title: Large-scale sequence analyses of Atlantic cod.
abstract: The Atlantic cod (Gadus morhua) is a key species in the North Atlantic ecosystem and commercial fisheries, with increasing aquacultural production in several countries. A Norwegian effort to sequence the complete 0.9Gbp genome by the 454 pyrosequencing technology has been initiated and is in progress. Here we review recent progress in large-scale sequence analyses of the nuclear genome, the mitochondrial genome and genome-wide microRNA identification in the Atlantic cod. The nuclear genome will be de novo sequenced with 25 times oversampling. A total of 120 mitochondrial genomes, sampled from several locations in the North Atlantic, are being completely sequenced by Sanger technology in a high-throughput pipeline. These sequences will be included in a new database for maternal marker reference of Atlantic cod diversity. High-throughput 454 sequencing, as well as Evolutionary Image Array (EvoArray) informatics, is used to investigate the complete set of expressed microRNAs and corresponding mRNA targets in various developmental stages and tissues. Information about microRNA profiles will be essential in the understanding of transcriptome complexity and regulation. Finally, developments and perspectives of Atlantic cod aquaculture are discussed in the light of next-generation high-throughput sequence technologies.
authors.affiliation: Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, Norway. Steinar. Johansen@uit.no
authors.forename: Steinar D
authors.initials: SD
authors.lastname: Johansen
authors.forename: Dag H
authors.initials: DH
authors.lastname: Coucheron
authors.forename: Morten
authors.initials: M
authors.lastname: Andreassen
authors.forename: Bård Ove
authors.initials: BO
authors.lastname: Karlsen
authors.forename: Tomasz
authors.initials: T
authors.lastname: Furmanek
authors.forename: Tor Erik
authors.initials: TE
authors.lastname: Jørgensen
authors.forename: Ase
authors.initials: A
authors.lastname: Emblem
authors.forename: Ragna
authors.initials: R
authors.lastname: Breines
authors.forename: Jarle T
authors.initials: JT
authors.lastname: Nordeide
authors.forename: Truls
authors.initials: T
authors.lastname: Moum
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Nederbragt
authors.forename: Nils C
authors.initials: NC
authors.lastname: Stenseth
authors.forename: Kjetill S
authors.initials: KS
authors.lastname: Jakobsen
mesh_terms: D000818:Animals; D001267:Atlantic Ocean; D001483:Base Sequence; D019143:Evolution, Molecular; D005398:Fisheries; D005544:Forecasting; D048389:Gadus morhua / Q000235:genetics*; D005819:Genetic Markers; D016678:Genome; D054629:Genome, Mitochondrial; D035683:MicroRNAs / Q000378:metabolism; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D005819:Genetic Markers; D035683:MicroRNAs