A chromosome-length assembly of the Hawaiian Monk seal (Neomonarchus schauinslandi) confirms genomic stability in the Pinnipeds and a prolonged history of “genetic purging”

The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here we report a chromosomal reference assembly for a male animal produced using a variety of methods including linked-read sequencing, Hi-C contiguity mapping, optical genome mapping, and nanopore long read sequencing. The final assembly consisted of 16 autosomes, an X and portions of the Y chromosomes. We compared variants in the reference animals to nine other HMS and to the human reference NA12878 confirming a low level of variation within the species and one-eighth that of the human reference. A lack of variation in several MHC genes was documented suggesting that this species may be at risk for infectious disease. Lastly, the HMS chromosomal assembly confirmed significant synteny with other pinnipeds. This reference should be a useful tool for long-term management of HMS and evolutionary studies of other carnivorans.

夏威夷僧海豹（HMS）是新僧海豹属中唯一现存的热带无耳海豹物种。该物种在19世纪末经历了一次严重的种群瓶颈，随后数量持续下降，直到1976年成为美国国家海洋和大气管理局（NOAA）主导的物种恢复工作的对象，当时其种群数量不足1000只。与其他正在恢复的物种一样，据报道，由于种群瓶颈和随后的近亲繁殖，夏威夷僧海豹的遗传异质性降低。在此，我们报告了一只雄性夏威夷僧海豹的染色体参考基因组组装结果，该组装使用了多种方法，包括linked - read测序、Hi - C连续图谱绘制、光学基因组图谱绘制以及纳米孔长读长测序。最终的组装结果包含16条常染色体、一条X染色体以及部分Y染色体。我们将参考个体中的变异与其他9只夏威夷僧海豹以及人类参考基因组NA12878进行了比较，证实了该物种内的变异水平较低，仅为人类参考基因组的八分之一。记录显示几个主要组织相容性复合体（MHC）基因缺乏变异，这表明该物种可能面临感染疾病的风险。最后，夏威夷僧海豹的染色体组装结果证实了它与其他鳍足类动物具有显著的同线性。这一参考基因组应该是夏威夷僧海豹长期管理以及其他食肉动物进化研究的有用工具。