Total codon usage across the protein-coding genes of the <i>Strigamia</i> mitochondrial genome.

<p>Standard one-letter abbreviations for amino acids (Aa) using invertebrate mitochondrial genetic code.</p><p>Total codon usage across the protein-coding genes of the <i>Strigamia</i> mitochondrial genome.</p

Comparisons of gene orders in the mitochondrial genomes of <i>Strigamia maritima</i>, the arthropod ‘ground-plan’ (<i>Limulus polyphemus</i>), three further chilopods, three diplopods and a symphylan.

<p>Genes are not drawn to scale; shaded genes indicate those that have moved from the original arthropod ‘ground-plan’.</p

Putative secondary structures of tRNAs from the mitochondrial genome of <i>Strigamia maritima</i> as predicted by MiTFi [40, 41].

<p>Putative secondary structures of tRNAs from the mitochondrial genome of <i>Strigamia maritima</i> as predicted by MiTFi [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121369#pone.0121369.ref040" target="_blank">40</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0121369#pone.0121369.ref041" target="_blank">41</a>].</p

The Complete Mitochondrial Genome of the Geophilomorph Centipede <i>Strigamia maritima</i>

<div><p><i>Strigamia maritima</i> (Myriapoda; Chilopoda) is a species from the soil-living order of geophilomorph centipedes. The Geophilomorpha is the most speciose order of centipedes with over a 1000 species described. They are notable for their large number of appendage bearing segments and are being used as a laboratory model to study the embryological process of segmentation within the myriapods. Using a scaffold derived from the recently published genome of <i>Strigamia maritima</i> that contained multiple mitochondrial protein-coding genes, here we report the complete mitochondrial genome of <i>Strigamia</i>, the first from any geophilomorph centipede. The mitochondrial genome of <i>S</i>. <i>maritima</i> is a circular molecule of 14,938 base pairs, within which we could identify the typical mitochondrial genome complement of 13 protein-coding genes and 2 ribosomal RNA genes. Sequences resembling 16 of the 22 transfer RNA genes typical of metazoan mitochondrial genomes could be identified, many of which have clear deviations from the standard ‘cloverleaf’ secondary structures of tRNA. Phylogenetic trees derived from the concatenated alignment of protein-coding genes of <i>S</i>. <i>maritima</i> and >50 other metazoans were unable to resolve the Myriapoda as monophyletic, but did support a monophyletic group of chilopods: <i>Strigamia</i> was resolved as the sister group of the scolopendromorph <i>Scolopocryptos sp</i>. and these two (Geophilomorpha and Scolopendromorpha), along with the Lithobiomorpha, formed a monophyletic group the Pleurostigmomorpha. Gene order within the <i>S</i>. <i>maritima</i> mitochondrial genome is unique compared to any other arthropod or metazoan mitochondrial genome to which it has been compared. The highly unusual organisation of the mitochondrial genome of <i>Strigamia maritima</i> is in striking contrast with the conservatively evolving nuclear genome: sampling of more members of this order of centipedes will be required to see whether this unusual organization is typical of the Geophilomorpha or results from a more recent reorganisation in the lineage leading to <i>Strigamia</i>.</p></div

Maximum Likelihood phylogenetic analysis of mitochondrial protein-coding genes from Arthropoda species including <i>S</i>. <i>maritima</i>.

<p>Support at nodes are SH-like support values. A monophyletic Chilopoda is resolved as sister group to Pancrustacea (SH-like support = 0.99) and Pauropoda (represented by <i>Pauropus longiramus</i>) placed as sister group to Chelicerata (SH-like support = 0.97). Within the Chilopoda, Scutigeromorpha (<i>Scutigera coleoptrata</i>) are resolved as sister group to the three other chilopod orders represented in our phylogeny (Lithobiomorpha, (<i>Bothropolys sp</i>., <i>Lithobius forficatus</i> and <i>Cermatobius longicornis</i>); Scolopendromorpha (<i>Scolopocryptos sp</i>.) and Geophilomorpha (<i>Strigamia maritima</i>) with SH-like support = 0.99.</p

Bayesian phylogenetic analysis of mitochondrial protein-coding genes from Arthropoda species including <i>S</i>. <i>maritima</i>.

<p>Support values at nodes are Bayesian Posterior Probability (BPP). Myriapoda and Chelicerata, ‘Myriochelata’ (BPP = 0.94) resolved as the sister group to Pancrustacea (Crustacea and Hexapoda, BPP = 1.0). A monophyletic Chilopoda is resolved with BPP = 0.99, within which Scutigeromorpha (<i>Scutigera coleoptrata</i>) are resolved as the sister group to the three remaining chilopod orders represented in our phylogeny (Lithobiomorpha, (<i>Bothropolys sp</i>., <i>Lithobius forficatus</i> and <i>Cermatobius longicornis</i>); Scolopendromorpha (<i>Scolopocryptos sp</i>.) and Geophilomorpha (<i>Strigamia maritima</i>)) with BPP = 1.</p

Organisation of the <i>Strigamia maritima</i> mitochondrial genome.

<p>Intergenic nucleotides shown as gaps (positive values) or overlap (negative values) between consecutive genes.</p><p>Organisation of the <i>Strigamia maritima</i> mitochondrial genome.</p

Overview of the mitochondrial genome of <i>Strigamia maritima</i> (Myriapoda: Chilopoda), genes not drawn to scale.

<p>Numbers inside the circle show intergenic spaces (positive values) or intergenic overlaps (negative values). Protein-coding genes are denoted by three letter abbreviations, ribosomal genes denoted by four letter abbreviations. tRNAs are indicated by single uppercase letters.</p

Ancestral protein kinases are extensively lost during arthropod evolution.

<p><i>S. maritima</i> is an exception and retains the largest number of ancestral kinases. Numbers of kinase subfamilies in selected species are shown in parentheses after species names. The gains, losses, and inferred content of common ancestors are listed on internal branches. Kinases found in at least two species from human, <i>C. elegans</i> and <i>Nematostella vectenesis</i> were used as an outgroup.</p

Presence and absence of immunity genes in different arthropods.

<p>Counts of immune genes are shown for <i>S. maritima</i>, <i>D. pulex</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-McTaggart1" target="_blank">[131]</a>, <i>A. mellifera</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-Evans1" target="_blank">[86]</a>, <i>T. castaneum</i>, <i>Anopheles gambiae</i>, and <i>D. melanogaster</i><a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002005#pbio.1002005-Dasmahapatra1" target="_blank">[132]</a>. ∼, identity of the gene is uncertain; -, not investigated.</p