Abstract Dinoflagellates of Order Suessiales include the diverse Family Symbiodiniaceae known for their role as essential coral reef symbionts, and the cold-adapted Polarella glacialis . These taxa inhabit a broad range of ecological niches and exhibit extensive genomic divergence, although their genomes are in the smaller size ranges (haploid size &lt; 3 Gbp) compared to most other dinoflagellates. Different isolates of a species are known to form symbiosis with distinct hosts and exhibit different regimes of gene expression, but intraspecies whole-genome divergence remains little known. Focusing on three Symbiodiniaceae species (the free-living Effrenium voratum , and the symbiotic Symbiodinium microadriaticum and Durusdinium trenchii ) and the free-living outgroup P. glacialis , all for which whole-genome data from multiple isolates are available, we assessed intraspecies genomic divergence at sequence and structural levels. Our analysis based on alignment and alignment-free methods revealed greater extent of intraspecies sequence divergence in symbiodiniacean species than in P. glacialis . Our results also reveal the implications of gene duplication in generating functional innovation and diversification of Symbiodiniaceae, particularly in D. trenchii for which whole-genome duplication was involved. Interestingly, tandem duplication of single-exon genes was found to be more prevalent in genomes of free-living species than in those of symbiotic species. These results in combination demonstrate the remarkable intraspecies genomic divergence in dinoflagellates under the constraint of reduced genome sizes, shaped by genetic duplications and symbiogenesis events during diversification of Symbiodiniaceae.

Intraspecies genomic divergence of coral algal symbionts shaped by gene duplication