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

Diversity and Distribution of Mites (ACARI) Revealed by Contamination Survey in Public Genomic Databases

Acari (mites and ticks) are a biodiverse group of microarthropods within the Arachnida. Because of their diminutive size, mites are often overlooked. We hypothesized that mites, like other closely related microorganisms, could also contaminate public genomic database. Here, using a strategy based on DNA barcodes previously reported, we scanned contaminations related to mites (Acari, exclusive of Ixodida) in Genbank WGS/TSA database. In 22,114 assemblies (17,845 animal and 4269 plant projects), 1717 contigs in 681 assemblies (3.1%) were detected as mite contaminations. Additional taxonomic analysis showed the following: (1) most of the contaminants (1445/1717) were from the specimens of Magnoliopsida, Insecta and Pinopsida; (2) the contamination rates were higher in plant or TSA projects; (3) mite distribution among different classes of hosts varied considerably. Additional phylogenetic analysis of these contaminated contigs further revealed complicated mite-host associations. Overall, we conducted a first systemic survey and analysis of mite contaminations in public genomic database, and these DNA barcode related mite contigs will provide a valuable resource of information for understanding the diversity and phylogeny of mites.

Complete mitochondrial genome of Hygrobates turcicus Pešić, Esen & Dabert, 2017 (Acari, Hydrachnidia, Hygrobatoidea)

The aim of the study was sequencing of the mitogenome of Hygrobates turcicus Pešić, Esen & Dabert, 2017 to expand knowledge of the polymorphism and cryptic or pseudocryptic diversity within Hydrachnidia. The samples originated from Bulgaria, Vidima River near Debnewo, 42°56'41.4''N, 24°48'44.6''E, depth 0.4 m, stones on the bottom, water flow 0.71 m/s, temperature 10 °C, pH 8.53, oxygen 110%, conductivity 279 µS/cm, hardness 121 CaO mg/l; 11 males, 27 females, 2 deutonymphs 12.x.2019 leg. Zawal, Michoński & Bańkowska; one male and one female dissected and slides mounted. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other populations of H. turcicus, and multigene phylogeny. As a result of the study, it was determined that the mitogenome is 15,006 bp long and encodes for 13 proteins, 2 rRNAs, and 22 tRNAs. The genome is colinear with those of H. longiporus and H. taniguchii, the difference in size originating from a non-coding region located between protein-coding genes ND4L and ND3. Five genes have alternative start-codon, and four display premature termination. The multigene phylogeny obtained using all mitochondrial protein-coding genes unambiguously associates H. turcicus with the cluster formed by H. longiporus and H. taniguchii.

The mitogenome of Halotydeus destructor (Tucker) and its relationships with other trombidiform mites as inferred from nucleotide sequences and gene arrangements

The redlegged earth mite, Halotydeus destructor (Tucker, 1925: Trombidiformes, Eupodoidea, Penthaleidae), is an invasive mite species. In Australia, this mite has become a pest of winter pastures and grain crops. We report the complete mitogenome for H. destructor, the first to represent the family Penthaleidae, superfamily Eupodoidea. The mitogenome of H. destructor is 14,691 bp in size, and has a GC content of 27.87%, 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. We explored evolutionary relationships of H. destructor with other members of the Trombidiformes using phylogenetic analyses of nucleotide sequences and the order of protein-coding and rRNA genes. We found strong, consistent support for the superfamily Tydeoidea being the sister taxon to the superfamily Eupodoidea based on nucleotide sequences and gene arrangements. Moreover, the gene arrangements of Eupodoidea and Tydeoidea are not only identical to each other but also identical to that of the hypothesized arthropod ancestor, showing a high level of conservatism in the mitogenomic structure of these mite superfamilies. Our study illustrates the utility of gene arrangements for providing complementary information to nucleotide sequences with respect to inferring the evolutionary relationships of species within the order Trombidiformes. The mitogenome of H. destructor provides a valuable resource for further population genetic studies of this important agricultural pest. Given the co-occurrence of closely related, morphologically similar Penthaleidae mites with H. destructor in the field, a complete mitogenome provides new opportunities to develop metabarcoding tools to study mite diversity in agro-ecosystems. Moreover, the H. destructor mitogenome fills an important taxonomic gap that will facilitate further study of trombidiform mite evolution.

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.

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).

Mitochondrial genome reorganization provides insights into the relationship between oribatid mites and astigmatid mites (Acari: Sarcoptiformes: Oribatida)

Oribatida s.l. represents one of the most species-rich mite lineages, including two recognized groups: oribatid mites (Oribatida s.s., non-astigmatan oribatids) and astigmatid mites (Astigmata). However, the relationship between these two groups has been debated. Here, we sequenced the complete mitochondrial (mt) genome of one oribatid mite and one astigmatid mite, retrieved complete mt genomes of three oribatid mites, and compared them with two other oribatid mites and 12 astigmatid mites sequenced previously. We find that gene orders in the mt genomes of both oribatid mites and astigmatid mites are rearranged relative to the hypothetical ancestral arrangement of the arthropods. Based on the shared derived gene clusters in each mt genome group, rearranged mt genomes are roughly divided into two groups corresponding to each mite group (oribatid mites or astigmatid mites). Phylogenetic results show that Astigmata nested in Oribatida. The monophyly of Astigmata is recovered, while paraphyly of Oribatida s.s. is observed. Our results show that rearranged gene orders in the mt genomes characterize various lineages of oribatid mites and astigmatid mites, and have potential phylogenetic information for resolving the high-level (cohort or supercohort) phylogeny of Oribatida.

The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost?

BACKGROUND

Mitochondrial (mt) genomes of animals typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. In sarcoptiform mites, the entire set of mt tRNA genes is present in Aleuroglyphus ovatus, Caloglyphus berlesei, Dermatophagoides farinae, D. pteronyssinus, Histiostoma blomquisti and Psoroptes cuniculi. Loss of 16 mt tRNA genes, however, was reported in Steganacarus magnus; loss of 2-3 tRNA genes was reported in Tyrophagus longior, T. putrescentiae and Sarcoptes scabiei. Nevertheless, convincing evidence for mt gene loss is lacking in these mites.

RESULTS

We sequenced the mitochondrial genomes of two sarcoptiform mites, Histiostoma feroniarum (13,896 bp) and Rhizoglyphus robini (14,244 bp). Using tRNAScan and ARWEN programs, we identified 16 and 17 tRNA genes in the mt genomes of H. feroniarum and R. robini, respectively. The other six mt tRNA genes in H. feroniarum and five mt tRNA genes in R. robini can only be identified manually by sequence comparison when alternative anticodons are considered. We applied this manual approach to other mites that were reported previously to have lost mt tRNA genes. We were able to identify all of the 16 mt tRNA genes that were reported as lost in St. magnus, two of the three mt tRNA genes that were reported as lost in T. longior and T. putrescentiae, and the two mt tRNA genes that were reported as lost in Sa. scabiei. All of the tRNA genes inferred from these manually identified genes have truncation in the arms and mismatches in the stems.

CONCLUSIONS

Our results reveal very unconventional tRNA structures in sarcoptiform mites and do not support the loss of mt tRNA genes in these mites. The functional implication of the drastic structural changes in these tRNA genes remains to be investigated.

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

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.

Characterization of the complete mitochondrial genome of the storage mite pest Tyrophagus longior (Gervais) (Acari: Acaridae) and comparative mitogenomic analysis of four acarid mites

Mites of the genus Tyrophagus are economically important polyphagous pest commonly living on stored products and also responsible for allergic reactions to humans. Complete mitochondrial genomes (mitogenomes) and the gene features therein are widely used as molecular markers in the study of population genetics, phylogenetics as well as molecular evolution. However, scarcity on the sequence data has greatly impeded the studies in these areas pertaining to the Acari (mites and ticks). Information on the Tyrophagus mitogenomes is quite critical for phylogenetic evaluation and molecular evolution of the mitogenomes within Acariformes. Herein, we reported the complete mitogenome of the allergenic acarid storage mite Tyrophagus longior (Astigmata: Acaridae), an important member of stored food pests, and compared with those of other three acarid mites. The complete mitogenome of T. longior was a circular molecule of 13,271 bp. Unexpectedly, only 19 transfer RNA genes (tRNAs) were present, lacking trnF, trnS1 and trnQ. Furthermore, it also contained 13 protein-coding genes (PCGs) and 2 genes for rRNA (rrnS and rrnL) commonly detected in metazoans. The four mitogenomes displayed similar characteristics with respect to the gene content, nucleotide comparison, and codon usages. Yet, the gene order of T. longior was different from that in other Acari. The J-strands of the four mitogenomes possessed high A+T content (67.4-70.0%), and exhibited positive GC-skews and negative AT-skews. Most inferred tRNAs of T. longior were extremely truncated, lacking either a D- or T-arm, as found in other acarid mites. In T. longior mitogenome the A+T-rich region was just 50 bp in length and can be folded as a stable stem-loop structure, whereas in the region some structures of microsatellite-like (AT)n and palindromic sequences was not present. Besides, reconstructing of the phylogenetic relationship based on concatenated amino acid sequences of 13 PCGs supported that monophyly of the family Acaridae and the order Astigmata, to which the former belongs. Our results were consistent with the traditional classifications.

The complete mitochondrial genomes of six species of Tetranychus provide insights into the phylogeny and evolution of spider mites

Many spider mites belonging to the genus Tetranychus are of agronomical importance. With limited morphological characters, Tetranychus mites are usually identified by a combination of morphological characteristics and molecular diagnostics. To clarify their molecular evolution and phylogeny, the mitochondrial genomes of the green and red forms of Tetranychus urticae as well as T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus, T. pueraricola were sequenced and compared. The seven mitochondrial genomes are typical circular molecules of about 13,000 bp encoding and they are composed of the complete set of 37 genes that are usually found in metazoans. The order of the mitochondrial (mt) genes is the same as that in the mt genomes of Panonychus citri and P. ulmi, but very different from that in other Acari. The J-strands of the mitochondrial genomes have high (∼ 84%) A+T contents, negative GC-skews and positive AT-skews. The nucleotide sequence of the cox1 gene, which is commonly used as a taxon barcode and molecular marker, is more highly conserved than the nucleotide sequences of other mitochondrial genes in these seven species. Most tRNA genes in the seven genomes lose the D-arm and/or the T-arm. The functions of these tRNAs need to be evaluated. The mitochondrial genome of T. malaysiensis differs from the other six genomes in having a slightly smaller genome size, a slight difference in codon usage, and a variable loop in place of the T-arm of some tRNAs by a variable loop. A phylogenic analysis shows that T. malaysiensis first split from other Tetranychus species and that the clade of the family Tetranychoidea occupies a basal position in the Trombidiformes. The mt genomes of the green and red forms of T. urticae have limited divergence and short evolutionary distance.

The complete mitochondrial genome of the brown leg mite, Aleuroglyphus ovatus (Acari: Sarcoptiformes): evaluation of largest non-coding region and unique tRNAs

The circular mitochondrial genome (mitogenome) of Aleuroglyphus ovatus was sequenced. It was 14,328 bp long, and consisted of 37 coding genes including 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. This is the first description of the complete mitogenome of a species in the Acaridae (Acari: Sarcoptiformes). The mtDNA gene order for A. ovatus is identical to those of Dermatophagoides farinae and D. pteronyssinus, but distinctly different from the mtDNA of other Acari. Most inferred tRNA genes of A. ovatus are extremely truncated (48-62 bp), lack stem-loops on either the T- or D-arm (except the trnK), and are unable to fold into the canonical tRNA cloverleaf structure. The largest non-coding region (378 bp) contained several conserved sequences involved in the regulation of mitogenome replication, including one core sequence (ACAT) associated with termination of the J-strand replication and several hypothetical stem-loop structures. The microsatellite-like (AT)n sequence in the largest non-coding region was observed in two other Astigmata species, but it has not been found in other Acari.