Planarian High Molecular Weight DNA Isolation by Spooling

The complete mitochondrial genome of Scatoglyphus polytrematus (Acari: Acaridae)

We assembled and annotated the complete mitochondrial genome of Scatoglyphus polytrematus. It is the first complete mitochondrial genome sequence from the genus Scatoglyphus. The mitogenome was 13,966 bp in length and contains 37 genes (including 13 protein-coding genes, 22 transfer RNA (tRNA), and two ribosomal RNA (rRNA)), and one largest non-coding region. The gene arrangement of S. polytrematus is consistent with the pattern of possible common ancestor of astigmatid mites. In the present study, phylogenetic analysis shows that genus Scatoglyphus was clustered into one branch with other Acaridae species.

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

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.

Graphic Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04719-0.