A rapid identification method for common astigmatid species based on multiplex polymerase chain reaction.

Astigmatid mites are economically significant pests of stored products and sources of inhalant allergens causing allergic rhinitis and asthma worldwide. The morphological identification of astigmatid mites at the species level is often a difficult task due to their small size, phenotypic similarity and lack of diagnostic characters. We used multiplex polymerase chain reaction (PCR) to identify astigmatid mite species, which could complement the morphological data for the species-specific identification of mites. Internal ribosomal transcribed spacer (ITS) sequences (i.e., partial 18S, the full length of ITS1-5.8S-ITS2 and partial 28S) from eight astigmatid species (Acarus siro, Tyrophagus putrescentiae, Suidasia nesbitti, Dermatophagoides pteronyssinus, Dermatophagoides farinae, Lepidoglyphus destructor, Chortoglyphus arcuatus and Gohieria fuscus) were obtained by DNA extraction and then sequenced after PCR amplification. Specific primers were designed in the ITS2 region manually. Results revealed that an identification method for eight common astigmatid species was established based on multiplex PCR, which should be effective for the identification of other species of mites by redesigning species-specific primers in future experiments.

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.

De novo sequence of the mitochondrial genome of Tyrophagus putrescentiae (Acari: Sarcoptiformes) including 22 tRNA sequences and the largest non-coding region.

In this study, we de novo sequenced and analyzed the circular mitochondrial genome (mitogenome) of Tyrophagus putrescentiae. It was 14,156 bp long and contained a complete set of 37 genes, contrary to the initial published sequences; it included 22 tRNA sequences and the largest non-coding region. The mtDNA gene order of T. putrescentiae was found to be identical to that of Aleuroglyphus ovatus, Caloglyphus berlesei, and Rhizoglyphus robini (all Acaroidea). Most tRNAs of T. putrescentiae lack at least a D-arm or T-arm. Tyrophagus putrescentiae tRNAs also shared considerable structural and sequence similarity with the tRNAs of other reported Acaroidea species that have the full set of tRNAs. The largest non-coding region was located between trnF and trnS1, and it contained a microsatellite-like (AT)n sequence, short palindromic sequences, and several hairpin loops, as observed in other reported Acaroidea species (excepting Tyrophagus longior).