Avian mitogenome organisation 

In the avian ground pattern, the mitogenome contains 37 coding genes (two rRNA genes, 22 tRNA genes, and 13 protein-coding genes) and an elongate non-coding control region. In addition, an extended tandem duplication might have been present. This ancient pattern (except the tandem duplication) is typical for almost all metazoans (Bernt et al., 2014). 

Short mitochondrial-derived peptides like MOTS-c may also pertain to the ground pattern of birds (Shu et al., 2025). Even though the mini-gene is located in the mitogenome, translation happens in the cytoplasm. 

Compared to other vertebrates, in avian mitogenomes the positions of the adjacent gene clusters [CYB:T:P] and [ND6:E] are interchanged, with the derived gene order [CYB:T:P:ND6:E] representing an avian ground-pattern apomorphy (Montaña-Lozano et al., 2022). 

Mitochondrial gene map, depicting the putative ancestral avian pattern (not to scale). The tandem duplication (TD), extending between the non-coding control region (CR) and gene F, is shown separately as it is unclear whether it pertains to the avian ground pattern. When fully developed, the TD contains a pseudogene Ψ (a degenerate copy of CYB), four functional genes (T, P, ND6 and E), and an extended control region (Urantówka et al., 2020). Note: tRNA genes are depicted by their one-letter amino-acid code; red colour indicates genes that are encoded on the secondary (-) strand; spacers and overlaps are not considered.

Avian tandem duplication

Most avian mitogenomes are distinguished from typical vertebrate mitogenomes by the presence of a large tandem duplication comprising the control region and several adjacent genes (Urantówka et al., 2018, 2020, 2021; Mackiewicz et al., 2019). Dating back to Haring et al. (1999) this region is also referred to as “pseudo-control region”. Duplicated genes are often nearly identical to their counterpart, a phenomenon referred to as “sequence homogenisation” or “concerted evolution” (Cadahía et al., 2009; Eberhard et al., 2001; Kim et al.,  2021; Morris-Pocock et al., 2010; Urantówka et al., 2021). The molecular mechanism underlying this phenomenon is unknown. 

In Galloanserae, tandem duplications are absent throughout. It is unclear, however, whether the lack is primary or secondary. Although the presence of a tandem duplication is a ground-pattern trait of most avian orders (Mackiewicz et al., 2019), there is a considerable amount of homoplasy in the observed configurations. Some authors refer to pseudogenes simply as long intergenic spacers (e.g. Bai et al., 2023). 

Various types of tandem duplications may be distinguished: 

Schematic map of the original tandem duplication (type 0) and variously derived configurations (types 1-7). The control region of copy 1 was lost in moa, Dinornithiformes, recently extinct palaeognaths from New Zealand (type 7). 

Retaining hallmarks of their endosymbiotic ancestry, mitochondria use a genetic code distinct from that of the nucleus and cytosol, and their translation proceeds on uniquely specialized mitochondrial ribosomes. 

DNA-level mitochondrial codon translation code (according to the Vertebrate Mitochondrial Code of NCBI Taxonomy). At RNA-level, the nucleotide T is replaced by U. (link) 

Critical comments

In mitogenomics, there is an obvious lack of conventions (Alexeyev, 2020), e.g.:

There is no unequivocal assignment of strands. Historically, the strand with the lower G+T content was referred to as (L)-strand (Anderson et al., 1981). However, present-day strand assignments in vertebrates do not comply with the original definition (Barroso Lima & Prosdocimi, 2017; Alexeyev, 2020). Recommendation: to avoid confusion, the strands should be distinguished by the relative number of genes contained, with the (+) strand being the primary or main coding strand containing more genes than the secondary (–) strand (Taanman 1999, fig.1; Gissi et al., 2008; Lima & Prosdocimi, 2017). [In insects, the complementary strands are referred to as minority and majority strand, respectively]. 

Circular maps may be oriented with functional elements (i.e. genes and control region) arranged either clockwise or counter-clockwise (Alexeyev, 2020). Recommendation: circular maps should always be displayed in clockwise orientation. 

Circular maps may display any gene or the control region at the top (12 o’clock) position. Recommendation: circular maps should display gene F (the DNA template for tRNA Phe) at the top center.

Annotations may start with any gene or the control region; they can even start within the control region (e.g. in human mitochondrial annotations). Recommendation: vertebrate annotations should start with gene F and have the control region at the end (see e.g. Montaña-Lozano et al., 2022, Fig. 3). 

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