**2. Sequence variation among Atlantic cod mitochondrial genomes**

**Figure 1.** The Atlantic cod mitochondrial genome. (A) Circular map presenting gene content and organization. The mitochondrial genome harbors 13 protein-coding genes (light blue), 2 rRNA genes (yellow), 22 tRNA genes (red), and

of heavy- and light-strand replication, respectively; HTR, heteroplasmic tandem repeat; T–P spacer, intergenic noncoding spacer. tRNA genes are indicated by the standard one-letter symbols for amino acids. All genes are H-strand encoded,

genes; ND1–ND6, NADH dehydrogenase subunit 1–6; COI–COIII, cytochrome c oxidase subunit I–III; Cyt b, cytochrome b; ATP6 and ATP8, ATPase subunit 6 and 8. (B) Schematic view of the OxPhos complexes embedded in the inner mitochondrial membrane. ATP is generated by oxidative phosphorylation. The mitochondrial genome encodes 13 of the approximately 85

, E, P, and ND6 (L-strand encoded). mtSSU and mtLSU, mitochondrial small- and large-subunit rRNA

, H-strand promoters; LSP, L-strand promoter; OH and OL, origins

and H2

subunits, belonging to complex I (blue), complex III (orange), complex IV (green), and complex V (yellow).

noncoding regions (gray). CR, control region; H1

except Q, A, N, C, Y, S1

96 Mitochondrial DNA - New Insights

Complete mitogenome sequences have been obtained from approximately 200 specimens representing major ecotypes and geographic locations of Atlantic cod. In one study, based on SOLiD deep sequencing, we performed pooled sequencing of 44 specimens from each of the migratory northeast arctic cod (NA) and the stationary Norwegian coastal cod (NC) [16]. The sequencing represented more than 1100 times mitogenome coverage of each ecotype and 25 times coverage of each individual. We found a total of 365 SNP loci in the dataset, where 121 SNPs were shared between the ecotypes. One hundred fifty-one SNPs and ninety-three SNPs were specific to NA and NC cod, respectively. From the dataset we determined the mitochondrial substitution rate to be 14 times higher compared to that of the nuclear genome [16, 17].

More recently we analyzed 156 Atlantic cod mitogenomes at the individual level [18], including 32 specimens previously reported by Carr and Marshall [19]. We found 1034 SNPs in total among the sequences, which were not evenly distributed throughout the mitogenome. The ND2 gene (Complex I) and the COII gene (Complex IV) were the least and most conserved, respectively, among the protein-coding genes. Furthermore, rRNA and tRNA genes showed a significantly lower density of overall SNPs per site compared to protein-coding genes. Thus, the Atlantic cod mitogenome follows a similar pattern of conservation as seen for other vertebrates like zebrafish and human [20–23] and corroborates the observation that mutation rate constrains in vertebrate mitogenomes appear linked to the position of genes in relation to OriH and OriH [24, 25].

The noncoding regions of the Atlantic cod mitogenome showed a mosaic pattern of sequence conservation. Whereas the OriL and the central domain of CR were almost invariant among specimens, the T–P spacer and 5′ domain of CR contain significant sequence variation [7, 10, 13, 18]. The 74-bp T–P spacer was found to contain 16 variable sites and 26 haplotypes among 225 specimens assessed, including a 29-bp sequence duplication in three individuals [10]. Similarly, the 5′ domain of CR was the most variable region within the mitochondrial genome (more than three times that of average substitution rate). The elevated sequence variation was due to hot-spot substitution sites, homopolymeric heterogeneity, and the HTR array [18].
