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International Team Sequences Genomes of Two Tiny Plankton Species

NEW YORK (GenomeWeb News) – A team of researchers from seven countries has sequenced the genomes of two strains of microalgae or picophytoplankton that are believed to represent a very early stage of plant evolution.

The two Micromonas isolates, previously thought to belong to the same species, actually had remarkably different genomes, despite the fact that they look alike and carry similar 18S ribosomal RNA sequences. Because Micromonas belong to a group of algae near the base of the green eukaryote tree of life, researchers say the results provide new clues about the evolution of green algae and land plants. The research appeared online today in Science.

"The Micromonas genomes reveal features of the ancestral algae that initiated the billion-year trajectory of the green lineage and the greening of Earth," senior author Igor Grigoriev, a researcher at the US Department of Energy's Joint Genome Institute, and his co-authors wrote.

In an editorial appearing in the same issue of Science, Dalhousie University biochemistry and molecular biology researcher John Archibald, who was not involved in the research, said the study provides "the foundation for further comparative genomic analyses on a much broader diversity of plants and animals."

"It is exciting to think that some of the smallest eukaryotes on our planet can provide key insights into the early history of multicellular green plants," Archibald wrote.

Green photosynthetic eukaryotes belong to two large groups: chlorophytes and streptophytes. Chlorophytes include single-celled picophytoplankton such as Micromonas and Ostreococcus and single-celled freshwater algae such as Chlamydomonas, among other groups, while streptophytes include single-celled aquatic organisms called Mesostigma, stoneworts, and land plants.

Micromonas and Ostreococcus belong to an early branching chlorophyte group called Prasinophytae that is thought to resemble the ancestor of all green eukaryotes. Some have suggested prasinophytes might also serve as harbingers of climate change in marine environments, because of their widespread distribution.

Previous research suggests organisms in the Ostreococcus genus have dramatically streamlined genomes. For instance, two recently sequenced Ostreococcus species had genomes that were about 13 million base pairs and coded for roughly 8,000 genes.

For the latest study, Grigoriev and his team focused on a closely-related picophytoplankton called Micromonas. Using whole-genome shotgun sequencing, the researchers sequenced the 20.9 million base pair genome of RCC299, a Micromonas isolate collected in the South Pacific, and the 21.9 million base pair CCMP1545, an isolate collected in the North Atlantic.

RCC299 and CCMP1545 are usually classified as a single species called Micromonas pusilla. But even though their 18S rRNA sequences are about 97 percent identical and the strains looked indistinguishable, the team found that the genomes were very different. RCC299 contained an estimated 10,056 genes, while CCMP1545 contained about 10,575 genes. The genes were only about 90 percent alike in the two species.

Consequently, the team concluded that RCC299 and CCMP1545 actually represent two different species. Even so, features of the two genomes suggest RCC299 and CCMP1545 share an evolutionary history.

The researchers identified a core group of more than 7,100 genes that were present in the four sequenced Micromonas and Ostreococcus genomes and nearly 1,400 more genes that were shared in the RCC299 and CCMP1545 genomes but not the Ostreococcus genomes.

Among the genes detected were some coding for components of the photosynthetic pathway and other genes that grouped with land plants. The team also found genes resembling those in diatoms and brown algae, which they speculated might have resulted from a loss of genes from the green lineage or horizontal gene transfer.

"Their divergence, combined with acquisition strategies that are consistent with [horizontal gene transfer], highlight the dynamic nature of marine protistan evolution and provide a springboard for unraveling functional aspects of phytoplankton populations," the authors wrote.

Both Micromonas genomes housed transcription factors that appear to have been present early since before the chlorophyte-streptophyte split in the green lineage, including at least one transcription factor family present in higher land plants but not basal land plants.

But the team also found differences between Micromonas and other green eukaryotes. For instance, the two species have more genes protecting them from heavy metal toxicity and reactive oxygen species than Ostreococcus species.

Meanwhile, researchers identified 793 unique genes in the RCC299 genome and 826 unique genes in the CCMP1545 genome. In particular, they noted CCMP1545 had intronic repeat sequences missing from RCC299. The species also had distinct riboswitches (gene expression regulating messenger RNAs), though, as a group, Micromonas riboswitches were more like bacterial than eukaryotic riboswitches.

Together, the results provide new insights into Micromonas biology and ecology as well as green plant evolution in general. "Their analyses provide crucial insights into the plasticity of the eukaryotic genome over short evolutionary time scales and also shed light on the genetic 'toolkit' that may have been present in the ancestors of today's land plants and green algae," Archibald noted in his editorial.

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