Complete mitochondrial genome sequences of the Arctic Ocean codfishes Arctogadus glacialis and Boreogadus saida reveal oriL and tRNA gene duplications

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A mitogenomic approach to the taxonomy of pollocks: Theragra chalcogramma and T. finnmarchica represent one single species

<p>Abstract</p> <p>Background</p> <p>The walleye pollock (<it>Theragra chalcogramma</it>) and Norwegian pollock (<it>T. finnmarchica</it>) 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 (<it>Gadus morhua</it>), and 2 specimens of haddock (<it>Melanogrammus aeglefinus</it>).</p> <p>Results</p> <p>A total number of 204 variable positions were identified among the 12 pollock specimens, but no specific substitution pattern could be identified between the walleye and Norwegian pollocks. Phylogenetic analysis using 16.500 homologous mtDNA nucleotide positions clearly identify the Norwegian pollock within the walleye pollock species cluster. Furthermore, the Norwegian pollock sequences were most similar to mitochondrial genotypes present in walleye pollock specimens from the Sea of Japan, an observation supported both by neighbor-joining, maximum parsimony, and maximum likelihood analyses.</p> <p>Conclusion</p> <p>We infer that walleye pollock and Norwegian pollock represent one single species and that Norwegian pollock has been recently introduced from the Pacific to the Atlantic Oceans.</p

Characterization of mitochondrial mRNAs in codfish reveals unique features compared to mammals

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

Complete mitochondrial genome sequences of the Arctic Ocean codfishes Arctogadus glacialis and Boreogadus saida reveal oriL and tRNA gene duplications

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

A mitogenomic approach to the taxonomy of pollocks: and represent one single species-0

<p><b>Copyright information:</b></p><p>Taken from "A mitogenomic approach to the taxonomy of pollocks: and represent one single species"</p><p>BMC Evolutionary Biology 2007;7():86-86.</p><p>Published online 7 Jun 2007</p><p>PMCID:PMC1894972.</p><p></p>genes (indicated by the standard one-letter symbols for amino acid below the diagram), are encoded by the H-strand. Abbreviations: SSU and LSU, mitochondrial small- and large-subunit ribosomal RNA genes; ND1-6, NADH dehydrogenase subunit 1 to 6; COI-III, cytochrome c oxidase subunit I to III; A6 and A8, ATPase subunit 6 and 8; Cyt b, cytochrome b; OH and OL, origin of H-strand and L-strand replication; CR, control region containing the D-loop. () Distribution of variable sites in pollock mtDNA numbered according to the sequence of the Norwegian pollock Tf 19 (AM489718, Table 1). The position 834+ in SSU rDNA indicates nucleotide insertion between positions 834 and 835 in Tf 19. The variable sites were aligned to that of Tf 19. Identical sites are indicated by dots and deletions by dashes. The proposed diagnostic single nucleotide polymorphism at ND4 of Sea of Japan and Bering Sea pollocks [14] is boxed at position 11578

A mitogenomic approach to the taxonomy of pollocks: and represent one single species-1

<p><b>Copyright information:</b></p><p>Taken from "A mitogenomic approach to the taxonomy of pollocks: and represent one single species"</p><p>BMC Evolutionary Biology 2007;7():86-86.</p><p>Published online 7 Jun 2007</p><p>PMCID:PMC1894972.</p><p></p> the TMV+I+G evolutionary model. Trees constructed by neighbour-joining (NJ, Jukes-Cantor substitution model) and maximum parsimony (MP, heuristic searches) displayed almost identical topologies with the ML tree. Bootstrap values (2000 replications) are shown at the branches (ML/MP/NJ). sequences are boxed. () Tree presenting the topology (same ML tree as in A) with bootstrap values (2000 replications) over 50% at the branches (ML/MP/NJ). The relationship between and the two speciemens J3 and J4 of from the Sea of Japan are boxed

Large-scale sequence analyses of Atlantic cod

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 0.9 Gbp 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

Mitochondrial genome variation of Atlantic cod

Objective: The objective of this study was to analyse intraspecifc sequence variation of Atlantic cod mitochondrial DNA, based on a comprehensive collection of completely sequenced mitochondrial genomes. Results: We determined the complete mitochondrial DNA sequence of 124 cod specimens from the eastern and western part of the species’ distribution range in the North Atlantic Ocean. All specimens harboured a unique mitochondrial DNA haplotype. Nine hundred and ffty-two polymorphic sites were identifed, including 109 non-synonymous sites within protein coding regions. Eighteen variable sites were identifed as indels, exclusively distributed in structural RNA genes and non-coding regions. Phylogeographic analyses based on 156 available cod mitochondrial genomes did not reveal a clear structure. There was a lack of mitochondrial genetic diferentiation between two ecotypes of cod in the eastern North Atlantic, but eastern and western cod were diferentiated and mitochondrial genome diversity was higher in the eastern than the western Atlantic, suggesting deviating population histories. The geographic distribution of mitochondrial genome variation seems to be governed by demographic processes and gene fow among ecotypes that are otherwise characterized by localized genomic divergence associated with chromosomal inversions

MOESM5 of Mitochondrial genome variation of Atlantic cod

Additional file 5: Figure S1. Complete secondary structure diagram of Atlantic cod mitochondrial small subunit rRNA. Variable positions among the 124 complete Atlantic cod mitogenomes are indicated, as well as frequency (%) and variable sites (red boxes)