RIBOSOMAL RNA

Lin, Chu-Yin, Lin, Wen-Wen & Kao, Hsiao-Wei, 2012, The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids, Zoological Journal of the Linnean Society 165 (3), pp. 521-533 : 527

RIBOSOMAL RNA AND TRANSFER RNA GENES

As is typical in vertebrates, the mackerel icefish mt genome contains two rRNAs: a small (12S) and a large subunit (16S) of rRNA ( Table 1; Fig. 3 ). The 12S rRNA is 946 bp and is located between tRNAPhe (F) and tRNAVa l (V). The 16S rRNA is 1691 bp and is located between tRNAVal and tRNALeu(UUR) (L).

Unlike a typical vertebrate genome, which contains 22 tRNA genes ( Lee & Kocher, 1995; Boore, Macey & Medina, 2005), 24 tRNA genes were found in the mackerel icefish mt genome. It has two identical tRNAPro (P) before the first and second control regions, and two identical tRNAGlu behind the first and second ND6. The transcriptional polarity of these duplicated and translocated tRNA genes has not changed. The lengths of all tRNA genes ranged from 67–74 bp. Each tRNA gene can fold into a clover-leaf secondary structure. The aminoacyl stem was 7 bp long with some noncomplementary pairs, such as A- C and T- C. The TYC (Y refers to pseudouridine) stem was generally 5 bp long, except for tRNALys and tRNAVal, which were shorter than 5 bp. Most dihydrouridine (DHU) stems were 4 bp long but some were 3 bp. The majority of anticodon stems were 5 bp but some were shorter than 5 bp.

Figures

Figure 3. Map of the mackerel icefish mitochondrial (mt) genome as a circular diagram. The map represents the mt genome of a type-1 individual in which ND6 and tRNAGlu were transposed to a position between tRNAThr and tRNAPro flanked by intergenic spacers (UN3 and UN4), and the ND6- to -CR segment was duplicated once. Fourteen protein-coding genes, two rRNA genes, and noncoding regions are labelled with abbreviations. Twenty-four tRNA genes are shown by a one-letter amino acid code. Different codons used by each of tRNALeu and tRNASer are shown in parentheses. Genes transcribed from the heavy strand and light strand are respectively presented outside and inside the circle. Heavy- and light-strand replication origins are represented by OH and OL, respectively. Abbreviations: 12S, 12S ribosomal RNA; 16S, 16S ribosomal RNA; A, tRNAAla; ATP, ATP synthase; C, tRNACys; CO, cytochrome oxidase; Cyt b, cytochrome b; D, tRNAAsp; E, tRNAGlu; F, tRNAPhe; G, tRNAGly; H, tRNAHis; I, tRNAIle; K, tRNALys; L, tRNALeu; M, tRNAMet; N, tRNAAsn; ND, nicotiamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; Q, tRNAGln; R, tRNAArg; S, tRNASer; T, tRNAThr; V, tRNAVal; W, tRNATrp; Y, tRNATyr.