Endangered Steppe Eagle (<i>Aquila nipalensis</i>) (Aves, Accipitriformes, Accipitridae) genome and mitogenome assembly: A resource for molecular evolution and comparative genomics

The Steppe Eagle, <i>Aquila nipalensis</i> Hodgson, 1833, is a migratory, endangered raptor experiencing population declines due to habitat loss and human persecution. This study aims to construct a high-quality <i>de novo</i> nuclear genome and complete mitochondrial genome assembly using PromethION Oxford Nanopore long-read and MGI short-read sequencing technologies. The assembled genome size was 1.21 Gb and contained 16,192 predicted protein-coding genes. Phylogenomic reconstruction based on ultraconserved elements (UCEs) robustly placed <i>A. nipalensis</i> within Aquilinae, with <i>Aquila chrysaetos</i> (Linnaeus, 1758) identified as its closest extant relative. Mitogenome-based analyses recovered congruent topology but revealed dataset-dependent differences in divergence time estimation. The most recent common ancestor of <i>A. nipalensis</i> and other <i>Aquila</i> species was estimated at approximately 3-13 million years ago, depending on dataset, whereas divergence between <i>Aquila</i> and <i>Nisaetus</i> occurred around 22 Mya. Comparative genomic analyses further identified positively selected genes associated with vesicle trafficking, secretion, and tissue development, suggesting potential adaptive signatures related to physiological performance. In conclusion, these genomic and evolutionary insights establish a foundational reference for future population genomic, adaptive, and conservation studies of this endangered raptor.