Norwegian Team Completes Cod Genome
Lex Nederbragt and Kjetill S. Jakobsen in front of the machine that they use in their analysis. During one afternoon, the machine can read 500 million bases, which appears as dots on the computer screen. Photo: Elin Fugelsnes.
Scientist from a consortium of Norwegian marine and aquaculture institutions has announced this week that they have generated the first ever draft sequence and assembly of the Atlantic cod genome.
The results, presented at the GenoFisk meeting in Oslo, Norway, include a high-quality genome assembly and preliminary annotation of the fish species, completed using only whole genome shotgun and paired-end data generated by the Genome Sequencer FLX System from 454 Life Sciences, a Roche Company.
By using the long-read GS FLX Titanium Series and the system’s accompanying GS Assembler software, the consortium was able to produce a draft assembly at a fraction of the time and cost of traditional sequencing methods. The researchers hope to use this information and the fully annotated genome to identify genes and genetic variations underlying important traits for cod aquaculture.
The cod farming industry is of growing importance in northern latitude countries such as Norway due to the fish’s high demand, declining wild stock, and relatively fast growth at low temperatures.
In 2008, the Norwegian Centre for Ecological and Evolutionary Synthesis (CEES) was awarded the funds to complete the sequencing of the 0.9 Gb cod genome and the consortium turned to 454 Life Science to take on the project.
“The cod is a large and complex eukaryote with a number of highly repetitive regions in its genome. We understood the value of long 400-base sequencing reads to get the quality of assembly required to achieve our research goals. In the end, we were able to generate 25x genome coverage and an assembly with few, large scaffolds, a major achievement given the diploid and non-inbred nature of our DNA source,” explained Kjetill Jakobsen, Professor at the University of Oslo (UiO) and consortium leader.
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Also read “Racing for the cod genome” on Forskningsradet.no
