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JGI, Collaborators Sequence Pennate Diatom Genome

NEW YORK (GenomeWeb News) – Scientists reported today that they have sequenced the genome of Phaeodactylum tricornutum, a pennate diatom.
An international team of researchers led by investigators at the US Department of Energy’s Joint Genome Institute, sequenced the P. tricornutum genome and then compared it to the genome of another sequenced diatom called Thalassiosira pseudonana. Their findings, appearing online today in Nature, reveal just how distinct the two diatoms are and provide new clues about diatom evolution and the nature of diatom diversity.
“These organisms represent a veritable melting pot of traits — a hybrid of genetic mechanisms contributed by ancestral lineages of plants, animals, and bacteria, and optimized over the relatively short evolutionary timeframe of 180 million years since they first appeared,” lead author Chris Bowler, a researcher affiliated with Paris’ Ecole Normale Supérieure and the Stazione Zoologica ‘Anton Dohrn’ in Naples, said in a statement.
Diatoms are tiny algae encased in silica (glass) shells that share features with both plants and animals. The organisms are separated into two main groups based on their structure and biology. Centric diatoms are usually disc shaped, while pennate diatoms come in other shapes and generally exhibit bilateral symmetry.
Based on fossil evidence, researchers believe pennate diatoms diverged much more recently than centric diatoms. But even though they are evolutionarily “younger,” these pennate diatoms are incredibly diverse.
In 2004, researchers from JGI and elsewhere sequenced the genome of a centric marine diatom called T. pseudonana. For the latest paper, the researchers sequenced the genome of P. tricornutum, using whole genome shotgun sequencing. They also used information gleaned from more than 130,000 expressed sequence tags to help characterize the genes and gene functions in this pennate diatom.
Their results suggest that the roughly 27.4 million base P. tricornutum genome contains an estimated 10,402 genes — fewer than the 11,776 found in the centric diatom T. pseudonana. And while about 57 percent of the P. tricornutum genes resemble those in T. pseudonana, about 40 percent of its genes are distinct.
In addition, P. tricornutum contains more species-specific gene families than T. pseudonana, a finding that the researchers suspect may reflect specialized pennate diatom functions.
Interestingly, researchers found that diatom-specific genes are evolving faster in both diatom genomes than other genes. Both diatoms also contain gene families that are expanded compared to other eukaryote genomes. For instance, both P. tricornutum and T. pseudonana contain an abundance of genes involved in polyamine metabolism — an expansion that may be related to the organisms’ ability to produce silica.
By identifying these and other cell wall silicification genes, the researchers may eventually understand how diatoms create glass at ambient temperature and pressure. “If we can learn how they do it, we could open up all kinds of new nanotechnologies,” Bowler said, “like for building miniature silicon chips or for biomedical applications.”
The team also uncovered evidence of extensive horizontal gene transfer between diatoms and other organisms. For instance, the P. tricornutum genome contained 171 genes resembling those found in red algae as well as 587 genes that clustered with bacteria-only clades. More than half of these bacterial genes were found in both P. tricornutum and T. pseudonana, while 42 percent appeared exclusively in P. tricornutum.
Overall, the results hint at extensive horizontal gene transfer between diatoms and bacteria as well as proteobacteria, cyanobacteria, and archea. These transfers seem to have helped diatoms acquire genes involved in metabolic processes such as organic carbon and nitrogen use, along with other genes involved in urea cycling, polyamine metabolism, cell wall formation, and other processes.
“Our findings show that gene transfer between diatoms and other organisms has been extremely common, making diatoms ‘transgenic by nature,’” Bowler said.
Although the team’s conclusions are based on just a few genome sequences, the results so far suggest that gene transfer between bacteria and diatoms may have occurred often, contributing to diatom evolution. Meanwhile, they noted, genome rearrangements and domain recombinations may have led to the development of diatom-specific genes.
“This study gets us closer to explaining the dramatic diversity across the genera of diatoms, morphologically, behaviorally, but we still haven’t yet explained all the differences conferred by the genes contributed by other taxa,” senior author Igor Grigoriev, a JGI researcher, said in a statement.
In the future, the researchers hope to delve even deeper into diatom genome functions. For instance, Bowler and his team are interested in understanding how diatoms use iron — insights that could have implications for carbon sequestration, since iron is a limiting nutrient in many marine environments. Some have suggested that seeding marine environments with iron could induce algal and diatom blooms that ultimately trap carbon deep beneath the sea.

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