Genome Assembly of the Endangered Patagonian Deer Hippocamelus bisulcus (huemul): The First Nuclear Genome for the Genus Hippocamelus

Abstract

The huemul (Hippocamelus bisulcus) is an endangered cervid endemic to the Andean-Patagonian region of South America, where it persists in small, fragmented populations. The lack of a reference genome has constrained genomic approaches to huemul conservation and evolutionary research. Despite moderate theoretical coverage (~22.8x), Oxford Nanopore long reads yielded the first highly contiguous and nearly complete nuclear genome assembly for H. bisulcus. The 2.50-Gb assembly achieved a contig N50 of 8.75 Mb, 99.0% BUSCO completeness, an estimated k-mer completeness of 95.63%, and an ONT k-mer-based QV estimate of 48.11. Reference-guided scaffolding against the white-tailed deer (Odocoileus virginianus) genome organized 94% of the assembly into 36 chromosome-scale pseudomolecules (34 autosomes, X, and Y; scaffold N50 = 68.56 Mb). Repeat annotation identified 38.09% of the assembly as repetitive, dominated by LINEs, consistent with other cervid genomes. Coordinate-based annotation transfer with LiftOn identified 20,042 protein-coding genes, with 95.9% BUSCO completeness in the representative predicted proteome. We also assembled a complete circular mitochondrial genome of 16,405 bp containing the expected 37-gene complement in the conserved vertebrate arrangement. Nuclear and mitochondrial phylogenies placed H. bisulcus within Odocoileini (Capreolinae), while the mitochondrial analysis recovered H. bisulcus and the Andean deer H. antisensis as a maximally supported sister pair. Comparative analysis across nine Cervidae proteomes assigned 98.8% of the representative H. bisulcus proteins to orthogroups shared with at least one other species, indicating broad recovery of the conserved cervid protein repertoire. This study provides the first nuclear genome for the South American genus Hippocamelus and the first nuclear and mitochondrial genomic resources for H. bisulcus, establishing a foundational framework for population genomics, conservation management, and evolutionary studies of this emblematic Patagonian deer.