Scientists Decode Massive Genome to Fill Gap in the "Tree of Life"

The White Cliffs of Dover have long served as an iconic feature of the England landscape, inspiring songs and movies as well as countless photographs. To scientists, however, they represent much more than a striking backdrop: as a massive conglomeration of the single-celled photosynthetic alga known as Emiliania huxleyi, the cliffs are a monument to the coccolithophore that serves as the basis of most food chains.

Though miniscule in size, phytoplankton biomass exceeds that of all marine animals combined and is constantly affecting climate processes, such as lowering ocean temperatures by reflecting sunlight and through carbon metabolism. Furthermore, its versatility contributes to primary production of organic compounds from carbon dioxide or adds to its emissions make "Ehux" a critical player in the marine carbon cycle.

Given its importance, scientists at the Department of Energy Joint Genome Institute (DOE JGI) went ahead and sequenced the Ehux genome, allowing them to compare its sequences with those from other algal isolates.

Part of the third most abundant group of phytoplankton, the Ehux strain was isolated from the South Pacific and is the first reference genome for coccolithophores. Due to the complexities and size of the genome, the project ended up taking longer than planned: originally estimated to be about 30 million bases, the genome ended up being closer to 141 million.

Overall, the project took more than 10 years and came to be called “The Beast” by those working on it. However, with the advent of next generation sequencing technologies, the researchers were then able to conduct a comparison of 13 Ehux trains, revealing the first ever algal “pan genome.”

The coccolithophore is unique in that it doesn’t exist as a clearly defined “species” with a uniform genome, but as a more diffuse community of genomes (a pan-genome) with different individuals possessing a shared “core” of genes supplemented by different gene sets thought to be useful in dealing with the particular challenges of its local environment.

“Ehux thrives in a broad range of physiochemical conditions in the ocean,” Igor Grigoriev, the senior author of the study, said. “It’s a complex genome, with lots of genes and repeats, the first reference for haptophytes and fills another gap in the Eukaryotic Tree of Life.”

Other discoveries included genes that allow the Ehux to thrive in low levels of phosphorus and to assimilate and break down nitrogen-rich compounds. In addition, the researchers discovered hints that it may also be involved in the global sulfur cycle as it is able to produce a compound that can influence cloud formation and thus climate.

In the end, the scientists see the availability of the Ehux genome sequence as an important first step in unlocking the molecular mechanisms that govern the nucleation, growth and nanoscale patterning of the calcium carbonate shells like those that comprise the Cliffs of Dover.

“We have clues,” team member Betsy Read said, “but what makes this more difficult is that proteins involved in calcification are not conserved across biomineralizing species, those that can grow into composite materials. What we desperately need in order to identify the genes is a genetic transformation system. Several labs – including my own – are aggressively working on this.”

Identifying the genes and proteins involved in this process, Read explained, could lead to the design of new composite materials and devices for applications related to bone replacement, periodontal reconstruction, sensing systems, optoelectronic devices and the treatment of diseases.