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. 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).
Circular map depicting the putative ancestral avian mitogenome (not to scale). The tandem duplication (TD), extending between the non-coding control region (CR) and gene F, is shown separately as it is absent in numerous bird taxa. 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 that the corresponding genes are encoded on the reverse (-) strand.
In mitogenomics, there is a remarkable lack of conventions (Alexeyev, 2020):
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 whether the lack is primary or secondary. Although the presence of a tandem duplication is a putative 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). CR 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 comparison of spacers and overlaps is provided by Haring et al., 2001.
Mitogenome annotation of the Western Capercaillie, Tetrao urogallus (after Aleix-Mata et al., 2019). The incomplete stop codon T-- becomes completed upon polyadenylation. Genes located on the (-) strand are represented in red. In the original study, the annotation started with the control region, not with gene F (tRNA Phe), so I had to adjust the nucleotide positions.
The D-arm of tRNA Leu-UUR contains a highly conserved transcription termination factor (5'-TGGCAGAGCCCGG-3') that may be involved in regulating the transcription of rRNA genes (Valverde et al, 1994; Guo et al., 2022).
The protein-coding gene ND3 is peculiar in having an extra nucleotide (mostly cytosine) at position 174. Its presence probably pertains to the avian ground pattern, but it 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).
The control region (CR), 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 a highly variable domain on either side. The authors did not, however, define an exact boundary to separate domain 1 from domain 2.
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