First draft genome assembly of sponge Halisarca dujardinii reveals key components of basement membrane and broad repertoire of aggregation factors.

How features characteristic of multicellular animals emerged in evolution is one of the key topics of modern evolutionary biology. We can get closer to answering that question by studying animals that occupy a sister taxon position to all other animals on the phylogenetic tree, such as sponges (Porifera). We sequenced the genome of the sponge Halisarca dujardinii using Oxford Nanopore and Illumina technologies and made an assembly of long reads, followed by polishing with short reads. The resulting assembly had a size of 176 Mb, and an N50 of about 785 Kb. By analyzing transposable elements in the genomes of H. dujardinii and a number of other sponges, we found that a significant portion of the genome (more than half for Demospongiae) is occupied by repeats, most of which are evolutionarily young. RNA-seq data were used to predict 13,989 genes in the genome, several times less than in other Demospongiae. By analyzing ortholog groups unique to H. dujardinii among sponges and other invertebrates, we found overrepresented genes related to the extracellular matrix. The extracellular matrix of H. dujardinii contains, among other components, key basement membrane components such as laminin, nidogen, fibronectin, and collagen IV, which phylogenetic analysis has confirmed that it belongs to this type of nonfibrillar collagen. In addition, we showed in H. dujardinii 14 aggregation factor genes responsible for cell recognition and adhesion. Our obtained assembly and annotation will further expand the understanding of genome evolution at the emergence of animal multicellularity.