Abstract
BackgroundMitochondrial genomes are widely utilized for phylogenetic and population genetic analyses among animals. In addition to sequence data the mitochondrial gene order and RNA secondary structure data are used in phylogenetic analyses. Arachnid phylogeny is still highly debated and there is a lack of sufficient sequence data for many taxa. Ricinulei (hooded tickspiders) are a morphologically distinct clade of arachnids with uncertain phylogenetic affinities.ResultsThe first complete mitochondrial DNA genome of a member of the Ricinulei, Pseudocellus pearsei (Arachnida: Ricinulei) was sequenced using a PCR-based approach. The mitochondrial genome is a typical circular duplex DNA molecule with a size of 15,099 bp, showing the complete set of genes usually present in bilaterian mitochondrial genomes. Five tRNA genes (trnW, trnY, trnN, trnL(CUN), trnV) show different relative positions compared to other Chelicerata (e.g. Limulus polyphemus, Ixodes spp.). We propose that two events led to this derived gene order: (1) a tandem duplication followed by random deletion and (2) an independent translocation of trnN. Most of the inferred tRNA secondary structures show the common cloverleaf pattern except tRNA-Glu where the TψC-arm is missing. In phylogenetic analyses (maximum likelihood, maximum parsimony, Bayesian inference) using concatenated amino acid and nucleotide sequences of protein-coding genes the basal relationships of arachnid orders remain unresolved.ConclusionPhylogenetic analyses (ML, MP, BI) of arachnid mitochondrial genomes fail to resolve interordinal relationships of Arachnida and remain in a preliminary stage because there is still a lack of mitogenomic data from important taxa such as Opiliones and Pseudoscorpiones. Gene order varies considerably within Arachnida – only eight out of 23 species have retained the putative arthropod ground pattern. Some gene order changes are valuable characters in phylogenetic analysis of intraordinal relationships, e.g. in Acari.
Highlights
Mitochondrial genomes are widely utilized for phylogenetic and population genetic analyses among animals
Gene order and non-coding parts The generation of overlapping PCR fragments and subsequent sequencing demonstrated that the mitochondrial genome of P. pearsei is a typical circular DNA molecule with a length of 15099 bp [GenBank:EU024483]
In comparison to the putative arthropod ground pattern we observed a derived gene order with five tRNA genes found in different relative positions compared to the gene order of Limulus
Summary
Mitochondrial genomes are widely utilized for phylogenetic and population genetic analyses among animals. In addition to sequence data the mitochondrial gene order and RNA secondary structure data are used in phylogenetic analyses. Ricinulei (hooded tickspiders) are a morphologically distinct clade of arachnids with uncertain phylogenetic affinities. Due to their bacterial origin [1,2] mitochondria have retained a circular DNA double-helix, which in animals is sized between 12–30 kb. The mitochondrial DNA of Bilateria typically contains 37 genes and one ATrich non-coding part, which putatively bears regulatory elements for transcription and translation and is referred to as the mitochondrial control region [4]. Rearrangements in mitochondrial genomes most often disrupt genes and are deleterious – a possible reason for the stability of mitochondrial gene order [4]
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