Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) and provide key insights into mammalian evolution^1,2. Here we generate and analyse reference genomes of the platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus), which represent the only two extant monotreme lineages. The nearly complete platypus genome assembly has anchored almost the entire genome onto chromosomes, markedly improving the genome continuity and gene annotation. Together with our echidna sequence, the genomes of the two species allow us to detect the ancestral and lineage-specific genomic changes that shape both monotreme and mammalian evolution. We provide evidence that the monotreme sex chromosome complex originated from an ancestral chromosome ring configuration. The formation of such a unique chromosome complex may have been facilitated by the unusually extensive interactions between the multi-X and multi-Y chromosomes that are shared by the autosomal homologues in humans. Further comparative genomic analyses unravel marked differences between monotremes and therians in haptoglobin genes, lactation genes and chemosensory receptor genes for smell and taste that underlie the ecological adaptation of monotremes.

卵生哺乳动物（单孔类）是兽类（有袋类和真兽类）现存的唯一哺乳动物外类群，为哺乳动物进化提供了重要见解^1,2 。在这里，我们生成并分析了鸭嘴兽（ Ornithorhynchus anatinus ）和针鼹（ Tachyglossus aculeatus ）的参考基因组，它们代表了现存的仅有的两个单孔类动物谱系。近乎完整的鸭嘴兽基因组组装将几乎整个基因组锚定在染色体上，显着提高了基因组连续性和基因注释。与我们的针鼹序列一起，这两个物种的基因组使我们能够检测塑造单孔类动物和哺乳动物进化的祖先和谱系特异性基因组变化。我们提供的证据表明单孔类性染色体复合体起源于祖先染色体环结构。这种独特染色体复合体的形成可能是由人类常染色体同源体共有的多 X 和多 Y 染色体之间异常广泛的相互作用促进的。进一步的比较基因组分析揭示了单孔类动物和兽类动物在触珠蛋白基因、哺乳基因和嗅觉和味觉化学感应受体基因方面的显着差异，这些差异是单孔类动物生态适应的基础。