Descriptive mitogenomics

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. 

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 main coding strand containing more genes than the (–)-strand (Taanman 1999, fig.1; Gissi et al., 2008; Lima & Prosdocimi, 2017).
  • 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 (Montaña-Lozano et al., 2022, Fig. 3) and have the control region at the end. 

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. 

tRNA Leu-UUR 

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). 

ND3

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). 

Control region

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. 

References/Literature

Al-Arab M, Höner zu Siederdissen C, Tout K, and Sahyoun AH (2017), Accurate annotation of protein-coding genes in mitochondrial genomes, Mol. Phylogenet. Evol. 106, 209-216. (abstract)

Aleix-Mata G, Ruiz-Ruano FJ, Perez JM, Sarasa M, and Sanchez A (2019), Complete mitochondrial genomes of the Western Capercaillie Tetrao urogallus (Phasianidae, Tetraoninae), Zootaxa 4550, 585-593. (pdf)

Alexeyev M (2020), Mitochondrial DNA: the common confusions, Mitochondrial DNA A 31, 45-47. (pdf)

Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, and Sanger F (1981), Sequence and organization of the human mitochondrial genome, Nature 290, 457-465. (abstract)

Andreu-Sánchez S, Chen W, Stiller J, and Zhang G (2020), Multiple origins of a frame shift insertion in a mitochondrial gene in birds and turtles, GigaScience 10, 1-11. (free pdf) 

Barroso Lima NCB, and Prosdocimi F (2017), The heavy strand dilemma of vertebrate mitochondria on genome sequencing age: number of encoded genes or G+T content?, Mitochondrial DNA A 29, 300-302. (abstract)

Brown GG, Gadeleta G, Pepe G, Saccone C, and Sbisá E (1986), Structural conservation and variation in the D-loop containing region of vertebrate mitochondrial DNA, J. Mol. Biol. 192, 503-511. (abstract)

Cadahía L, Pinsker W, Negro JJ, Pavlicev M, Urios V, and Haring E (2009), Repeated sequence homogenisation between the control and pseudo-control regions in the mitochondrial genomes of the subfamily Aquilinae, J. Exp. Zool. 312B, 171-185. (abstract)

Eberhard JR, Wright TF, and Bermingham E (2001), Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona, Mol. Biol. Evol. 18, 1330-1342. (free pdf) 

Gissi C, Ianneli F, and Pesole G and (2008), Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species, Heredity 101, 301-320. (pdf)

Guo ZL, Zhang Y, Yang H, Wang TS, Wang WW, Zeng SS, Guo Y, Ye L, Du A, Wang ZW, Zeng SM, Tuan J, and Wang L (2022), Sequencing and structural characteristic analysis of  mitochondrial genome in Zhijin White Goose (Anser cygnoides), Res. Square (pdf)

Haring E, Riesing MJ, Pinsker W, and Gamauf A (1999), Evolution of a pseudo-control region in the mitochondrial genome of Palearctic buzzards (genus Buteo), J. Zool. Syst. Evol. Res. 37, 185-194. (abstract)

Haring E, Kruckenhauser L, Gamauf A, Riesling MJ, and Pinsker W (2001), The complete sequence of the mitochondrial genome of Buteo buteo (Aves, Accipitridae) indicates an early split in the phylogeny of raptors, Mol. Biol. Evol. 18, 1892-1904. (free pdf)

Jing M, Yang H, Li K, and Huang L (2020), Characterization of three new mitochondrial genomes of Coraciiformes (Megaceryle lugubris, Alcedo atthis, Halcyon smyrnensis) and insights into their phylogenetics, Genet. Mol. Biol. 43, e:20190392. (pdf)

Kim JI, Do TD, Choi Y, Yeo Y, and Kim CB (2021), Characterization and comparative analysis of complete mitogenomes of three Cacatua parrots (Psittaciformes: Cacatuidae), Genes 12, e:209. (pdf)

Mackiewicz P, Urantówka AD, Kroczak A, and Mackiewicz D (2019), Resolving phylogenetic relationships within Passeriformes based on mitochondrial genes and inferring the evolution of their mitogenomes in terms of duplications, Genome BiolEvol. 11, 2824-49. (free pdf)

Mindell DP, Sorenson MD, and Dimcheff DE (1998b), An extra nucleotide is not translated in mitochondrial ND3 of some birds and turtles, Mol. Biol. Evol. 15, 1568-71. (free pdf)

Montaña-Lozano P, Moreno-Carmona M, Ochoa-Capera M, Medina NS, Boore JL, and Prada CF (2022), Comparative genomic analysis of vertebrate mitochondria reveals a differential of rearrangement rate between taxonomic class, Sci. Rep. 12, e:5479. (pdf)

Morris-Pocock JA, Taylor SA, Birt TP, and Friesen VL (2010), Concerted evolution of duplicated mitochondrial control regions in three related seabird species, BMC Evol. Biol. 10, e:14. (pdf)

Nicholls TJ, and Minczuk M (2014), In D-loop: 40 years of mitochondrial 7S DNA, Exp. Geront. 56, 175-181. (abstract)

Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC, and Amorim A (2008), Evidence for variable selective pressures at a large secondary structure of the hunan mitochondrial DNA control region, Mol. Biol. Evol. 25, 2759-70. (free pdf) 

Slack KE, Janke A, Penny D, and Arnason U (2003), Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features, Gene 302, 43-52. (abstract)

Taanman JW (1999), The mitochondrial genome: structure, transcription, translation and replication, Biochim. Biophys. Acta 1410, 103-123. (free reading)

Urantówka AD, Kroczak A, Silva T, Padrón RZ, Gallardo NF, Blanch J, Blanch B, and Mackiewicz P (2018), New insight into parrot’s mitogenomes indicates that their ancestor contained a duplicated region, MolBiolEvol. 35, 2989-3008. (free pdf)

Urantówka AD, Kroczak A, and Mackiewicz P (2020), New view on the organization and evolution of Palaeognathae mitogenomes poses the question on the ancestral rearrangement in Aves, BMC Genomics 21, e:874. (pdf)

Urantówka AD, Kroczak A, Strzala T, Zaniewicz G, Kurkowski M, and Mackiewicz P (2021), Mitogenomes of Accipitriformes and Cathartiformes were subjected to ancestral and recent duplications followed by gradual degradation, Genome BiolEvol. 13, e:evab193. (pdf)  

Valverde JR, Marco R, and Garesse R (1994), A conserved heptamer motif for ribosomal RNA transcription termination in animal mitochondria, Proc. Natl. Acad. Sci. USA 91, 5368-71. (pdf)