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International Team Sequences Seaweed Genome

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – An international team reported online in Nature today that they have sequenced the genome of Ectocarpus siliculosus, a filamentous brown seaweed.

The French-led research group sequenced and analyzed the 214 million base pair E. siliculosus genome and also examined small RNA, methylation, and transposon patterns in the brown algae's genome. In the process, they identified a slew of signal transduction genes, tricked out light harvesting systems, and other genomic patterns that are providing clues to the organism's evolution and adaptation to the unforgiving rocky habitats found near coastlines.

"The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further," senior author Patrick Wincker, a researcher with Génoscope's Genomic Institute, and his colleagues wrote.

In order to gain a better understanding of brown algae — which have evolved separately from and are distantly related to green plants — Wincker and his team used paired-end sequencing to tackle the 214 million base genome of a haploid male E. siliculosus seaweed from the Ec 32 strain.

They also sequenced assessed genome methylation and transposon content in the seaweed and used the Illumina Genome Analyzer to characterize its small RNA repertoire.

Among the 16,256 protein-coding genes identified in the genome was a large family of genes coding for light harvesting complex proteins as well as clusters of light stress-related genes and pigment biosynthesis genes — a genomic toolkit that appears to suit the algae's adaptation to coastal waters where light conditions are variable.

The genome also contained genes that may help Ectocarpus withstand biotic stresses such as temperature and salinity changes in its habitat, the researchers noted, including potential antioxidants and genes coding for enzymes used in reactive oxygen species metabolism and the production of cell wall polysaccharides called alginates and fucans.

When they compared the newly sequenced genome to sequences from many other organisms, the researchers found that the seaweed appears to have expanded its receptor kinase collection since diverging from unicellular diatoms. Consequently, the receptor kinases present in Ectocarpus today appear to represent a monophyletic brown algal clade distinct from those in animals or green plants.

These and other genes, including some coding for integrin-like and ion channel proteins, were among those that the researchers highlighted as potentially having helped nudge the brown algal species toward multicellularity.

"Analysis of the Ectocarpus genome has revealed traces both of its ancient evolutionary past and of more recent events associated with the emergence of the brown algal lineage," the team concluded.

The researchers also noted that nearly a quarter of the brown algae's genome is comprised of repeat sequences, including DNA transposons, retrotransposons, and helitrons. Because small RNAs often mapped to the same parts of the genome as transposons, they speculated that these RNAs might help curb transposon activity in the genome, which appears to lack cytosine methylation mediated silencing.

In addition, the team turned up dozens of microRNAs in the genome, consistent with the idea that these sorts of small RNAs emerged early on in eukaryotic evolution.