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Sequencing Study Reveals Pan Genome for Marine Phytoplankton Species

NEW YORK (GenomeWeb News) – A large international team has uncovered unexpected genetic diversity in the miniscule marine algae Emiliania huxleyi, a species now known to have the type of variable 'pan genome' previously described in some bacterial species.

"In the sea, we thought that only bacteria were shuffling around their genes in this way," co-senior author Sonya Dyhrman, a researcher with the Columbia University Lamont-Doherty Earth Observatory, said in a statement, "so it was a real shock to see that [E. huxleyi] was doing the same thing."

As they reported online today in Nature, the researchers began by using genomic DNA from an E. huxleyi strain isolated in the Equatorial Pacific to generate a reference genome sequence for the phytoplankton species.

Together with re-sequencing data on 13 more E. huxleyi representatives, the reference sequence helped the team define a shared set of sequences within E. huxleyi's core genome, including genes that help the phytoplankton grow in locales with low phosphorus or iron levels.

Across the phytoplankton's broader pan genome, researchers detected an array of genes and repetitive sequences that are present in some E. huxleyi strains but not in others, varying with each strain's habitat, physical features, and metabolic capabilities, among others.

"Until now, the underlying mechanisms for the physiological and morphological variations between [E. huxleyi] isolates have been elusive," Dyhrman and colleagues wrote.

"Evidence presented here indicates that this capacity can be explained, in part, by its pan genome," they noted, "the first of its kind for what was thought to be a single microbial eukaryotic algal species."

The discovery of the pan genome has researchers speculating that the ability to swap certain genes may have helped the far-reaching phytoplankton adapt to the range of ocean sites where it is found.

Given the genetic patterns being uncovered in E. huxleyi, along with the phytoplankton's physiological capabilities and influence over the ocean and other environments, those involved in the study argued that the species could serve as a useful model to examine organisms' responses to environmental change.

In addition to its ability to grow across diverse environments, E. huxleyi belongs to a group of single-celled algae known as the coccolithophores — a nod to the calcium carbonate plates or "coccoliths" that make up the organisms' external skeleton.

As a group, coccolithophore species appear to have a pronounced effect on ocean carbon cycles and global climate patterns, researchers noted. The organisms take up and store carbon during photosynthesis and growth, for instance. But they also release carbon dioxide while forming their calcified coccolith coats.

"Carbon dioxide is fixed during photosynthesis and calcification," the study's first author Betsy Read, a biology researcher at the California State University San Marcos, said in a statement.

"It is also released during the process of calcification, but we do not know how this release balances with the amount of CO2 that is buried when [E. huxleyi] sinks to the bottom of the ocean," Read added. "This is an important, yet unresolved, question."

A decade or more in the making, the E. huxleyi genome comes in at just shy of 142 million bases in its haploid form.

The study's authors used a traditional Sanger sequencing-centered approach, plus DNA from an E. huxleyi strain called CCMP1516, to sequence a diploid version of the genome.

Once annotated — with the help of transcript sequences and NimbleGen tiling array data — the reference genome was found to contain 30,569 predicted protein-coding genes and a large set of repetitive elements.

Through analysis of the reference genome and comparisons with other algal sequences, the team got a glimpse at some of E. huxleyi's protein-coding capabilities and phylogenetic relationships.

But it wasn't until they re-sequenced the genomes of another 13 E. huxleyi strains using high-throughput Illumina sequencing that the researchers saw the extent to which the E. huxleyi genome can vary in its gene-coding capabilities and repeat sequence content.

With that data in hand, they determined that as many as one third of protein-coding sequences present in E. huxleyi fall outside of the species' core genome.

"[I]f the genetic information of two humans is compared, an agreement of about 99 percent is found," co-senior author Uwe John, an Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research investigator, said in a statement.

"However, if, for example, we take two [E. huxleyi] strains from different ocean regions, we find a degree of similarity of only 70 or 80 percent," he added. "The rest of the genome differs."

Going forward, researchers plan to continue mining the minute algal species' pan genome for information. Of particular interest are genetic pathways related to phytoplankton features affecting climate — from the physical reflection of sunlight off of the phytoplankton's exterior to the organism's contributions to carbon, nitrogen, and sulfur cycles.

Beyond that, though, the genome holds hints about biological pathways that may be of broader interest as well. For example, some members of the E. huxleyi sequencing team are set to delve further into the pathways that produce the phytoplankton's calcium carbonate-based coccolith shells — a process that might inform future work to design biomaterials for bone and tooth replacement or other applications.