The complete mitochondrial genome of Pseudocellus pearsei (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida

<p>Abstract</p> <p>Background</p> <p>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. 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.</p> <p>Results</p> <p>The first complete mitochondrial DNA genome of a member of the Ricinulei, <it>Pseudocellus pearsei </it>(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 (<it>trnW</it>, <it>trnY</it>, <it>trnN</it>, <it>trnL</it>(CUN), <it>trnV</it>) show different relative positions compared to other Chelicerata (e.g. <it>Limulus polyphemus</it>, <it>Ixodes </it>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 <it>trnN</it>. 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.</p> <p>Conclusion</p> <p>Phylogenetic 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.</p

ein neuer Ansatz zur Beantwortung phylogenetischer Fragestellungen

Die Phylogenie der Arachnida ist bis heute umstritten, einerseits wegen widersprüchlicher Interpretationen von Verwandtschaftsverhältnissen der übergeordneten Taxa, andererseits durch die fragliche Eingliederung der marinen Xiphosura in diese vorwiegend terrestrische Tiergruppe. Die konträren Hypothesen beruhen hauptsächlich auf morphologischen Merkmalen und 18S- Sequenzen, deren Verwendung in diesem Zusammenhang wenig geeignet erscheint, da mehrere morphologische Merkmale als homoplastisch angenommen werden und sich das 18S-Gen während der Evolution der Chelicerata offenbar nur wenig verändert hat. Mitochondriale Genome stellen einen weiteren Datensatz phylogenetisch wertvoller Merkmale dar. Dabei können neben den Aminosäure- bzw Nucleotid-Sequenzen auch strukturelle Merkmale dieser eher kleinen Genome analysiert werden. Diese „Genom-morphologischen“ Merkmale umfassen vergleichende Untersuchungen der Genreihenfolge, der RNASekundärstrukturen und der Kontroll-Region, aber auch z. B. die Nukleotidzusammensetzung von protein- kodierenden und ribosomalen Genen. In dieser Arbeit werden neue mitochondriale Genomsequenzen mehrerer Arachniden präsentiert und vor dem Hintergrund der Verwendbarkeit dieser molekularen Methode für die Phylogenie der Arachniden diskutiert. In diese Überlegungen werden sowohl Sequenzanalysen als auch Vergleiche von „Genom morphologischen“ Merkmalsbefunden einbezogen. Insgesamt konnten zehn Genome der Arachniden-Taxa Ricinulei, Opiliones, Araneae, Scorpiones und Amblypygi komplett sequenziert werden. Rückschlüsse über die frühe Diversifi kation übergeordneter Arachniden-Taxa konnten unter Verwendung von mitochondrialen Sequenzen bzw. Genreihenfolgen nicht gezogen werden. Allerdings konnte ein klarer Nutzen für Aussagen auf untergeordneten taxonomischen Ebenen gezeigt werden. Die gewonnenen Daten unterstützen u.a. die aus morphologischer Sicht etabliertende Phylogenie übergeordneter Spinnen- Taxa. Vor allem waren aber Belege vielversprechend, welche eine Abgrenzung einzelner Gruppen innerhalb der opisthothelen Spinnen erlauben, da hier die Schwestergruppen-Beziehungen der Subtaxa längst nicht geklärt ist. Eine ähnliche Bedeutung mitochondrialer Daten zeigt sich auch bei Skorpionen. Auch wenn mitochondriale Genome derzeit keine Aufklärung der Verwandschaftsbeziehungen hochrangiger Arachniden- Taxa vermögen, so können sie dennoch auf etwas niedrigerem taxonomischem Niveau wertvolle Hilfe zur Aufklärung der Phylogenie darstellen.The phylogeny of the predominantly terrestrial Arachnida is still controversial, due to confl icting interpretations of the relatedness of the major lineages as well as the questionable inclusion of the marine Xiphosura. The confl icting hypotheses were produced by using basically morphological and nuclear sequence-based data, in that case both with doubtful convenience as many characters must have emerged convergently and the prevalent used 18S rRNA gene appears to have changed too sparsely during chelicerate evolution. Another large dataset of phylogenetic information is provided by mitochondrial genomes, which have served as models for comparative genomics for some time. Besides the sequence information retained in mitochondrial genomes in form of amino acid or nucleotide sequences of proteincoding and rRNA genes, other features of those rather small genomes bear phylogenetic information. These structural characters are often considered as `genome morphology` and comprise gene order, secondary structures of transfer and ribosomal RNAs, control region features, codon usage patterns, and the nucleotide compositional strand bias of proteincoding and rRNA genes. In this thesis several new mitochondrial genomes from arachnids are presented against the background of an evaluation of the usability and effi ciency of these molecular character complexes concerning arachnid systematics. Included in these considerations are sequence analyses as well as comparisons of fi ndings in terms of different characters belonging to `genome morphology`. Altogether, sequencing was successful in case of ten complete genomes from the arachnid orders Ricinulei, Opiliones, Araneae, Scorpiones, and Amblypygi. It appears diffi cult to deduce the progression of early diversifi cation among arachnid orders from mitochondrial genome sequence data or gene rearrangements. However, a real benefit is gained on lower taxonomic levels. In case of Araneae, e.g., mitochondrial sequences and genome organisations largely support morphological based phylogenetic relationships of the three major clades. Furthermore, it even could be proven that gene rearrangements are useful for in-depth phylogenetic analysis of the Opisthothelae, in which sister group relationships of some taxa still deserve study. Similarily, inverted repeat sequences in the control region of Scorpiones demarcate clades on different levels. So even if mitochondrial genomes can hardly shed light on the relationships of major arachnid lineages, the data is promising for a resolution of disputed intraordinal relationships

Changes in gene order in mitochondrial genomes of Arachnida compared to the putative ancestral arthropod gene order

<p><b>Copyright information:</b></p><p>Taken from "The complete mitochondrial genome of (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida"</p><p>http://www.biomedcentral.com/1471-2164/8/386</p><p>BMC Genomics 2007;8():386-386.</p><p>Published online 25 Oct 2007</p><p>PMCID:PMC2231378.</p><p></p> Transfer RNA genes are labelled according to the one letter amino acid code. Genes marked white show the same relative position as in the arthropod ground pattern; genes marked orange have relative positions differing from the arthropod ground pattern; the gene marked black indicates a duplicated gene in . Horizontal lines above genes illustrate adjacent genes which were probably translocated together; dotted lines indicate regions where tandem duplication and random deletion events may have occurred; connected arrows show adjacent genes which have switched their position, making it difficult to assess which gene was translocated. Braces accentuate the duplicated regions in the mitochondrial genome of . lnr: large non-coding region, putative mitochondrial control region; other non-coding regions (> 50 bp) are illustrated by gaps between genes. Numbers refer to rearrangement events, compare Fig. 6. For GenBank accession numbers see Table 2

Phylogenetic trees of chelicerate relationships, inferred from nucleotide (upper) and amino acid (lower) datasets

<p><b>Copyright information:</b></p><p>Taken from "The complete mitochondrial genome of (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida"</p><p>http://www.biomedcentral.com/1471-2164/8/386</p><p>BMC Genomics 2007;8():386-386.</p><p>Published online 25 Oct 2007</p><p>PMCID:PMC2231378.</p><p></p> All protein coding gene sequences were aligned and concatenated; ambiguously aligned regions were omitted by Gblocks. Trees were rooted with outgroup taxa (, , ). Topologies and branch lengths were taken from the best scoring trees of the maximum likelihood (ML) analyses. Numbers behind the branching points are percentages from ML bootstrapping (left), Bayesian posterior probabilities (BPP, middle) and maximum parsimony bootstrap percentages (MP, right). Stars indicate that values are 100 (ML), 1.0 (BI) and 100 (MP). See Table 2 for accession numbers