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

Abstract

BackgroundAtypical 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.ResultsMitochondrial 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.ConclusionsMitochondrial 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.

Mitochondrial genome sequence of Unionicola parkeri (Acari: Trombidiformes: Unionicolidae): molecular synapomorphies between closely-related Unionicola gill mites

“…The developing significance of gene-boundary and tRNA structural character states can only be fully realized if both protein-coding and structural RNA sequences can be accurately annotated. While the annotation of protein-coding genes is relatively straightforward, our work, along with that of other authors annotating mitochondrial genome sequences in the Acari have demonstrated that a number of complementary approaches are required to identify tRNA genes (Murrell et al 2003;Jeyaprakash and Hoy 2007;Ernsting et al 2009;Klimov and O'Connor 2009;Dermauw et al 2010). Even when multiple approaches are utilized, some Acari genome sequences have been reported to lack subsets of tRNA genes.…”

“…All tRNA annotations were confirmed by sequence alignment. Our U. parkeri annotation predicts the non-canonical tRNAs that is typical of Acari and some other arachnids (Masta and Boore 2004;Shao et al 2005;Fahrein et al 2007;Masta and Boore 2008;Ernsting et al 2009;Klimov and O'Connor 2009). Sequence alignments (Fig.…”

“…tRNA search programs such as tRNAscan-SE (Lowe and Eddy 1997) and ARWEN (Laslett and Canback 2008) are not able to recognize many tRNAs within the Prostigmata. An accurate annotation of these genes must combine covariant search algorithms with alignments of tRNA sequence from related species, and by-eye inspections (Klimov and O'connor 2009;Yuan et al 2010). This is especially important when the resulting annotations will be used for phylogenetic inference.…”

“…In addition to a wealth of unique gene orders, the annotation of Acari mitochondrial genomes has shown predicted transfer RNA (tRNA) structures that represent departures from the canonical tRNA model more extreme than those seen in nematodes (Klimov and O'connor 2009). Typically, Acari tRNAs lack either the T-arm or D-arm, and occasionally part of the acceptor stem (Ernsting et al 2009;Masta and Boore 2004;Shao et al 2005;Fahrein et al 2007).…”

Complete mitochondrial genome of the feather mite Ardeacarus ardeae (Acari, Sarcoptiformes, Pterolichidae)

“…However, A. ardeae has a shorter mitogenome than two closely related species, Dermatophagoides farinae (14,266 bp) and D. pteronyssinus (14,203 bp). These length differences are mainly due to the CR, which is 214 bp long in A. ardeae, while D. farinae and D. pteronyssinus have CRs composed of 410 and 286 bp, respectively (Dermauw et al 2009;Klimov & Oconnor 2009). …”