly related Gallus gallus. TEs account for 7.43-8.44% of the genomes, with LINEs (CR1) and DNA transposons (Mutator, CACTA) predominating. Contigs belonging to the W sex chromosome were identified based on their significantly higher TE content (30% or more) compared to autosomes and the Z chromosome. Gene prediction, informed by long-read RNA Iso-Seq, identified 18,638-19,858 genes per genome, aligning with prior falcon annotations. Importantly we recovered key immune and sensory gene families, including MHC class I/II, innate immune receptors, and 24-25 olfactory receptor genes. We detected 8,746 structural variants, over 40% of which involved TEs, underscoring their role in genome polymorphism. These assemblies provide a valuable resource for investigating avian chromosome evolution, TE dynamics, and species-specific adaptations. They also establish a foundation for comparative genomics, population genetics, and conservation efforts in falcons.
Zuccolo et al. (Mon,) studied this question.