Chromosome-Scale Genome Architecture and Historical Demography of the Southern White Rhinoceros

The white rhinoceros (<i>Ceratotherium simum</i>) offers a unique model for investigating the genomic consequences of extreme demographic bottlenecks. However, the fragmented southern white rhinoceros genome assembly has limited chromosome-scale structural and evolutionary comparisons with the functionally extinct northern subspecies. Here, we report a chromosome-scale genome assembly for the southern white rhinoceros by integrating Oxford Nanopore Technology long-read sequencing, Illumina short-read polishing and high-throughput chromosome conformation capture (Hi-C) scaffolding. The final assembly spans 2.48 Gb and achieves a contig N50 of 42.06 Mb, representing a 452-fold improvement in contiguity over the previous assembly. In total, 2.46 Gb of sequence was anchored to 40 autosomes plus the X and Y chromosomes. Genome annotation identified 1.13 Gb of repetitive elements (45.7% of the assembly), 22,593 protein-coding genes, and 100.68 Mb of segmental duplications. Inspection of the major histocompatibility complex class II gene region further supported the local assembly and annotation reliability, revealing conserved gene composition and order between the southern and northern white rhinoceroses. Whole-genome comparison with the northern white rhinoceros assembly indicated extensive chromosome-scale synteny, along with localized structural variants between the two subspecies, including 111 inversions spanning 33.48 Mb and 497 translocations spanning 36.48 Mb. Furthermore, coalescent demographic reconstruction indicated asynchronous Pleistocene population dynamics for southern and northern white rhinoceroses, reflecting divergent responses to historical climate oscillations. Both subspecies also exhibit lower recent effective population sizes than estimated Pleistocene ancestral levels, underscoring persistent conservation concern. This assembly provides a useful resource for evaluating the genomic consequences of historical bottlenecks, informing future genomic-rescue plans, and strengthening the comparative framework for rhinoceros conservation and evolutionary genomics.