NEW YORK (GenomeWeb News) – Roche today said that a Norwegian consortium has completed the first Atlantic cod draft genome and assembly.
The team, which presented their research at the recent GenoFisk meeting in Oslo, used whole genome shotgun sequencing and paired end sequencing with the Roche 454 FLX Titanium platform to get about 25 times coverage of the highly repetitive 0.9 gigabase cod genome. They have since assembled and done preliminary annotation for a high quality version of the genome, made up of a few large scaffolds.
GWDN's sister publication In Sequence reported in June that members of the cod genome consortium also planned to use some Sanger sequencing to aid in the cod genome assembly.
"A preliminary transcriptome survey revealed that 95 percent of all sequenced transcripts are found in the current version of the assembly, confirming the quality of these results," University of Oslo researcher Kjetill Jakobsen, who led the consortium, said in a statement. "With this project, we have made significant steps towards the creation of a highly annotated reference genome that can be mined for genes and genetic variations associated with important traits for cod aquaculture."
With a draft version of the genome in hand, the researchers will now begin applying information from the cod genome to better understand the fish's biology and find genetic variants related to economically important cod traits, such as temperature tolerance and growth following cod harvesting.
The team reportedly plans to do cod transcriptome sequencing, which is expected to aid in further genome annotation, as well as genetic evaluations of wild cod stocks.