Chromosome-Scale Genome Assembly Provides Insights Into Condor Evolution and Conservation

Rare species are highly vulnerable to anthropogenic threats due to their unique life-history traits and specialised adaptations. The Andean condor (Vultur gryphus), the world's largest soaring bird, exemplifies these challenges with exceptional flight efficiency, delayed maturity, long lifespan, extreme sexual dimorphism and a critical scavenging role. The species faces significant threats, including habitat loss, persecution and poisoning. Meanwhile, conservation efforts have been hindered by knowledge gaps, including limited genetic data. Herein, we present the first chromosome-scale reference genome for the species, a key resource for investigating its evolution and ecology, as well as informing conservation measures. The assembly spans 1.19 Gb with 97.4% completeness, including 29 autosomes and the Z chromosome. High synteny with the California condor (Gymnogyps californianus) genome reflects their close evolutionary relationship. Genomic diversity in Andean condors (~0.65He/Kbp; π: 6.73^e-4) was lower than in California condors (~0.97 He/Kbp; π: 1.09^e-3). Runs of Homozygosity (RoH) analyses revealed a smaller genomic proportion (~15%) with shorter elements in Andean condors (> 5 Mb covering 1.43% of the genome). In contrast, California condors showed a higher genomic proportion (~40%), with longer RoH segments (> 5 Mb covering 7.3% of the genome). Analyses of gene family evolution revealed divergent patterns of expansion and contraction between Andean and California condors, including genes linked to detoxification metabolism, high-altitude adaptation and immune response. Shared genomic trends among avian scavengers highlight convergent evolution in stress response and metabolic pathways. This study provides a key genomic resource for advancing avian research and guiding conservation strategies for threatened vultures.