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Dinoflagellate Genome Sequenced in Search of Coral Symbiosis Insights

NEW YORK (GenomeWeb) – A new genome sequencing analysis is helping researchers untangle the contributions that a photosynthetic dinoflagellate species called Symbiodinium kawagutii makes in its endosymbiotic relationship with coral reef species such as the anthozoan Acropora.

"This study provides a portrait of a symbiotic dinoflagellate and the molecular basis of coral-Symbiodinium symbiosis," senior author David Morse, a plant biology researcher at the University of Montreal, and his colleagues wrote in a study published online today in Science.

"Our results are a stepping stone to understanding how the genetic complementarity between anthozoans and Symbiodinium can explain host specificity and to determining the molecular mechanisms responsible for coral bleaching," they noted.

Morse and members of an international team led by investigators in China and the US put together a high-quality genome assembly for a S. kawagutii dinoflagellate acquired from a reef ecosystem in Hawaii. Their analyses uncovered genes expressed by both the dinoflagellate and its coral counterpart, along with expansions to S. kawagutii gene families suspected of contributing to coral symbiosis.

"We found biochemical complementarity between genomes of S. kawagutii and the anthozoan Acropora," the researchers noted, "indicative of host-symbiont co-evolution, providing a resource for studying the molecular basis and evolution of coral symbiosis."

The researchers used Illumina instrument to shotgun sequence the 1.18-billion-base S. kawagutii genome using DNA from a clade F strain from Hawaii.

From the more than 150 billion base pairs of sequences generated, they assembled a 935-million-base genome assembly for the dinoflagellate, which contains an estimated 36,850 protein-coding genes and more than 350 potential mature miRNAs, including dozens of miRNAs resembling those in animals, 11 plant-like miRNAs, and one miRNA that was most similar to a viral sequence.

By comparing the genome to sequences from higher plants; diatoms; chlorophyte, rhodophyte, and phaeophyte algae; alveolate protists; and cnidarian invertebrates, the team identified more than 25,000 gene family clusters and 12,516 S. kawagutii gene families.

As expected, the dinoflagellate genome contained genes associated with standard photosynthetic processes in other eukaryotes. It also housed genes known for their role in sexual reproduction, germination, and cyst formation as well as distinctive gene promoter elements.

Some 7,663 gene families appear to have been gained in the Symbiodinium lineage, the researchers explained — a collection marked by an over-representation of genes with suspected metabolic functions.

While fewer than 100 gene families have contracted in Symbiodinium, their results suggest that there have been expansions affecting around 265 other gene families.

The S. kawagutii genome appears to have had help from transposable elements and horizontal gene transfer in distinguishing itself from sequences in a related species called S. minutum, the team noted. On the other hand, there were no signs of historical whole-genome duplications in the S. kawagutii lineage.

In the hunt for genes contributing to endosymbiosis with coral, meanwhile, the researchers focused in on dinoflagellate genes involved in everything from amino acid and sugar biosynthesis to transport and stress tolerance. They noted that some 1,500 coral genes may be targetable by miRNAs produced by dinoflagellates, including a subset of transporter genes shared by S. kawagutii and Acropora.

Still other genes were missing in S. kawagutii but present in A. digitifera, the team found, perhaps reflecting the intimate ties between the endosymbiotic species.

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