The genome of the choanoflagellate *Monosiga brevicollis* has been sequenced and analyzed to understand the molecular mechanisms underlying the evolution of metazoans. Choanoflagellates are the closest known relatives of metazoans, and their genome contains approximately 9,200 intron-rich genes, including those encoding cell adhesion and signaling protein domains typically restricted to metazoans. The study reveals that the last common ancestor of choanoflagellates and metazoans had genes with high intron content, suggesting that intron gain occurred before the origin of metazoans. The genome also contains a diverse array of cell adhesion and extracellular matrix (ECM) protein domains, such as cadherins, C-type lectins, integrin-α, and immunoglobulin domains, which are crucial for stable cell adhesion and multicellularity. However, many metazoan-specific signaling pathways, such as NHR, WNT, and TGF-β, are absent in *M. brevicollis*. The genome also encodes abundant tyrosine kinase domains and their downstream signaling targets, indicating that pTyr-based signaling may have evolved before the separation of choanoflagellates and metazoans. The study highlights the importance of domain shuffling in the evolution of intercellular signaling pathways and suggests that the common ancestor of choanoflagellates and metazoans had an early form of multicellularity that became more robust in metazoans. The availability of the *M. brevicollis* genome provides a valuable resource for studying the evolution of metazoan biology and the transition to multicellularity.The genome of the choanoflagellate *Monosiga brevicollis* has been sequenced and analyzed to understand the molecular mechanisms underlying the evolution of metazoans. Choanoflagellates are the closest known relatives of metazoans, and their genome contains approximately 9,200 intron-rich genes, including those encoding cell adhesion and signaling protein domains typically restricted to metazoans. The study reveals that the last common ancestor of choanoflagellates and metazoans had genes with high intron content, suggesting that intron gain occurred before the origin of metazoans. The genome also contains a diverse array of cell adhesion and extracellular matrix (ECM) protein domains, such as cadherins, C-type lectins, integrin-α, and immunoglobulin domains, which are crucial for stable cell adhesion and multicellularity. However, many metazoan-specific signaling pathways, such as NHR, WNT, and TGF-β, are absent in *M. brevicollis*. The genome also encodes abundant tyrosine kinase domains and their downstream signaling targets, indicating that pTyr-based signaling may have evolved before the separation of choanoflagellates and metazoans. The study highlights the importance of domain shuffling in the evolution of intercellular signaling pathways and suggests that the common ancestor of choanoflagellates and metazoans had an early form of multicellularity that became more robust in metazoans. The availability of the *M. brevicollis* genome provides a valuable resource for studying the evolution of metazoan biology and the transition to multicellularity.