The genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits such as nervous systems arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here we present its 326 Mbp genome, assembled to high contiguity (N50: 9.88 Mbp) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, highly shared synteny, and offer clarity on the changes allowing adaptation to the extreme temperatures and conditions found in freshwater. The pancontinental distribution, sexual and asexual development, and ready laboratory culture of E. muelleri make this a highly practical model system. Alongside RNAseq, DNA methylation and amplicon data spanning its development and range, the E. muelleri genome offers a multifaceted resource for examining genomic changes both within sponges and in early animal evolution.
