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. 2016 Jan 6:6:18920.
doi: 10.1038/srep18920.

Mitochondrial genome evolution and tRNA truncation in Acariformes mites: new evidence from eriophyoid mites

Xiao-Feng Xue  1   2 , Jing-Feng Guo  1 , Yan Dong  1 , Xiao-Yue Hong  1 , Renfu Shao  2
Affiliations

Mitochondrial genome evolution and tRNA truncation in Acariformes mites: new evidence from eriophyoid mites

Xiao-Feng Xue et al. Sci Rep. .

Abstract

The subclass Acari (mites and ticks) comprises two super-orders: Acariformes and Parasitiformes. Most species of the Parasitiformes known retained the ancestral pattern of mitochondrial (mt) gene arrangement of arthropods, and their mt tRNAs have the typical cloverleaf structure. All of the species of the Acariformes known, however, have rearranged mt genomes and truncated mt tRNAs. We sequenced the mt genomes of two species of Eriophyoidea: Phyllocoptes taishanensis and Epitrimerus sabinae. The mt genomes of P. taishanensis and E. sabinae are 13,475 bp and 13,531 bp, respectively, are circular and contain the 37 genes typical of animals; most mt tRNAs are highly truncated in both mites. On the other hand, these two eriophyoid mites have the least rearranged mt genomes seen in the Acariformes. Comparison between eriophyoid mites and other Aacariformes mites showed that: 1) the most recent common ancestor of Acariformes mites retained the ancestral pattern of mt gene arrangement of arthropods with slight modifications; 2) truncation of tRNAs for cysteine, phenylalanine and histidine occurred once in the most recent common ancestor of Acariformes mites whereas truncation of other tRNAs occurred multiple times; and 3) the placement of eriophyoid mites in the order Trombidiformes needs to be reviewed.

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Figures

Figure 1
Figure 1. Map of the mitochondrial genomes of Phyllocoptes taishanensis (A) and Epitrimerus sabinae (B).
Protein-coding genes are color-coded (cox: blue; nad: green; atp: orange; cob: yellow); rRNA genes are in grey; control regions are in black; tRNA genes are in red or purple. Abbreviations of protein-coding genes are: atp6 and atp8 for ATP synthase subunits 6 and 8, cox1–3 for cytochrome oxidase subunits 1–3, cob for cytochrome b, nad1-6 and nad4L for NADH dehydrogenase subunits 1-6 and 4 L, rrnL and rrnS for large and small rRNA subunits. tRNA genes are indicated by the single letter IUPAC-IUB abbreviations for their corresponding amino acids. Arrows and arrowheads show the direction of gene transcription. Numbers at gene junctions indicate the length of non-coding sequences; negative numbers indicate overlap between genes.
Figure 2
Figure 2. Mitochondrial gene arrangements in the hypothetical ancestor of Acariformes, Phyllocoptes taishanensis and Epitrimerus sabinae.
Underlined genes are on the N-strand. Translocated or inverted genes are color-coded (blue: inversion and translocation; green: translocation; orange: inversion). rRNA genes are in grey; control regions are in black. Abbreviations of gene names are the same as in Fig. 1. Lines between genes indicate gene rearrangement. The positions of trnQ and trnY are unclear. Question marks after tRNA genes indicate uncertain locations.
Figure 3
Figure 3. Inferred secondary structures of the 12 mt tRNAs of P. taishanensis (Pt) and E. sabinae (Es).
tRNAs are labeled with the abbreviations of their corresponding amino acids. Dashes indicate Watson–Crick bonds; dots indicate bonds between U and G. Shared identical sequences between tRNA genes are circled in P. taishanensis.
Figure 4
Figure 4. Inferred secondary structures of the 10 mt tRNAs of P. taishanensis (Pt) and E. sabinae (Es).
tRNAs are labeled with the abbreviations of their corresponding amino acids. Dashes indicate Watson–Crick bonds; dots indicate bonds between U and G. Shared identical sequences between tRNA genes are circled in P. taishanensis.
Figure 5
Figure 5. Maximum likelihood trees inferred with nucleotide sequences by 16 partitions (13 PCGs, 2 rRNA genes and concatenated tRNA genes).
Asterisks indicate the branches with >75% BSPs and>95% BPPs in the majority of the 13 topologies (Figures S1 and S2). Translocated genes are in green; inverted genes are in orange; inverted and translocated genes are in blue. rRNAs are in grey. Control regions are in black. Abbreviations of gene names are the same as in Fig. 1. Genes are transcribed from left to right except for those underlined, which are transcribed from right to left.
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