The accurate and complete assembly of both haplotype sequences of a diploid organism is essential to understanding the role of variation in genome functions, phenotypes and diseases¹. Here, using a trio-binning approach, we present a high-quality, diploid reference genome, with both haplotypes assembled independently at the chromosome level, for the common marmoset (Callithrix jacchus), an primate model system that is widely used in biomedical research^2,3. The full spectrum of heterozygosity between the two haplotypes involves 1.36% of the genome—much higher than the 0.13% indicated by the standard estimation based on single-nucleotide heterozygosity alone. The de novo mutation rate is 0.43 × 10⁻⁸ per site per generation, and the paternal inherited genome acquired twice as many mutations as the maternal. Our diploid assembly enabled us to discover a recent expansion of the sex-differentiation region and unique evolutionary changes in the marmoset Y chromosome. In addition, we identified many genes with signatures of positive selection that might have contributed to the evolution of Callithrix biological features. Brain-related genes were highly conserved between marmosets and humans, although several genes experienced lineage-specific copy number variations or diversifying selection, with implications for the use of marmosets as a model system.

二倍体生物的两个单倍型序列的准确和完整的组装对于了解变异在基因组功能、表型和疾病中的作用至关重要¹。在这里，我们使用 trio-binning 方法，为常见的狨猴（ Callithrix jacchus ）提供了一个高质量的二倍体参考基因组，两种单倍型在染色体水平上独立组装，这是一种广泛用于生物医学研究的灵长类动物模型系统^2,3。两种单倍型之间的全谱杂合性涉及 1.36% 的基因组——远高于仅基于单核苷酸杂合性的标准估计所指示的 0.13%。从头突变率为0.43 × 10 ^-8每代每个位点，父系遗传基因组获得的突变数量是母系的两倍。我们的二倍体组装使我们能够发现最近性别分化区域的扩展和狨猴 Y 染色体的独特进化变化。此外，我们鉴定了许多具有正选择特征的基因，这些基因可能有助于Callithrix生物学特征的进化。脑相关基因在狨猴和人类之间高度保守，尽管有几个基因经历了谱系特异性拷贝数变异或多样化选择，这对使用狨猴作为模型系统有影响。