The unique genome structure of coral symbionts

“The genome for S. microadriaticum had already been sequenced and arranged into scaffolds,” says Manuel Aranda at KAUST, who worked on the study. “However, value really lies in identifying exactly which genes are located on each chromosome. It has taken us ten years to structure this genome into continuous pieces and map the genes and nucleotides on the chromosomes in three dimensions.”

The team used a technique called Hi-C, which captures the conformation of chromosomes by searching for interactions in chromatin: the combination of DNA and protein that builds chromosomes. Dinoflagellates do not have the classical superstructure of DNA strands wound around histone proteins. Instead, their DNA strands are in a highly condensed state inside the cell nucleus. The team discovered that, rather than having genes randomly distributed across chromosomes like humans do, S. microadriaticum has well-organised, orientated blocks of genes arranged in domains in rod-shaped chromosomes. Further, the genes are arranged by function (at least in some instances), so that genes associated with specific traits are grouped together and their transcription might be co-regulated. 

“Forget what you’ve learned about eukaryotic genetics,” says Aranda. “This creature has developed a different way of carrying out the tasks required to survive. Each domain is structured with two blocks of genes – the genes are orientated in one direction in one block, and in the other they face the opposite direction. This structure is linked to how they are transcribed. In fact, when we knocked out transcription, the structural domains disappeared.”

This orientation and grouping of genes could mean the organism might be able to control all its genes at once. Chromosome duplication might be a tactic in dinoflagellates in response to stress, doubling their power to tolerate specific stresses by boosting certain traits. If true, the team believes this natural process could be manipulated to help corals and their symbiotic partners survive future oceans. 

“This is a significant step forward in understanding dinoflagellate genome architecture,” says marine scientist, Senjie Lin, of the University of Connecticut, US, who was not involved in the study. “The findings of domain boundaries formed primarily by convergence of unidirectional gene blocks, and increasing gene density towards the ends of DNA strands, are particularly novel. These will prompt many more studies on dinoflagellate chromosome organization and gene expression regulation.”

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