A group of researchers at the Center for Mathematical Modeling (CMM) and the Center for the Genome Regulation (CGR) at the Universidad de Chile joined in an investigation about the genome of Atlantic salmon that was published on Monday, April 18 in Nature journal.
Alejandro Maass and Alex di Génova were part of the International Cooperation to Sequence the Atlantic Salmon Genome, with Canadian, Chilean, Norwegian, and American scientists. This group had already given its first results in 2014. That year, they publish the complete sequencing of this fish. The information published now is equally or more important. It analyzes the genome with its characteristics and peculiarities. This will give relevant information for the development of new technologies and products in direct benefit of the industry.
In the scientific field, this new work takes significant findings. Unlike many terrestrial vertebrate species, the Atlantic salmon genome presents an important and challenging feature: duplication. This means you have two versions of each functional or non-functional gene in their genome. This phenomenon is a product of a duplication produced millions of years ago.
This work contradicts the classical hypothesis about the inability to sustain over time two copies or versions of genes in a genome. The key is that duplicated copies were not lost in time, but adopted new functions. This allowed Atlantic salmon to adapt and create new functions. So, this genome represents a new and important paradigm. It gives information for comparative genomics studies to understand the process of genomic evolution in other species of fish.
Bioinformatics expertise
Scientists and public and private institutions from the four countries were involved in this research. Chile participated through Corfo, which called Alejandro Maass as scientific advisor. He, Patricia Iturra (Faculty of Medicine of the Universidad de Chile) and Rodrigo Vidal (Universidad de Santiago), joined the Chilean scientific committee of the study.
“Our contribution and expertise were in the bioinformatics area, which plays a crucial role in these complex projects to assemble organisms,” says Maass.
“All available algorithms were used to decipher the salmon,” recalls Di Génova. In total, the consortium used ten strategies to solve the genome of the fish. One of them took place in Chile, where Bruijn graphs and All-Paths method of assembly were used.
“This was possible thanks to the calculation capacity of Mathomics laboratory; ie we use our expertise bioinformatics developed for almost ten years working at CMM and CGR,” explained Maass, director of the lab.
James Yorke, a mathematician at University of Maryland and member of the scientific committee of Center for Mathematical Modeling was also incorporated into the research. He was contacted by Maass. His work on a new strategy for assembling complex genomes introducing mathematical ideas from symbolic dynamics to the traditional methods was key to ending the deciphering the Atlantic salmon.
The consortium generated eleven versions at the end. Two of them were created in the CMM-CGR, explained Di Génova: “The final version is a mixture of that we did, the JCVI’s version and that made by Maryland’s group, plus the genetic map provided by Norwegian.”
With the results published in 2014 and the information disclosed now, you can develop technology in the creation of vaccines and medical devices, plan genetic selection and develop and validate of new formulas or food products for the third Chilean exporter sector that ships more than 800 thousand tons per year -equivalent to US $ 4.3 billion- and employs nearly 60,000 people.
For Chilean researchers, meanwhile, new challenges in assembling complex genomes open. American entities asked them to work with Chinook salmon, which is as difficult to decipher as the Atlantic. In the same vein, the group collaborated in the production of a genotyping chip to analyze Chilean salmon families. This technology allows the genetic selection of fishes to improve their offspring, which previously made using traditional genetics. These are just two of the challenges that could be addressed.
“In the genomes of Chile, its people and its adapted to extreme conditions wildlife and flora, are hidden many secrets that have to do with the mechanisms used by nature -and possibly by humans- to improve his life,” concludes Maass. “If Chileans do not research that, nobody will do it for us.”
