Background: The walleye pollock (Theragra chalcogramma) and Norwegian pollock (T. finnmarchica) are confined to the North Pacific and North Atlantic Oceans, respectively, and considered as distinct species within the family Gadidae. We have determined the complete mtDNA nucleotide sequence of two specimens of Norwegian pollock and compared the sequences to that of 10 specimens of walleye pollock representing stocks from the Sea of Japan and the Bering Sea, 2 specimens of Atlantic cod (Gadus morhua), and 2 specimens of haddock (Melanogrammus aeglefinus).

Expression and processing of mitochondrial gene transcripts are fundamental to mitochondrial function, but information from early vertebrates like teleost fishes is essentially lacking. We have analyzed mitogenome sequences of ten codfishes (family Gadidae), and provide complete sequences from three new species (Saithe, Pollack and Blue whiting). Characterization of the mitochondrial mRNAs in Saithe and Atlantic cod identified a set of ten poly(A) transcripts, and six UAA stop codons are generated by posttranscriptional polyadenylation. Structural assessment of poly(A) sites is consistent with an RNaseP cleavage activity 5′ of tRNA acceptor-like stems. COI, ND5 and ND6 mRNAs were found to harbor 3′ UTRs with antisense potential extending into neighboring gene regions. While the 3′ UTR of COI mRNA is complementary to the tRNASer (UCN) and highly similar to that detected in human mitochondria, the ND5 and ND6 3′ UTRs appear more heterogenic. Deep sequencing confirms expression of all mitochondrial mRNAs and rRNAs, and provides information about the precise 5′ ends in mature transcripts. Our study supports an overall evolutionary conservation in mitochondrial RNA processing events among vertebrates, but reveals some unique 5′ and 3′ end characteristics in codfish mRNAs with implications to antisense regulation of gene expression.Electronic supplementary materialThe online version of this article (doi:10.1007/s00294-011-0338-2) contains supplementary material, which is available to authorized users.

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.

We have determined the complete mitochondrial genome sequences of the codWshes Arctogadus glacialis and Boreogadus saida (Order Gadiformes, Family Gadidae). The 16,644 bp and 16,745 bp mtDNAs, respectively, contain the same set of 37 structural genes found in all vertebrates analyzed so far. The gene organization is conserved compared to other Gadidae species, but with one notable exception. B. saida contains heteroplasmic rearrangement-mediated duplications that include the origin of light-strand replication and nearby tRNA genes. Examination of the mitochondrial control region of A. glacialis, B. saida, and four additional representative Gadidae genera identiWed a highly variable domain containing tandem repeat motifs in A. glacialis. Mitogenomic phylogeny based on the complete mitochondrial genome sequence, the concatenated protein-coding genes, and the derived protein sequences strongly supports a sister taxa aYliation of A. glacialis and B. saida.

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