The avian mitogenome contains two rRNA genes, MT-RNR1 and MT-RNR2, coding for the mito-ribosomal 12S rRNA and 16S rRNA components, respectively. [The standard symbols for vertebrate genes follow the HUGO (Human Genome Organisation) Gene Nomenclature Committee (link)]

MT-RNR1

• tRNA Phe (F) connection: 1 bp overlap (A)
• Length: variable (965-995 bp)
• Indels: numerous
• tRNA Val (V) connection: usually none, sometimes 1 bp spacer (A, T, C)

The mitochondrial 12S rRNA exhibits numerous hypervariable regions of varying length. Due to the co-occurrence of indels, these regions cannot be reliably aligned and must be excluded from phylogenetic analyses. 

Secondary structure of the mitochondrial 12S rRNA ascribed to the reconstructed ground pattern of Galliformes (comprising 966 nucleotides). Following the seminal paper of de los Monteros (2003), the rRNA strand has been broken down into four domains (Domains I-IV) and 40 stems (S1-40). Stems are numbered in sequential order from the 5' to 3' terminal ends. The backbone of the depicted graphic has been created via the online platform R2DT. (link)

MT-RNR2

• tRNA Val (F) connection: 0-2 bp overlaps, or 0-2 bp spacers (?)
• Length: variable (1593-1625 bp)
• Indels: numerous
• tRNA Leu-UUR (L1) connection: 0-2 bp spacer (?)

Comment: The mitochondrial 16S rRNA exhibits numerous hypervariable regions of varying length. Due to the co-occurrence of indels, these regions cannot be reliably aligned and therefore must be excluded from phylogenetic analyses. 

References

Bi D, Ding H, Wang Q, Jiang L, Lu W, Wu X, Zhu R, Zeng J, Zhou S, Yang X, and Kan X (2019), Two new mitogenomes of Picidae (Aves, Piciformes): Sequence, structure and phylogenetic analyses, Int. J. Biol. Macromol. 133, 683-692. (abstract)

Chen H, Chen Y, Wang Z, Wu D, Chen P, and Chen Y (2024), The complete mitochondrial genome of the Siberian Scoter Melanitta stejnegeri and its phylogenetic relationship in Anseriformes, Int. J. Mol. Sci., 25, e:10181. (free pdf)

de los Monteros AE (2003), Models of the primary and secondary structure for the 12S rRNA of birds: a guideline for sequence alignment, DNA Sequence 14, 241-256. (abstract)

Han S, Ding H, Peng H, Dai C, Zhang S, Yang J, Gao J, and Kan X (2024), Sturnidae sensu lato mitogenomics: novel insights into codon aversion, selection, and phylogeny, Animals 14, e:2777. (free pdf)

Houde P, Cooper A, Leslie E, Strand A, and Montaño GA (1997), Phylogeny and evolution of 12S rDNA in Gruiformes (Aves), in: Avian Molecular Evolution and Systematics (Mindell DP, ed.), chapter 5, pp. 121-158. Academic Press. (abstract)

Li XJ, Huang Y, and Lei FM (2014), Complete mitochondrial genome sequence of Bonasa sewerzowi (Galliformes: Phasianidae) and phylogenetic analysis, Zool. Syst. 39, 358-371. (free pdf)

Li F, Niu G, Du R, Wan K, Smith DR, Wei M, and Shi H (2025), Refining the vertebrate mitochondrial 12S rRNA secondary structure by comparative analysis, Integr. Zool. (pdf)

Raposo do Amaral F, Sheldon FH, and Wajntal A (2010), Towards an assessment of character interdependence in avian RNA phylogenetics: A general secondary structure model for the avian mitochondrial 16S rRNA, Mol. Phylogenet. Evol. 56, 498-506. (free viewing)

Shu X, Liu J, Xu B, Wang H, Liu L, Zheng X, and Chen J (2025), Characterization of the avian mitochondrial-derived peptide MOTS-c and its potential role as a metabolic regulator, Animals 15, e:2230. (free pdf)

Yang C, Lei FM, and Huang Y (2010), Sequencing and analysis of the complete mitochondrial genome of Pseudopodoces humilis (Aves, Paridae), Zool. Res. 31, 333-344. (free pdf) [in Chinese]

Yang L, Tan Z, Wang D, Xue L, Guan MX, Huang T, and Li R (2014), Species identification through mitochondrial RNA genetic analysis, Sci. Rep. 4, e;4089. (free pdf)

Zhou T, Zhou F, Yao Y, Xie M, Ni Q, Zhang M, and Xu H (2022), Comparative analysis of the complete mitochondrial genomes of related species of Chrysolophus amherstiae and Chrysolophus pictus, Mitochondrial DNA Part B Resour. 7, 144-152. (free pdf)