Chromosome-level genome assembly of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni)
)
Traditional conservation methods have failed to save the northern white rhinoceros (NWR: Ceratotherium simum cottoni), leaving only two non-reproductive females. Scientists are exploring assisted reproductive technologies (ARTs), including artificial gametes produced from induced pluripotent stem cells (iPSCs) and somatic cell nuclear transfer, together with Southern white rhinoceros (SWR: Ceratotherium simum simum) surrogate mothers as potential methods to save functionally extinct NWR. The development of ARTs requires a high-quality reference genome. Fibroblast and iPSCs were cultured from a male NWR ‘Angalifu’ and deeply sequenced using four complementary platforms. We developed an assembly strategy to generate a chromosomal-level (2n = 82) NWR reference genome, including 40 acrocentric autosomes, the X and partially resolved Y chromosomes, as well as the mitochondria genome, that meets or exceeds the metrics proposed by the Vertebrate Genome Project (VGP). The high quality genome not only confirms the gene order and chromosome conservation between horse and rhino, but also shows that no chromosomal-level structure variants exists between NWR and SWR. Although gaps still exist in the generated NWR reference genome, recent development of ONT ultralong sequencing techniques has demonstrated that a gap-less telomere-telomere NWR genome assembly is highly achievable