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Team Sequences Sea Anemone Genome In Search of Coral Reef Symbiosis Model

NEW YORK (GenomeWeb) – A research team from Saudi Arabia, Germany, the UK, and the US has sequenced and started analyzing the genome of the sea anemone Aiptasia in the hopes of understanding the dynamic relationships between endosymbiotic cnidarian animals, algae, and microorganisms that make up coral reefs.

As they reported online yesterday in the Proceedings of the National Academy of Sciences, the researchers focused on Aiptasia in an effort to develop genetic resources for studying this and other anthozoans — reef-forming animals from the cnidarian phylum that harbor photosynthetic dinoflagellate algae in their cells.

Through comparisons with previously sequenced cnidarians, including anthozoans such as the starlet sea anemone and stony coral, the team found genome rearrangements and adaptions that appear to equip the endosymbiotic coral species for interactions with the algae within them.

"Although differences are likely to exist between different symbiotic anthozoans, our analyses have revealed a variety of conserved features that should help illuminate the evolution of the symbiotic lifestyle," the study's authors wrote, "and provide the basis for the continued development of Aiptasia as a critically needed model of coral-dinoflagellate endosymbiosis, which underlies one of the most important marine ecosystems, coral reefs."

While ecological features of coral reefs have been relatively well studied, the researchers noted, not as much is known about the molecular mechanisms that make it possible for a cnidarian animal host to tightly couple its metabolism with those of dinoflagellate algae in their cells, making up a larger unit known as a holobiont.

Genomic and transcriptomic studies of the sea anemone Nematostella vectensis and the stony coral Acropora digitifera have started offering clues to this process, though more research is needed to understand coral reef functions and to combat their deterioration.

"The ongoing decline of corals worldwide due to anthropogenic influences, including global warming, ocean acidification, and pollution, heightens the need for an experimentally tractable model system to elucidate the molecular and cellular biology underlying the symbiosis and its susceptibility or resilience to stress," the team explained.

Using Illumina instruments, the researchers sequenced short-read and long-insert mate-pair libraries containing DNA from a clonal population of the Aiptasia strain CC7, producing a roughly 258 million base genome that was predicted to contain more than 29,000 protein-coding gene models.

With the help of transcriptome sequence data generated with RNA from CC7 and from larvae produced by crossing the CC7 strain with a strain called H2, the team verified 26,658 of these as complete gene models — a collection that included 26,162 genes with documented homologs in other organisms.

The team then compared the Aiptasia genome with sequences from other anthozoans, such as the starlet sea anemone and the stony coral, and with sequences from the Hydra, a freshwater cnidarian sequenced in 2010, to search for genomic features coinciding with the holobiont lifestyle.

For example, both the Aiptasia and stony coral (A. digitifera) genomes contained ancient transposable element expansions that are missing in the starlet sea anemone (N. vectensis), which does not form symbiotic associations with intracellular dinoflagellate algae.

Nevertheless, the researchers cautioned that "it remains to be determined if these genomic rearrangements were functionally associated with some common event affecting their symbiotic lifestyles."

Within a collection of 3,107 predicted Aiptasia genes without known homologs, meanwhile, the team saw an over-representation of genes with altered expression during symbiosis or Aiptasia development, hinting that they may be important to these processes.

Finally, the analysis highlighted gene families that have been expanded and/or nabbed from bacteria, dinoflagellates, or other organisms by horizontal gene transfer in Aiptasia and other anthozoan species.