**1. Introduction**

The mitochondrial genome (mitogenome) is highly conserved among vertebrates [1]. All species investigated to date contain mitogenomes encoding the same 37 canonical gene products, organized in a highly similar gene order in most species. Complete mitogenome sequences have been determined from almost 5000 vertebrate species, where about 50% is represented by the bony fishes [2].

The Atlantic cod (*Gadus morhua*) is a benthopelagic fish in the Gadidae family, belonging to the order of Gadiformes [3, 4]. The 16.7 kb circular mitogenome was one of the first to be

© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. © 2018 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

completely sequenced from a fish species [5–7]. Atlantic cod possesses the same mitogenome organization as most vertebrate species, including that of humans and vertebrate model sys-

Expanding the Coding Potential of Vertebrate Mitochondrial Genomes: Lesson Learned…

http://dx.doi.org/10.5772/intechopen.75883

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Among the canonical gene products encoded by the Atlantic cod mitogenome, 13 represent hydrophobic proteins essential for oxidative phosphorylation (OxPhos), two are ribosomal RNAs (rRNAs) of the mitochondrial ribosome, and 22 are transfer RNAs (tRNAs) necessary for mitochondrial translation. The OxPhos system consists of five large protein complexes embedded in the inner mitochondrial membrane. However, only 13 of the approximately 85

Both strands (H- and L-strands) have coding potential (**Figure 1A**). Most mitochondrial genes are encoded by the H-strand and include the small and large subunit rRNAs (mtSSU rRNA and mtLSU rRNA), 14 tRNAs, and 12 protein-coding genes. The L-strand, however, encodes only eight tRNAs and one protein. The control region (CR), located between the genes of tRNAPro and tRNAPhe, is the major noncoding region in the mitogenome and constitutes approximately 1000 bp in Atlantic cod [7, 9]. The CR harbors the genetic control elements for H-strand replication origin (OriH), the transcription initiation sites for H- and L-strands, as well as the displacement loop (D-loop) located between OriH and the termination associated sequence (TAS) [7, 9, 10]. Furthermore, a 30-bp spacer located between the genes of tRNAAsp and tRNACys contains the origin of L-strand synthesis. OriL appears functionally conserved in

Hallmarks of Atlantic cod mitogenomes are the noncoding intergenic T–P spacer, and the heteroplasmic tandem repeat (HTR) array at the 5′ domain of CR (**Figure 1A**). The 74-bp Atlantic cod T–P spacer [5, 13], located between the tRNAThr and tRNAPro genes, represents an evolutionary preserved feature present in all gadiform species [10, 13]. The T–P spacer is variable in sequence and size among gadiforms but still harbors two conserved 17-bp sequence motifs forming potential hairpin structures at the RNA level [10]. The HTR array consists of a 40-bp sequence motif usually present in two to five copies within an individual [5, 14, 15] and thus results in size heterogeneity and heteroplasmy of Atlantic cod mitogenomes. Here, we review recent developments in the characterization of Atlantic cod mitogenomes with focus on interindividual sequence variation, mitochondrial transcriptome, noncoding RNAs, and putative mitochondrial-derived peptides.

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

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

tems like mouse, rat, *Xenopus*, and zebrafish (**Figure 1A**).

most vertebrates [11, 12], including the Atlantic cod [5].

OxPhos proteins are encoded by the mitogenome (**Figure 1B**) [8].

**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 noncoding regions (gray). CR, control region; H1 and H2 , H-strand promoters; LSP, L-strand promoter; OH and OL, origins 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, except Q, A, N, C, Y, S1 , E, P, and ND6 (L-strand encoded). mtSSU and mtLSU, mitochondrial small- and large-subunit rRNA 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 subunits, belonging to complex I (blue), complex III (orange), complex IV (green), and complex V (yellow).

completely sequenced from a fish species [5–7]. Atlantic cod possesses the same mitogenome organization as most vertebrate species, including that of humans and vertebrate model systems like mouse, rat, *Xenopus*, and zebrafish (**Figure 1A**).

Among the canonical gene products encoded by the Atlantic cod mitogenome, 13 represent hydrophobic proteins essential for oxidative phosphorylation (OxPhos), two are ribosomal RNAs (rRNAs) of the mitochondrial ribosome, and 22 are transfer RNAs (tRNAs) necessary for mitochondrial translation. The OxPhos system consists of five large protein complexes embedded in the inner mitochondrial membrane. However, only 13 of the approximately 85 OxPhos proteins are encoded by the mitogenome (**Figure 1B**) [8].

Both strands (H- and L-strands) have coding potential (**Figure 1A**). Most mitochondrial genes are encoded by the H-strand and include the small and large subunit rRNAs (mtSSU rRNA and mtLSU rRNA), 14 tRNAs, and 12 protein-coding genes. The L-strand, however, encodes only eight tRNAs and one protein. The control region (CR), located between the genes of tRNAPro and tRNAPhe, is the major noncoding region in the mitogenome and constitutes approximately 1000 bp in Atlantic cod [7, 9]. The CR harbors the genetic control elements for H-strand replication origin (OriH), the transcription initiation sites for H- and L-strands, as well as the displacement loop (D-loop) located between OriH and the termination associated sequence (TAS) [7, 9, 10]. Furthermore, a 30-bp spacer located between the genes of tRNAAsp and tRNACys contains the origin of L-strand synthesis. OriL appears functionally conserved in most vertebrates [11, 12], including the Atlantic cod [5].

Hallmarks of Atlantic cod mitogenomes are the noncoding intergenic T–P spacer, and the heteroplasmic tandem repeat (HTR) array at the 5′ domain of CR (**Figure 1A**). The 74-bp Atlantic cod T–P spacer [5, 13], located between the tRNAThr and tRNAPro genes, represents an evolutionary preserved feature present in all gadiform species [10, 13]. The T–P spacer is variable in sequence and size among gadiforms but still harbors two conserved 17-bp sequence motifs forming potential hairpin structures at the RNA level [10]. The HTR array consists of a 40-bp sequence motif usually present in two to five copies within an individual [5, 14, 15] and thus results in size heterogeneity and heteroplasmy of Atlantic cod mitogenomes. Here, we review recent developments in the characterization of Atlantic cod mitogenomes with focus on interindividual sequence variation, mitochondrial transcriptome, noncoding RNAs, and putative mitochondrial-derived peptides.
