Genomics

Decrypting Duplication

The genome of the Paramecium–a famous example of unicellular organisms–has been decrypted and is now shedding light on long speculated theories concerning evolutionary biology.

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© H. Raguet/CNRS Photothèque

The sequencing of the Paramecium genome was conducted at the Genoscope (Evry, France).

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Paramecia are microscopic unicellular organisms that live in fresh water, where they feed on bacteria and decaying organic matter. Because they are easily cultivated and because the cell is relatively large, they have long been a model for investigating cellular organization and heredity. Four years ago, laboratories studying paramecia in France, Germany, and Poland combined their efforts into Paramecium Genomics, a European research group (GDRE), promoted and financially supported by CNRS. On the strength of its collaborative structure, the group convinced Genoscope, the French National Sequencing Center, to decrypt the genome of the Paramecium tetraurelia.

“This international collaboration was one of the persuasive arguments in convincing Genoscope that their data would lead to something concrete rather than just end up sitting in a drawer,” relates CNRS researcher Jean Cohen.¹

The two organizations have now sequenced and annotated the Paramecium genome, which, they discovered, is made up of 40,000 genes–nearly twice the number of genes in humans. Their findings, published in the November 9th issue of Nature,² indicate that this incredible heritage is the result of at least three duplications of the organism's entire genome, occurring over a few hundred million years.

Based on the study of other species, researchers have long alleged that whole genome duplications–during which all genes are doubled, giving rise to twin genes–could be responsible for major evolutionary transitions. But because most duplications lead to unstable cells, and because they often trigger genetic recombinations, it has been difficult to provide evidence of their occurrence. As a result, understanding the role of duplications in evolution has been mostly speculative.

“For some unknown reason, the last three duplications inside the Paramecium genome led to very few genetic recombinations; it was therefore easy to identify genetic pairs. So the Genoscope team was able to recreate what these ancestral chromosomes theoretically looked like,” explains Cohen.

The team thus verified a previously unconfirmed theory suggesting that, after duplication, genes lose their copies gradually rather than abruptly, a process that can take millions of years. The researchers also realized that the ultimate objective of keeping two copies of the same gene is to maintain a balance inside the cell, rather than to trigger the emergence of new functions.

“You often hear that duplicated genes are a source of diversity. It's true; when you have two copies of a gene, one can retain its initial function while the other may have more liberty to acquire new functions,” comments Cohen. “This certainly occurs, but it's infrequent. Maintaining a balance is the prime goal.”

Cohen gives the example of proteins involved in multi-subunit complexes or in a metabolic pathway. “If one protein is expressed by fewer genes than the others, the complex or the sequence of reactions might not function properly,” he clarifies.

Another striking result is the confirmation that these duplications can lead to an explosive creation of new species. According to the authors, the last duplication was immediately followed by the creation of 15 new species of Paramecium. The Paramecium Genomics laboratories are now exploring the functions of genes that remained doubled throughout all three duplications.

“We hope this will lead to general rules that can apply to other species,” remarks Cohen. “What we understand in a simple cell can often be extrapolated to much more complex organisms –fungus, plants, and even humans.”

Clémentine Wallace