Genomic Characterization of Dinoflagellate Species

Dinoflagellates encompass a diverse clade of unicellular algae whose genomic architecture is among the most complex in eukaryotes. Genome sizes range from a few gigabases to over 100 Gb, with high G + C content, extensive repetitive elements and minimal histone packaging. Many genes occur in tandem arrays, often as single-exon units, and nearly all transcripts undergo trans-splicing with a conserved splice leader. Such features challenge assembly and annotation, but advances in sequencing, long-read technology and multi-omics integration have begun to resolve gene content, regulatory pathways and adaptation strategies. Genomic insights illuminate mechanisms underlying photosynthesis, toxin biosynthesis, stress responses, symbiosis and harmful algal bloom formation. Furthermore, the discovery of virus-derived nucleoproteins points to horizontal gene transfer events that have remodelled chromatin and influenced genome condensation. Comprehensive characterisation of these genomes offers a window into the evolutionary innovations that underpin the ecological success and global impact of dinoflagellate species.

Research from Nature Portfolio

Recent studies have uncovered the integration of virus-related genes into dinoflagellate genomes, notably the presence of dinoflagellate/viral nucleoproteins (DVNPs) originally encoded by giant viruses. Comprehensive proteomic and phylogenomic analyses reveal that these DVNPs influence chromatin compaction and may have been acquired from the Imitervirales order, implicating viral-host interactions in the evolution of genome architecture. Electron microscopy shows that virus infection remodels host nuclear structure to create viral replication factories, emphasising the role of horizontal gene transfer in shaping dinoflagellate chromatin and genome function.

Genomic Characterization of Dinoflagellate Species publication trend

The graph below shows the total number of articles in genomic characterization of dinoflagellate species across all publications each year (not limited to Nature Index journals).

Technical terms

De novo assembly: Reconstruction of a genome sequence directly from sequencing reads without a reference.

Multi-omics: Integrated analysis of genomic, transcriptomic, proteomic and metabolomic data to study biological systems.

Trans-splicing: A form of RNA processing in which exons from separate pre-mRNA molecules are joined to form mature mRNA.

Tandem gene cluster: A series of identical or similar genes arranged consecutively on a chromosome.

Dinoflagellate/viral nucleoprotein (DVNP): A chromatin-associated protein encoded by giant viruses and dinoflagellates, implicated in genome condensation and horizontal gene transfer.

References

1. Multi-omics analysis reveals the molecular response to heat stress in a “red tide” dinoflagellate. Genome Biology (2023).
2. Haptophyte-infecting viruses change the genome condensing proteins of dinoflagellates. Communications Biology (2025).
3. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biology (2020).
4. From Stop to Start: Tandem Gene Arrangement, Copy Number and Trans-Splicing Sites in the Dinoflagellate Amphidinium carterae. PLOS ONE (2008).
5. Distinct Gene Number-Genome Size Relationships for Eukaryotes and Non-Eukaryotes: Gene Content Estimation for Dinoflagellate Genomes. PLOS ONE (2009).