Dataset Information

The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs.

ABSTRACT: BACKGROUND: Complete mitochondrial (mt) genomes and the gene rearrangements therein are increasingly used as molecular markers for investigating phylogenetic relationships, especially for elucidating deep splits. Contributing to the complete mt genomes of arthropods, especially Arachnida, available so far, we provide the first complete mt genome of a sarcoptiform mite species, the sexually reproducing oribatid mite Steganacarus magnus (Acari, Oribatida) which was determined by sequencing of long PCR products. RESULTS: The mt genome of S. magnus lacks 16 tRNAs, only those for leucine, histidine, proline, tryptophan, glutamine and serine are present. Within those tRNAs only tRNA-His and tRNA-Pro have kept their original position, the others are translocated. Furthermore, the mt genome of S. magnus consists of 13,818 bp and it is composed of 13 protein-coding genes and two genes for the ribosomal RNA subunits that are typically found in metazoan mt genomes. The gene order in S. magnus differs from the hypothetical ancestral chelicerate arrangement as conserved in Limulus polyphemus: instead of nad1-rrnL-rrnS-LNR-nad2 (tRNAs excluded) S. magnus is nad2-rrnL-nad1-rrnS-LNR. Phylogenetic analyses of a concatenated amino acid dataset of all mt protein-coding genes of 28 arthropod species suggest a sister-group relationship of sarcoptiform and prostigmatid mites (S. magnus and Leptotrombidium). CONCLUSION: The mt gene arrangement of S. magnus differs from the hypothetical ground plan of arthropods and from that of other mites further contributing to the variety of mt gene arrangements found in Arachnida. The unexpected lack of tRNAs is enigmatic, probably showing that the loss of mt genes is an ongoing evolutionary process. For solving phylogenetic relationships of oribatid mite lineages and their position within Acari further complete mt genomes are needed.

SUBMITTER: Domes K

PROVIDER: S-EPMC2588462 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs.

Domes Katja K Maraun Mark M Scheu Stefan S Cameron Stephen L SL

BMC genomics 20081107

<h4>Background</h4>Complete mitochondrial (mt) genomes and the gene rearrangements therein are increasingly used as molecular markers for investigating phylogenetic relationships, especially for elucidating deep splits. Contributing to the complete mt genomes of arthropods, especially Arachnida, available so far, we provide the first complete mt genome of a sarcoptiform mite species, the sexually reproducing oribatid mite Steganacarus magnus (Acari, Oribatida) which was determined by sequencing ...[more]

PMID: 18992147

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Project description:The dominance of sex in Metazoa is enigmatic. Sexual species allocate resources to the production of males, while potentially facing negative effects such as the loss of well-adapted genotypes due to recombination, and exposure to diseases and predators during mating. Two major hypotheses have been put forward to explain the advantages of parthenogenetic versus sexual reproduction in animals, that is, the Red Queen hypothesis and the Tangled Bank/Structured Resource Theory of Sex. The Red Queen hypothesis assumes that antagonistic predator-prey/ parasite-host interactions favor sex. The Structured Resource Theory of Sex predicts sexual reproduction to be favored if resources are in short supply and aggregated in space. In soil, a remarkable number of invertebrates reproduce by parthenogenesis, and this pattern is most pronounced in oribatid mites (Oribatida, Acari). Oribatid mites are abundant in virtually any soil across very different habitats, and include many sexual and parthenogenetic (thelytokous) species. Thereby, they represent an ideal model group to investigate the role of sexual versus parthenogenetic reproduction across different ecosystems and habitats. Here, we compiled data on oribatid mite communities from different ecosystems and habitats across biomes, including tropical rainforests, temperate forests, grasslands, arable fields, salt marshes, bogs, caves, and deadwood. Based on the compiled dataset, we analyzed if the percentage of parthenogenetic species and the percentage of individuals of parthenogenetic species are related to total oribatid mite density, species number, and other potential driving factors of the reproductive mode including altitude and latitude. We then interpret the results in support of either the Red Queen hypothesis or the Structured Resource Theory of Sex. Overall, the data showed that low density of oribatid mites due to harsh environmental conditions is associated with high frequency of parthenogenesis supporting predictions of the Structured Resource Theory of Sex rather than the Red Queen hypothesis.

Project description:BACKGROUND: The family Tetranychidae (Chelicerata: Acari) includes ~1200 species, many of which are of agronomic importance. To date, mitochondrial genomes of only two Tetranychidae species have been sequenced, and it has been found that these two mitochondrial genomes are characterized by many unusual features in genome organization and structure such as gene order and nucleotide frequency. The scarcity of available sequence data has greatly impeded evolutionary studies in Acari (mites and ticks). Information on Tetranychidae mitochondrial genomes is quite important for phylogenetic evaluation and population genetics, as well as the molecular evolution of functional genes such as acaricide-resistance genes. In this study, we sequenced the complete mitochondrial genome of Panonychus citri (Family Tetranychidae), a worldwide citrus pest, and provide a comparison to other Acari. RESULTS: The mitochondrial genome of P. citri is a typical circular molecule of 13,077 bp, and contains the complete set of 37 genes that are usually found in metazoans. This is the smallest mitochondrial genome within all sequenced Acari and other Chelicerata, primarily due to the significant size reduction of protein coding genes (PCGs), a large rRNA gene, and the A + T-rich region. The mitochondrial gene order for P. citri is the same as those for P. ulmi and Tetranychus urticae, but distinctly different from other Acari by a series of gene translocations and/or inversions. The majority of the P. citri mitochondrial genome has a high A + T content (85.28%), which is also reflected by AT-rich codons being used more frequently, but exhibits a positive GC-skew (0.03). The Acari mitochondrial nad1 exhibits a faster amino acid substitution rate than other genes, and the variation of nucleotide substitution patterns of PCGs is significantly correlated with the G + C content. Most tRNA genes of P. citri are extremely truncated and atypical (44-65, 54.1 ± 4.1 bp), lacking either the T- or D-arm, as found in P. ulmi, T. urticae, and other Acariform mites. CONCLUSIONS: The P. citri mitochondrial gene order is markedly different from those of other chelicerates, but is conserved within the family Tetranychidae indicating that high rearrangements have occurred after Tetranychidae diverged from other Acari. Comparative analyses suggest that the genome size, gene order, gene content, codon usage, and base composition are strongly variable among Acari mitochondrial genomes. While extremely small and unusual tRNA genes seem to be common for Acariform mites, further experimental evidence is needed.

Dataset Information

The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs.

Publications

The complete mitochondrial genome of the sexual oribatid mite Steganacarus magnus: genome rearrangements and loss of tRNAs.

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