Genomic map of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni)

• 成果类型: Article
• 署名作者: Wang, Gaojianyong; Korody, Marisa L.; Braendl, Bjoern; Hernandez-Toro, Camilo Jose; Rohrandt, Christian; Hong, Karl; Pang, Andy Wing Chun; Lee, Joyce; Migliorelli, Giovanna; Stanke, Mario; Ford, Sarah M.; Pollmann, Iris; Houck, Marlys L.; Lewin, Harris A.; Lear, Teri L.; Ryder, Oliver A.; Meissner, Alexander; Loring, Jeanne F.; Mueller, Franz-Josef
• 署名单位: Max Planck Society; University of Kiel; University of Kiel; Schleswig Holstein University Hospital; University of Kiel; Universitat Greifswald; Universitat Greifswald; University of California System; University of California Santa Cruz; University of California System; University of California Davis; University of California System; University of California Davis; University of California System; University of California Davis; University of Kentucky; Scripps Research Institute
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-15273
• DOI: 10.1073/pnas.2401207122
• 发表日期: 2025-05-20
• 关键词: embryonic stem-cells; copy number; in-vitro; domestic horse; SYSTEM; pluripotency; karyotype

摘要

The northern white rhinoceros (NWR; Ceratotherium simum cottoni) is functionally extinct, with only two nonreproductive females alive. Efforts to rescue the NWR from its inevitable demise have inspired the exploration of unconventional conservation methods, including the development of induced pluripotent stem cells (iPSCs) for the in vitro generation of artificial gametes. The integrity of iPSC genomes is critical for in vitro gametogenesis to be used for assisted reproductive technologies using NWR iPSCs. We generated a chromosome-level NWR reference genome that meets or exceeds the metrics proposed by the Vertebrate Genome Project, using complementary sequencing and mapping methods. The genome represents 40 autosomes, an X and a partially resolved Y chromosome, and the mitochondrial genome. Using comparative FISH mapping, we confirmed a general gene order conservation between the NWR and horse genomes. We aligned the NWR genome with that of the southern white rhinoceros (SWR; Ceratotherium simum simum), a population that has been physically separated from the NWR for tens of thousands of years, and we found that the two subspecies are very similar on the chromosome level. Comparing long-read data from NWR iPSC lines and the fibroblast cultures used for reprogramming, we identified copy number variations that were likely to have been introduced during in vitro iPSC expansion. The NWR reference genome allows for efficient, rapid, and accurate assessment of the genomic integrity of iPSC lines to direct their differentiation. This will assist in strategies to rescue the NWR through extraordinary measures like cloning and the generation of embryos from iPSC-derived gametes.