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Study Suggests Diatom Genome Contains More Green Than Red Algal Genes

NEW YORK (GenomeWeb News) - Although diatoms are thought to have procured their photosynthetic capability from interactions with red algae, green genes actually appear to be more common in the organisms' genomes, according to a paper appearing online today in Science.

An international research team used phylogenomic analyses to investigate the origin of genes in two diatom genomes. Their results suggest that diatoms contain some genes from red algae, the organisms from which they apparently developed their plastids or photosynthetic compartments. But the diatom genomes harbor more — and older — genes from green algae, they found, suggesting an even earlier endosymbiotic relationship.

"In contrast to current thinking, our findings show that chromalveolates were already green before they acquired the red plastid," senior author Debashish Bhattacharya, a genetics and genomics researcher at the University of Iowa, and co-authors wrote.

"Given that diatoms are known to have acquired their plastids from red algae via a process known as secondary endosymbiosis, one would have expected their search to uncover many nuclear genes with a red algal origin," University of Düsseldorf researchers Tal Dagan and William Martin wrote in a perspectives article also appearing online in Science. "Yet, the authors find that most symbiont-derived genes in the diatom genome have a green algal origin."

Diatoms are tiny single-celled photosynthetic organisms with glass-like silica cell walls. Because of their role in primary production in the oceans, and potential applications for biofuel and nanotechnology research, Bhattacharya and his co-authors explained, diatom genetics and genomics is on the rise.

Diatoms are thought to have descended from flagellated cells that formed an endosymbiotic relationship with red algae, which contain similar photosynthetic pigments to those found in diatom plastids. And recent classification schemes have placed the organisms in a group called the chromalveolates, which also contains non-photosynthetic organisms such as water molds and ciliated protists.

To explore diatoms' evolutionary history, including the contribution of endosymbionts to diatom nuclear genomes, Bhattacharya and his colleagues conducted a phylogenomic analysis, comparing the genomes of two diatoms — Thalassiosira and Phaeodactylum — with sequences in a genomic database containing RefSeq data as well as genome sequence information for red and green algae and other organisms.

The researchers detected thousands of algal genes in the nuclear genomes of both diatoms: the Phaeodactylum genome contained nearly 3,500 algal, while the Thalassiosira genome contained almost 3,700.

Unexpectedly though, given the proposed endosymbiotic relationship between diatoms and red algae, the researchers saw far more green algal than red algal genes. More than 70 percent of the genes in the diatom genome — and about 16 percent of the diatom proteome — apparently originated in green algae.

Based on their subsequent analyses, the researchers concluded that diatoms likely picked up green algal genes through a combination of endosymbiosis and horizontal gene transfer. And because the green algal genes seem to have been hanging around the diatom nuclear genome longer than the red algal genes, the team suggested that green algal endosymbiosis preceded red algae's relationship with diatoms.

The authors argue that the dual endosymbiotic events, followed by horizontal gene transfer, have "supplied chromalveolates such as diatoms with the genetic potential to become some of the most ecologically successful and dominant marine primary producers on our planet."

In their perspectives article, Dagan and Martin said the results of the new study are bound to be controversial, given the widespread belief that diatoms pigments have been acquired through endosymbiosis with red algae.

They pointed out that some of the difference in green versus red algal gene content detected might be a consequence of comparing diatom genomes with a small red algae genome that has far fewer genes than most green algae genomes. They argued that sequencing additional, large red algal genomes might help clarify the diatom-algal relationships. "More data from red algae would soothe all concerns," they wrote, "if anyone is searching for a reason to sequence larger red algal genome, there it is."

Still, since the new study pinpoints not just a few genes of green algal origin but about 1,000, the duo noted, the results do indicate that diatom and algal relationships are more complex than previously supposed. "A phylogenetic signal of that magnitude surely tells us something important about algal evolution," Dagan and Martin wrote.