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Background  Atypical tRNAs are functional minimal tRNAs, lacking either the D- or T-arm. They are significantly shorter than typical cloverleaf tRNAs. Widespread occurrence of atypical tRNAs was first demonstrated for secernentean nematodes and later in various arachnids. Evidence started to accumulate that tRNAs of certain acariform mites are even shorter than the minimal tRNAs of nematodes, raising the possibility that tRNAs lacking both D- and T-arms might exist in these organisms. The presence of cloverleaf tRNAs in acariform mites, particularly in the house dust mite genus  Dermatophagoides , is still disputed.    Results  Mitochondrial tRNAs of  Dermatophagoides farinae  are minimal, atypical tRNAs lacking either the T- or D-arm. The size (49-62, 54.4 ± 2.86 nt) is significantly (p = 0.019) smaller than in  Caenorhabditis elegans  (53-63, 56.3 ± 2.30 nt), a model minimal tRNA taxon. The shortest tRNA (49 nt) in  Dermatophagoides  is approaching the length of the shortest known tRNAs (45-49 nt) described in other acariform mites. The D-arm is absent in these tRNAs, and the inferred T-stem is small (2-3 bp) and thermodynamically unstable, suggesting that it may not exist in reality. The discriminator nucleotide is probably not encoded and is added postranscriptionally in many  Dermatophagoides  tRNAs.    Conclusions  Mitochondrial tRNAs of acariform mites are largely atypical, non-cloverleaf tRNAs. Among them, the shortest known tRNAs with no D-arm and a short and unstable T-arm can be inferred. While our study confirmed seven tRNAs in  Dermatophagoides  by limited EST data, further experimental evidence is needed to demonstrate extremely small and unusual tRNAs in acariform mites.

Improved tRNA prediction in the American house dust mite reveals widespread occurrence of extremely short minimal tRNAs in acariform mites