Mitochondrial analysis of oribatid mites provides insights into their atypical tRNA annotation, genome rearrangement and evolution

Abstract

Background: The mitochondrial (mt) genomes of Sarcoptiformes mites typically contain 37 genes. Although the loss of genes is rare in Sarcoptiformes mite mitogenomes, two of the six previously reported oribatid mites (Acariforms: Sarcoptiformes) are reported to have lost parts of their tRNA genes. To confirm whether the tRNA genes were indeed lost and whether the loss is universal, we re-annotated the available oribatid mite sequences and sequenced the mitogenome of Oribatula sakamorii.

Methods: The mitogenome of O. sakamorii was sequenced using an Illumina HiSeq sequencer. The mt tRNA gene was annotated using multi-software combined with a manual annotation approach. Phylogenetic analyses were performed using the maximum likelihood and Bayesian inference methods with concatenated nucleotide and amino acid sequences.

Results: The mitogenomes of O. sakamorii contained 37 genes, including 22 tRNA genes. We identified all mt tRNA genes that were reported as "lost" in Steganacarus magnus and Paraleius leontonychus and revealed certain atypical tRNA annotation errors in oribatid mite sequences. Oribatid mite mitogenomes are characterized by low rates of genetic rearrangement, with six or seven gene blocks conserved between the mitogenome of all species and that of ancestral arthropods. Considering the relative order of the major genes (protein-coding genes and rRNAs), only one or two genes were rearranged with respect to their positions in the ancestral genome. We explored the phylogenetic relationships among the available oribatid mites, and the results confirmed the systematic position of Hermannia in the Crotonioidea superfamily. This was also supported by the synapomorphic gene-derived boundaries.

Conclusions: The tRNA "lost" phenomenon is not universal in oribatid mites. Rather, highly atypical secondary structure of the inferred mt tRNA genes made them unidentifiable using a single type of tRNA search program. The use of multi-software combined with a manual annotation approach can improve the accuracy of tRNA gene annotation. In addition, we identified the precise systematic position of Hermannia and validated that Astigmata is nested in Oribatida.

Keywords: Mitochondrial genome; Oribatid mites; Phylogeny; TRNA re-annotation.

Fig. 1

a AT% vs AT-skew and b GC% vs GC-skew. Values are calculated on the (−)-strands for full-length mitochondrial genomes. The X-axis indicates the level of nucleotide skew, and the Y-axis indicates the nucleotide percentages

Fig. 2

Mitochondrial gene orders of the six oribatid mite species. The mitogenome orders obtained from different annotations for Steganacarus magnus, Paraleius leontonychus, Oribatula sp., Hermannia gibba and Platynothrus peltifer. The gray boxes indicate re-annotated genes. The green boxes indicate the newly predicted tRNAs. The underlined genes were present on the (−)-strand. The genes are presented in the original order. Intergenic distances are not included, and sizes of genes are not to scale. The tRNA annotation methods are indicted in different colors at the end of each sequence (tRANscan-SE in yellow, ARWEN in orange, minimum free energy in light blue, MITOS in black, MITOS2 in purple, manual annotation using anticodon and secondary structure in blue and manual annotation using sequence alignmentsin pink)

Fig. 3

Comparison of the secondary structures of tRNAs. Two Paraleius leontonychus (Pl) tRNAs were retrieved. MFE: minimum free energy

Fig. 4

Relative synonymous codon usage (RSCU) and codon numbers of the 22 amino acids. The X-axis indicates the oribatid mite species; the Y-axis indicates the RSCU or total number of codons

Fig. 5

Evolution of gene orders [protein-coding genes (PCGs) and rRNAs] in mitogenomes explained using CREx. Rearrangement operations occurred from an inferred ancestral arthropod gene order to oribatid mites followed by astigmatid mites. Type I indicates the mt PCG and rRNA gene orders in six oribatid mites. Type II indicates the mt PCG and rRNA gene order in Steganacarus magnus. Type III indicates the mt PCG and rRNA gene orders in astigmatid mites. Underlined genes are present on the (−)-strand. The genes are presented in their original order; intergenic distances are not included, and the gene sizes are not true to scale. The rrnL and rrnS genes are color-coded (black gray in color)

Fig. 6

Gene order representation. Underlined genes were present on the (−)-strand. The ancestral gene blocks a–g are underlined in the Limulus polyphemus gene order and also indicated by different colors. Different codes were used to label the boundaries

Fig. 7

Representation of derived characters on a phylogenetic tree. A part of Bayesian inference is used for the representation of the ancestral and shared derived characters. The shared derived character states are shown on the node. The ancestral gene blocks (a–g) are indicated using different colors and codes, which are shown at the terminal end of the branch. Partial ancestral characters are marked with an asterisk

Fig. 8

Phylogenetic tree inferred from mitochondrial genome sequences using maximum likelihood and Bayesian inference methods. The branch lengths presented here follow the Bayesian analysis. The node numbers indicate Bayesian posterior probabilities (BPP) and maximum likelihood bootstrap proportion (BSP). “−” indicates the absence of the node in the corresponding analysis. The numbers indicate BPP and BSP values from the analyses of datasets consisting of without third codon positions of protein coding genes