Egg-laying mammals monotremes are the oldest surviving mammalian lineage. It only comprises of five extant species including platypus (Ornithorhynchus anatinus) from family Ornithorhynchidae, short-beak echidna (Tachyglossus aculeatus) and long-beak echidna (Zaglossus ssp.) from family Tachyglossa. These animals possess an intermediate position between reptiles and mammals from both phylogenetic and biologic aspects. For example, they lay eggs to produce offspring but also lactate to feed them. Moreover, platypus and echidna exhibit distinct appearance and live in different ecological niches. Platypus is a semiaquatic mammal covered with dark brown fur and only detect for food underwater with its bill; echidna is a terrestrial species with spiny hair and widely spread in Australia and New Guinea, and feed on ants and termites. The sex chromosome system in monotremes is also intriguing. There are 5 X and 5 Y chromosomes in platypus and 5 X and 4 Y chromosomes in echidna. They have been showed not homologous to human X chromosomes but instead to avian Z chromosomes. Genomic sequences have always been an important resource for the understanding of evolution. Monotreme genome no doubt contains molecular evidences for early mammal evolution and their adaptation. Although the platypus genome has been published in 2008, its quality is not good enough because of the low sequence continuity. The absence of echidna genome also hinders people from studying the strategies monotremes take to adapt to different environments. Moreover, the sequenced platypus individual is a female, which harbors only a full set for X chromosomes but completely lack Y chromosomes. This would hinder the research on sex chromosome evolution and divergence in monotremes as well. Here in this thesis I present two de novo monotremes assemblies covering all the two extant families. Both assemblies had been scaffolded with various of technologies and underwent extensive curation to ensure assembly quality. Both showed improvement compared with the published one. Then I utilized these assemblies to resolve the uncertain divergent time between platypus and echidna, and gave insights into mammalian macro evolution. For the first time mammalian ancestral karyotype was reconstructed, which further revealed rearrangement events in the three major mammalian lineages. The multiple sex chromosome system was further studied in detail, where we found a circular pairing pattern among the 5 X and 5 Y chromosomes and suggested that X1 is the oldest X. An unexpected excessive intersex chromosome interaction was discovered even in mitotic cells. At last I presented some genomics signals for both mammal evolution and monotreme adaptation to their different lifesty