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Phytoplankton Drowning in Genomic Diversity

06/13/2013
Sarah C.P. Williams

A new study has found that different strains of Emiliana huxleyi have very different genomes, with some diverging up to 10%. So what facilitates this remarkable plasticity? Find out...


The phytoplankton Emiliana huxleyi, which causes massive blooms that can alter the ocean’s carbon cycles, thrives in many diverse spots around the world. Now, a team of researchers has found that the plankton has a large genome that varies drastically between strains, providing one potential mechanism for the adaptability of E. huxleyi to different environments.

A new study has found that different strains of Emiliana huxleyi have very different genomes, with some diverging up to 10%. Source: Jeremy Young




“This incredible plasticity of the genome between strains explains its global distribution and its ecological success in the world’s oceans,” said biologist Betsy Read of California State University, San Marcos, the first author of the new paper published this week in Nature that describes the study (1).

A decade ago, Read and her collaborators began with the goal of sequencing just one strain of E. huxleyi, namely CCMP1516. They hoped the sequence would help them understand how the plankton forms its elegantly sculpted shells, what mediates its changing use of carbon and generation of large blooms, and how it is affected by climate change.

Overall, they expected the E. huxleyi genome to be similar to the recently sequenced diatom, which is also a phytoplankton. So their first surprise came with the size of the genome—it was 5 times larger than that of the diatom, about 141 million base pairs in length. Moreover, repetitive elements made up almost two thirds of the sequence, much higher than in the diatom. To investigate these surprise findings further, the team began sequencing strains of E. huxleyi from other regions.

“We noticed all this diversity when we started comparing strains,” said Read. “People actually initially thought that it was bacterial contamination.”

But when they double-checked their data, the diversity was real: the sequences varied by up to ten percent between strains (the human genome by comparison varies by less than half a percent between individuals). Nearly a quarter of the predicted genes from the CCMP1516 strain were missing in at least three other strains. The researchers concluded that E. huxleyi has a core set of genes shared between species, but a much broader pan-genome among strains. Among highly conserved core genes were those encoding photoreceptors, phosphorus and nitrogen transporters, and other metal and vitamin processing enzymes.

With the E. huxleyi sequences now at their disposal, Read and her colleagues plan to ask questions about the life cycle, nutrient processing, and shell formation of phytoplanktons.

“The biggest challenge for us right now is that we don’t have a genetic transformation system,” said Read. “So there are many of us that are working aggressively toward developing methods that will enable us to knock out or overexpress genes.”

They’ll also delve further into studying which parts of the E. huxleyi genome are most malleable and how the species developed such a large amount of genetic diversity. The research could lead to broader conclusions about how genetic diversity arises in other species as well.

“The only hint we have from the genome right now is this huge amount of repetitive sequences,” said Read. “So that may be what’s facilitating the plasticity, but we don’t yet know for sure.”

Reference

  1. Read, B.A., Kegel, J., Klute, M.J., Kuo, A. et. al. 2013. Pan genome of the phytoplankton Emiliana underpins its global distribution. Nature. Published online June 12, 2013.

Keywords:  genomics