A consensus genome sequence for the social amoeba <i>Dictyostelium giganteum</i>

The dictyostelid or cellular slime moulds (CSMs) are recognised as models in cell, developmental and human disease biology. Their unusual life cycle alternates between a free-living solitary phase and an aggregative social phase. We generated short Illumina reads and assembled a consensus genome, comprising nuclear and mitochondrial genomes, representative of six naturally-occurring strains of the CSM Dictyostelium giganteum. The nuclear genome has an AT content of 75.76%, accounting for 38.52 Mb with a N50 of 3.01 Mb and L50 of 5, and resolves into five chromosome-scale scaffolds consistent with the karyotype. BUSCO analysis recovered 95.5% complete single-copy orthologs and 0.6% duplicated orthologs, corresponding to an overall completeness of 96.1%, with 0.3% fragmented and 3.6% missing orthologs. ∼5500 deduced gene sequences from a publicly available transcriptome further validate the genome assembly and completeness. The genome encodes 13,251 predicted proteins including ABC transporters, polyketide synthases, Ras/Rho GTPases, and expanded families of protein kinases. A comparative analysis shows extensive conservation of syntenic blocks with D. discoideum and D. firmibasis. About 18% of the nuclear genome is made up of repetitive DNA, mostly in the form of simple repeats. Comparative proteome-level orthology analysis across Dictyostelium species and Entamoeba identifies a conserved Amoebozoan core and a substantial dictyostelid-specific gene repertoire. Domain-level comparisons indicate widespread conservation of intracellular signalling and cytoskeletal modules with animals, whereas canonical metazoan extracellular adhesion domains are absent.