The avian mitogenome contains 22 tRNA-encoding genes, three of which (MT-TE, MT-TP and MT-TT) are sporadically duplicated in many orders (but not in Galliformes and Anseriformes). The 22 mito-tRNAs decode all 60 sense codons by means of expanded wobble pairing (where a single anticodon recognises either two or four different codons). Thus, there are far fewer mitochondrial tRNAs than in the standard cytosolic system. This reduced tRNA set is characteristic of all vertebrate mitogenomes, including birds. 

The standard symbols for vertebrate genes follow the HUGO (Human Genome Organisation= Gene Nomenclature Committe (HGNC) (link): 

 

 

Note that tRNAs are transcribed from the template strand of the respective tRNA genes, not from the coding strand. Therefore, the coding strand (sense strand) has the same sequence as the tRNA (except T in DNA is replaced by U in RNA). 

 

The production of functional (mature) tRNAs from DNA templates is a multi-step procedure that occurs entirely in the mitochondrial matrix and encompasses: 

• transcribing both DNA strands via mitochondrial RNA polymerase (POLRMT)
• cleaving polycistronic transcripts via RNase P (mitochondrial form) [cleaving the 5’ end] and RNase Z (ELAC2) [cleaving the 3’ end] to release individual pre-tRNAs
• adding 3’ CCA tail to the terminal discriminator nucleotide via tRNA nucleotidyltransferase
• modifying several bases (e.g. taurine-containing modification at wobble position 34; methylations at position 37)
• attaching the respective amino acid to the fully modified tRNA by aminoacylation via nuclear-encoded aminoacyl-tRNA synthetases

Schematic cloverleaf-like secondary structure of a generalised mitochondrial pre-tRNA. The numbering system follows Sprinzl et al. (1996), except that nucleotides 26 and 44 are not forming part of the stem. (link) Note that in mitochondrial tRNAs, non-canonical G-U base pairings (wobble pairs) are frequently found in the stems, because the mitochondrial translation machinery is adapted to these atypical tRNAs. [G-U pairs form two hydrogen bonds instead of three in G-C pairs, so they are slightly less stable.]

 

In the following, the secondary structures of all 22 mitochondrial pre-tRNAs in the putative ground pattern of Galliformes are shown. I chose landfowl as an example, because it is the avian order with the oldest crown group (ca. 70 Ma) and because it is lacking the tandem duplication containing additional tRNAs. 

Secondary structures of mitochondrial tRNAS have been created with the aid of the online platform R2DT (Sweeney et al., 2025). (link)

pre-tRNA-Ala

• anticodon: UGC; accepted codons: GCU, GCC, GCA, GCG
• number of nucleotides: 69 (variation within Galliformes: no indels)
• coding strand: (-) strand
• peculiarities: amino acid acceptor stem with 6 bp (instead of 7 bp); probably, a combination of G3:C70 and translocated G4:U69 serves as the major recognition determinant; D-loop with 5 nucleotides (instead of 8 nucleotides)

pre-tRNA-Arg

• anticodon: UCG; accepted codons: CGU, CGC, CGA, CGG
• number of nucleotides: 68 (variation within Galliformes: 69  or 70 due to one insertion in D-loop and one insertion in T-loop)
• coding strand: (+) strand
• peculiarities: D-loop with 5 nucleotides (instead of 8 nucleotides); T-loop with 6 nucleotides (instead of 7 nucleotides)

pre-tRNA-Asn

• anticodon: GUU; accepted codons: AAU, AAC
• number of nucleotides: 72 (variation within Galliformes: or 73 due to 1 nucleotide insertion between D-loop and D-stem) 
• coding strand: (-) strand
• peculiarities: amino acid acceptor stem with one base pair mismatch; D-stem with 3 bp (instead of 4 bp due to one nucleotide deletion); variable loop with 5 nucleotides

pre-tRNA-Asp

• anticodon: GUC; accepted codons: GAU, GAC
• number of nucleotides: 69 (variation within Galliformes: no indels)
• coding strand: (+) strand
• peculiarities: D-loop with 5 nucleotides (instead of 8 nucleotides); amino acid acceptor stem and anticodon stem with base pair mismatches

pre-tRNA-Cys

• anticodon: GCA; accepted codons: UGU, UGC
• number of nucleotides: 67 (variation within Galliformes: from 66 to 68 due to one deletion in T-loop and one insertion in 5' acceptor stem)
• coding strand: (-) strand
• peculiarities: D-loop with 3 nucleotides (instead of 8 nucleotides); anticodon stem with 4 bp (instead of 5 bp)

pre-tRNA-Gln

• anticodon: UUG; accepted codons: CAA, CAG
• number of nucleotides: 71 (variation within Galliformes: no indels)
• coding strand: (-) strand
• peculiarities: D-loop with 7 nucleotides (instead of 8 nucleotides)

pre-tRNA-Glu

• anticodon: UUC; accepted codons: GAA, GAG
• number of nucleotides: 68 (variation within Galliformes: sometimes 69 due to one insertion in T-stem)
• coding strand: (-) strand
• peculiarities: D-loop with 4 nucleotides (instead of 8 nucleotides)

pre-tRNA-Gly

• anticodon: UCC; accepted codons: GGU, GGC, GGA, GGG
• number of nucleotides: 69 (variation within Galliformes: sometimes 70 due to one insertion in T-loop)
• coding strand: (+) strand
• peculiarities: D-stem with 3 bp (instead of 4 bp); D-loop with 7 nucleotides (instead of 8 nucleotides); anticodon stem with two adjacent base pair mismatches; T-stem with 4 bp (instead of 5 bp)

pre-tRNA-His

• anticodon: GUG; accepted codons: CAU, CAC
• number of nucleotides: 69 (variation within Galliformes: sometimes 70 due to one insertion in D-loop)
• coding strand: (+) strand
• peculiarities: one base pair mismatch in amino acid acceptor stem

pre-tRNA-Ile

• anticodon: GAU; accepted codons: AUU, AUC
• number of nucleotides: 72 (variation within Galliformes: from 70 to 73 nucleotides due to one or two deletions and one insertion in D-loop)
• coding strand: (+) strand
• peculiarities: D-stem with 3 bp (instead of 4 bp); T-loop with 9 nucleotides (instead of 7 nucleotides)

pre-tRNA-Leu CUN

• anticodon: UAG; accepted codons: CUU, CUC, CUA, CUG
• number of nucleotides: 71 (variation within Galliformes: no indels)
• coding strand: (+) strand
• peculiarities: D-loop with 7 nucleotides (instead of 8 nucleotides)

pre-tRNA-Leu UUR

• anticodon: UAA; accepted codons: UUA, UUG
• number of nucleotides: 75 (variation within Galliformes: sometimes 76 due to one insertion in variable arm) 
• coding strand: (+) strand
• peculiarities: one base pair mismatch in amino acid acceptor stem; two insertions  in D-loop

pre-tRNA-Lys

• anticodon: UUU; accepted codons: AAA, AAG
• number of nucleotides: 70 (variation within Galliformes: from 66-72 due to 1 nucleotide insertion in D-loop and 2 nucleotides insertion and 5 nucleotides deletion in T-loop)
• coding strand: (+) strand
• peculiarities: D-stem with 3 bp (instead of 4 bp); D-loop with 5/7 nucleotides (instead of 7/9); variable arm with 5 nucleotides (instead of 4 nucleotides); T-arm highly variable

pre-tRNA-Met

• anticodon: CAU; accepted codons: AUG, AUA
• number of nucleotides: 69 (variation within Galliformes: from 68 nucleotides due to deletion in T-stem to 70 nucleotides due to insertion in D-loop)
• coding strand: (+) strand
• peculiarities: D-loop with 5 nucleotides (instead of 8nucleotides); T-stem with one base pair mismatch

pre-tRNA-Phe

• anticodon: GAA; accepted codons: UUU, UUC
• number of nucleotides: 71 (variation within Galliformes: highly variable, from 68 to 73 nucleotides)
• coding strand: (+) strand
• peculiarities: one  base pair mismatch in amino acid acceptor stem; D-loop and T-loop highly variable with numerous indels; homologisation of positions difficult

pre-tRNA-Pro

• anticodon: UGG; accepted codons: CCU, CCC, CCA, CCG
• number of nucleotides: 70 (variation within Galliformes: no indels)
• coding strand: (-) strand
• peculiarities: D-loop with 6 nucleotides (instead of 8 nucleotides)

pre-tRNA-Ser AGY

• anticodon: GCU; accepted codons: AGU, AGC
• number of nucleotides: 67 (variation within Galliformes: from 66 to 69 nucleotides due to one deletion and two insertions in D-arm)
• coding strand: (+) strand
• peculiarities: one unpaired nucleotide in amino acid acceptor stem; D-arm without stem-loop structure (an ancient metazoan apomorphy); anticodon stem with one mismatch; T-loop with 8 nucleotides (instead of 7 nucleotides)

pre-tRNA-Ser UCN

• anticodon: UGA; accepted codons: UCU, UCC, UCA, UCG
• number of nucleotides: 75 (variation within Galliformes: no indels)
• coding strand: (-) strand
• peculiarities: D-loop with 11 nucleotides (instead of 8 nucleotides)

pre-tRNA-Thr

• anticodon: UGU; accepted codons: ACU, ACC, ACA, ACG
• number of nucleotides: 69 (variation within Galliformes: sometimes 70 nucleotides due to one insertion in either D-loop or T-loop)
• coding strand: (+) strand
• peculiarities: D-loop with 5 nucleotides (instead of 8 nucleotides); variable arm with 5 nucleotides; T-stem with 4 bp (instead of 5 bp); T-loop with 8 nucleotides (instead of 7 nucleotides)

pre-tRNA-Trp

• anticodon: UCA; accepted codons: UGA, UGG
• number of nucleotides: 78 (variation within Galliformes: from 76 to 79 nucleotides due to up to three deletions and one insertion in T-loop)
• coding strand: (+) strand
• peculiarities: T-stem with one mismatch; T-loop with 14 nucleotides (instead of 8 nucleotides)

pre-tRNA-Tyr

• anticodon: GUA; accepted codons: UAU, UAC
• number of nucleotides: 72 (variation within Galliformes: 71 due to to deletion of nucleotide T/U18 or T/U19 in D-loop)
• coding strand: (-) strand
• peculiarities: D-stem with 3 bp (instead of 4 bp); anticodon stem with 3 bp (instead of 5 bp)

pre-tRNA-Val

• anticodon: UAC; accepted codons: GUU, GUC, GUA, GUG
• number of nucleotides: 73 (variation within Galliformes: between 70 and 74 nucleotides due one insertion and up to two deletions in D-loop and one insertion and up to three deletions in T-loop)
• coding strand: (+) strand
• peculiarities: T-loop with  8 nucleotides (instead of 7 nucleotides)

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