A consensus genome sequence for the social amoeba Dictyostelium giganteum

Abstract

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.