In a study published online this week in Nature, an international team of researchers report the first complete sequence of the Atlantic cod genome and an unexpected discovery of the unique immune system of this important fish species.
Led by researchers from the University of Oslo, a consortium of Norwegian universities and aquaculture institutions turned to 454 Sequencing Systems from Roche (SIX: RO, ROG; OTCQX: RHHBY) to obtain a comprehensive de novo assembly of the highly complex cod genome at a fraction of the time and cost of traditional sequencing methods. Strikingly, the researchers found that Atlantic cod has lost genes that are essential for a critical component of its immune system. The findings call to question fundamental ideas on the evolution of the immune system in all vertebrate species.
“The overall aim of this initiative was to obtain the entire genome sequence of the Atlantic cod utilizing cutting edge sequencing technology,” said study lead Professor Kjetill S. Jakobsen from the Centre for Ecological and Evolutionary Synthesis, University of Oslo. “We had not expected to find that the Atlantic cod had lost such a crucial component of its immune system.” Despite lacking genes essential for the function of the major histocompatibility (MHC) II pathway, the Atlantic cod appears to function normally and relies on an increased number of MHC I genes and Toll-like receptor genes for its immune response. This finding will potentially allow for the development of more targeted vaccine development – aiding disease management and the process of domestication of Atlantic cod.
The complete genome sequence was generated exclusively using 454 Sequencing Systems with a combination of GS FLX Titanium shotgun, 3 kb, 8 kb and 20 kb paired end reads. In the end, the researchers obtained 40x genome coverage and generated a high-quality draft assembly using the 454 GS De Novo Assembler Software (Newbler). The consortium plans to use the assembly and fully annotated genome to identify genes and genetic variations associated with important traits for cod aquaculture and wild stocks.
“Our study shows quite clearly that this approach solely using 454 Systems gives excellent results for large genome sequencing and de novo assembly projects. We found that the long reads were essential to obtaining the desired quality of results to achieve our research goals,” explained Jakobsen. “Our next step is to improve the cod assembly using read length improvements offered by the recently launched GS FLX+ System. We believe the extended 800 bp reads will be particularly powerful for transcriptome sequencing and further refinement of our cod genome annotation.”
“This is another example of how 454 Sequencing Systems have helped a group make the transition from sequence to assembly to biological understanding,” said James Knight, R&D Fellow at 454 Life Sciences. “With our long, accurate reads and optimized assembly software, laboratory of any size can effectively carry out this type of large-scale project.”
Headquartered in Basel, Switzerland, Roche is a leader in research-focused healthcare with combined strengths in pharmaceuticals and diagnostics. Roche is the world’s largest biotech company with truly differentiated medicines in oncology, virology, inflammation, metabolism and CNS. Roche is also the world leader in in-vitro diagnostics, tissue-based cancer diagnostics and a pioneer in diabetes management. Roche’s personalised healthcare strategy aims at providing medicines and diagnostic tools that enable tangible improvements in the health, quality of life and survival of patients. In 2010, Roche had over 80’000 employees worldwide and invested over 9 billion Swiss francs in R&D. The Group posted sales of 47.5 billion Swiss francs. Genentech, United States, is a wholly owned member of the Roche Group. Roche has a majority stake in Chugai Pharmaceutical, Japan.