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

Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea

<p>Abstract</p> <p>Background</p> <p>The new animal phylogeny established several taxa which were not identified by morphological analyses, most prominently the Ecdysozoa (arthropods, roundworms, priapulids and others) and Lophotrochozoa (molluscs, annelids, brachiopods and others). Lophotrochozoan interrelationships are under discussion, e.g. regarding the position of Nemertea (ribbon worms), which were discussed to be sister group to e.g. Mollusca, Brachiozoa or Platyhelminthes. Mitochondrial genomes contributed well with sequence data and gene order characters to the deep metazoan phylogeny debate.</p> <p>Results</p> <p>In this study we present the first complete mitochondrial genome record for a member of the Nemertea, <it>Lineus viridis</it>. Except two <it>trnP </it>and <it>trnT</it>, all genes are located on the same strand. While gene order is most similar to that of the brachiopod <it>Terebratulina retusa</it>, sequence based analyses of mitochondrial genes place nemerteans close to molluscs, phoronids and entoprocts without clear preference for one of these taxa as sister group.</p> <p>Conclusion</p> <p>Almost all recent analyses with large datasets show good support for a taxon comprising Annelida, Mollusca, Brachiopoda, Phoronida and Nemertea. But the relationships among these taxa vary between different studies. The analysis of gene order differences gives evidence for a multiple independent occurrence of a large inversion in the mitochondrial genome of Lophotrochozoa and a re-inversion of the same part in gastropods. We hypothesize that some regions of the genome have a higher chance for intramolecular recombination than others and gene order data have to be analysed carefully to detect convergent rearrangement events.</p

Branchiopoda und Astacida (Arthropoda, Crustacea)

Innerhalb der Arthropodensystematik sind die phylogenetischen Beziehungen der höheren Crustaceataxa seit langem von besonderen Interesse. Ziel dieser Arbeit ist die Rekonstruktion der phylogenetischen Verwandtschaftsverhältnisse mit Hilfe molekularer Datensätze für die Phyllopoda, die zusammen mit den Anostraca die Branchiopoda bilden und der Astacoidea (Astacida), einer Teilgruppe der Flusskrebse. Folgende molekulare Marker kamen zum Einsatz: 1) Für die Phyllopoda: Die 3. Domäne der mitochondrial codierten 12S rRNA, unter Berücksichtigung von Sekundärtrukturinformationen, das nukleare Gen EF-1 alpha und die Positionen von Introns im Gen EF-1 alpha. 2) Für die Astacoidea: Die 3. Domäne der 12S rRNA und das mitochondrial codierte Gen cox1. Durch die Wahl der molekularen Marker, die mit unterschiedlichen computerkladistischen Methoden ausgewertet wurden, konnten für die meisten Fragen eine eindeutige und im Fall der Astacoidea überraschende phylogenetische Aussage getroffen werden. Die gewonnenen Hypothesen werden ausführlich im Licht morphologischer Hypothesen diskutiert.The phylogenetic relationships of the higher arthropod taxa are still of special interest. Especially the interrelationships of the different Crustacea taxa have long been debated. The focus of this investigation is to make a contribution to the phylogenies of two Crustacea taxa using molecular markers: The Phyllopoda which belong together with the Anostraca to the branchiopods, and of the Astacoidea, one of the two higher crayfish taxa (Astacida). The following molecular markers were used: 1) Phyllopoda: the 3rd domain of the mitochondrial encoded 12S rRNA taking into account informations of the secondary structure, the nuclear encoded proteingene EF-1 alpha and the positions of introns found in the coding region of EF-1 alpha. 2) Astacoidea: the 3rd domain of the 12S rRNA and the mitochondrial encoded proteingene cox1. The choice of the mentioned markers in combination with different computercladistical methods allowed to give a satisfying, and in the case of the Astacoidea a more surprising answer to most addressed phylogenetic questions. The gained hypotheses are then discussed in detail in the light of morphological features and hypotheses

The complete mitochondrial genome of the sea spider <it>Nymphon gracile </it>(Arthropoda: Pycnogonida)

<p>Abstract</p> <p>Background</p> <p>Mitochondrial genomes form units of genetic information replicating indepentently from nuclear genomes. Sequence data (most often from protein-coding genes) and other features (gene order, RNA secondary structure) of mitochondrial genomes are often used in phylogenetic studies of metazoan animals from population to phylum level. Pycnogonids are primarily marine arthropods, often considered closely related to chelicerates (spiders, scorpions and allies). However, due to their aberrant morphology and to controversial results from molecular studies, their phylogenetic position is still under debate.</p> <p>Results</p> <p>This is the first report of a complete mitochondrial genome sequence from a sea spider (<it>Nymphon gracile</it>, class Pycnogonida). Gene order derives from that of other arthropods so that presumably 10 single tRNA gene translocations, a translocation of the mitochondrial control region, and one large inversion affecting protein-coding genes must have happened in the lineage leading to <it>Nymphon gracile</it>. Some of the changes in gene order seem not to be common to all pycnogonids, as those were not found in a partial mitochondrial genome of another species, <it>Endeis spinosa</it>. Four transfer RNAs of <it>Nymphon gracile </it>show derivations from the usual cloverleaf secondary structure (truncation or loss of an arm). Initial phylogenetic analyses using mitochondrial protein-coding gene sequences placed Pycnogonida as sister group to Acari. However, this is in contrast to the majority of all other studies using nuclear genes and/or morphology and was not recovered in a second analysis where two long-branching acarid species were omitted.</p> <p>Conclusion</p> <p>Extensive gene rearrangement characterizes the mitochondrial genome of <it>Nymphon gracile</it>. At least some of the events leading to this derived gene order happened after the split of pycnogonid subtaxa. Nucleotide and amino acid frequencies show strong differences between chelicerate taxa, presumably biasing phylogenetic analyses. Thus the affinities between Pycnogonida and Acari (mites and ticks), as found in phylogenetic analyses using mitochondrial genes, may rather be due to long-branch attraction and independently derived nucleotide composition and amino acid frequency, than to a real sister group relationship.</p

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

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