Avian mitogenome organisation

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

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.

Critical comments

In mitogenomics, there is a remarkable lack of conventions (Alexeyev, 2020): 

• 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). 

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 (largely) 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. Various types 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). 

Annotation of mitogenomes

For sequenced mitogenomes, all functional elements (i.e. tRNA genes, rRNA genes, protein-coding genes, and the control region) and intergenic transitions (i.e. spacers and overlaps) should be identified. For protein-coding genes, putative start and stop codons should be determined. Process and outcome of this analytical process are referred to as "annotation". It should be noted, however, that the exact limits of genes are often not recognisable with certainty (Slack et al., 2003). A limited comparison of spacers and overlaps is provided by Haring et al., 2001 and Zhao et al., 2022. 

Avian mitochondrial codon translation code (according to the Vertebrate Mitochondrial Code of NCBI Taxonomy, link). 

tRNA Leu-UUR 

The D-arm of tRNA Leu-UUR contains a conserved motif (5'-TGGCAGAGCCCGG-3') that may be involved in regulating the transcription of rRNA genes (Valverde et al, 1994; Guo et al., 2022). 

COI

In the avian ground pattern the protein-coding COI gene is characterised by the start codon GTG. It is retained as start codon in most taxa, but has independently been changed to ATG in some families (eg. in Accipitridae, Jacanidae, Meropidae, Strigidae, and several passeriform families). The gene comprises 1551 nucleotides, thus encoding 516 amino acids. AGG serves as stop codon. 

ATP8

This gene comprises either 165 bp or 168 bp, depending on the presence/absence of a 3 bp indel between positions 132 and 133 (corresponding to codons 44 and 45). The terminal region of the gene is characterised by a highly conserved 10 bp overlap with ATP6 (motifs: ATGAACCTAA or ATGAACTTAA). ATG serves as start and TAA as stop codon. 

ND3

The protein-coding gene ND3 is peculiar in having an extra nucleotide (mostly cytosine) at position 174. The insertion probably pertains to the avian ground pattern, but has been lost many times during avian evolution (Jing et al., 2020, suppl. 12). The extra base, however, appears not to be processed during translation as the downstream reading frame and amino-acid sequence are conserved due to a translational (+1)-frameshift (Mindell et al., 1998b; Al-Arab et al., 2017; Andreu-Sánchez et al., 2020). 

ND6

ND6 is the only protein-coding gene that is encoded on the secondary (-)-strand. It comprises 522 bp. ATG serves as start codon, and TAG (TAA, AGG) as stop codons. 

Control region

The control region, which typically has a length of about 1,150 bp, is the only extended non-coding region of the mitogenome. This region is also referred to as ‘D-loop’, although the true D-loop does neither span the entire control region nor is it found in all mtDNA molecules at any given time (Pereira et al., 2008; Nicholls & Minczuk, 2014). 

For descriptive purposes, Brown et al. (1986) first divided the control region into three domains, with a conserved central domain being flanked by highly variable domains on either side. The authors did not, however, define an exact boundary to separate domains 1 and 2 from each other. 

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