cientists at the Department of Energy’s Joint Genome Institute (DOE JGI) have announced completion of sequencing the Emiliania huxleyi (Ehux) genome, allowing them to compare the sequences of this bottom of the food chain alga with those from other algal isolates.
Ehux represent the most abundant species of coccolithophore, the unicellular, eukaryotic phytoplankton distinguished by calcium carbonate scales (think White Cliffs of Dover) which are also important microfossils. An important part of the planktonic base of a large proportion of marine food webs, coccolithophores are of particular interest to those studying global climate change because as ocean acidity increases, their coccoliths may become even more important as a carbon sink.
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 more than ten years. Originally estimated to be about 30 million bases, the genome ended up being closer to 141 million. 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. Additionally, the researchers discovered hints that Ehux may also be involved in the global sulfur cycle as it is able to produce a compound that can influence cloud formation and thus affect climate.
The project researchers 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. Long term, this work 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.