Mitogenome sequence variation in migratory and stationary ecotypes of North-east Atlantic cod.
Sequencing of mitochondrial gene fragments from specimens representing a wide range of geographical locations has indicated limited population structuring in Atlantic cod (Gadus morhua). We recently performed whole genome analysis based on next-generation sequencing of two pooled ecotype samples representing offshore migratory and inshore stationary cod from the North-east Atlantic Ocean. Here we report molecular features and variability of the 16.7kb mitogenome component that was collected from the datasets. These sequences represented more than 25 times coverage of each individual and more than 1100 times coverage of each ecotype sample. We estimated the mitogenome to have evolved 14 times more rapidly than the nuclear genome. Among the 365 single nucleotide polymorphism (SNP) sites identified, 121 were shared between ecotypes, and 151 and 93 were private within the migratory and stationary cod, respectively. We found 323 SNPs to be located in protein coding genes, of which 29 were non-synonymous. One synonymous site in ND2 was likely to be under positive selection. FST measurements indicated weak differentiation in ND1 and ND2 between ecotypes. We conclude that the Atlantic cod mitogenome and the nuclear genome apparently evolved by distinct evolutionary constraints, and that the reproductive isolation observed from whole genome analysis was not visible in the mtDNA sequences.
Department of Medical Biology - RNA Lab, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway; Marine Genomics Group, Faculty of Biosciences and Aquaculture, University of Nordland, N-8059 Bodø, Norway.
Bård O
BO
Karlsen
Department of Medical Biology - RNA Lab, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway.
Åse
Å
Emblem
Marine Genomics Group, Faculty of Biosciences and Aquaculture, University of Nordland, N-8059 Bodø, Norway.
Tor E
TE
Jørgensen
Marine Genomics Group, Faculty of Biosciences and Aquaculture, University of Nordland, N-8059 Bodø, Norway.
Kevin A
KA
Klingan
Marine Genomics Group, Faculty of Biosciences and Aquaculture, University of Nordland, N-8059 Bodø, Norway.
Jarle T
JT
Nordeide
Marine Genomics Group, Faculty of Biosciences and Aquaculture, University of Nordland, N-8059 Bodø, Norway.
Truls
T
Moum
Department of Medical Biology - RNA Lab, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway; Marine Genomics Group, Faculty of Biosciences and Aquaculture, University of Nordland, N-8059 Bodø, Norway. Electronic address: steinar.johansen@uit.no.
Steinar D
SD
Johansen
D000818:Animals; D001267:Atlantic Ocean; D001483:Base Sequence; D017753:Ecosystem; D019143:Evolution, Molecular; D048389:Gadus morhua / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population; D054629:Genome, Mitochondrial / Q000235:genetics*; D008969:Molecular Sequence Data; D009245:NADH Dehydrogenase / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D060047:Reproductive Isolation; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
D009245:NADH Dehydrogenase
Atlantic cod; Marine genomics; Population mitogenomics; SOLiD sequencing; mtDNA