Mitochondrial genomics in Orthoptera using MOSAS

Phylomitogenomics of two Neotropical species of long-legged crickets Endecous Saussure, 1878 (Orthoptera: Phalangopsidae)

Mitochondrial genomes have provided significant insights into the evolution of several insects. A typical mitogenome contains 37 genes, and variations in gene order can indicate evolutionary relationships between species. In this study, we have assembled the first complete mitogenomes of Endecous chape and E. onthophagus and analyzed the phylogenetic implications for the Gryllidea infraorder. We performed DNA extractions and genome sequencing for both Endecous species. Subsequently, we searched for raw data in the Sequence Read Archive (SRA) in NCBI. Using the SRA data, we assembled the partial mitogenome of Dianemobius nigrofasciatus and annotated the protein-coding genes (PCGs) for nine species. Phylogenomic relationships were reconstructed using Maximum Likelihood (ML) and Bayesian Inference (BI), utilizing the PCGs from 49 Gryllidea species. The mitogenome lengths of E. chape and E. onthophagus are 16,266 bp and 16,023 bp, respectively, while D. nigrofasciatus has a length of 15,359 bp. Our results indicate that species within the infraorder exhibit four types of gene order arrangements that align with their phylogenetic relationships. Both phylogenomic trees displayed strong support, and the ML corroborated with the literature. Gryllidea species have significantly contributed to various fields, and studying their mitogenomes can provide valuable insights into this infraorder evolution.

Complete mitochondrial genome sequences of two ground crickets, Dianemobius fascipes nigrofasciatus and Polionemobius taprobanensis (Orthoptera: Grylloidea: trigonidiidae)

The authors sequenced the complete mitochondrial (mt) genomes of the band-legged ground cricket (Dianemobius fascipes nigrofasciatus Matsumura, 1904) and a temperate form of the lawn ground cricket (Polionemobius taprobanensis Walker, 1869), collected in Japan. The length of the mt genome sequences was 15,354 bp in D. fascipes nigrofasciatus and 16,063 bp in P. taprobanensis. Annotation of the mt genome sequences revealed 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The orientation of the genes was the same as in other Grylloidea species, and the order was the same as in other Trigonidiidae species. In our phylogenetic analysis, D. fascipes nigrofasciatus formed a clade with D. fascipes collected in China, and the temperate form of P. taprobanensis formed a clade with P. taprobanensis collected in China. Comparison of the numbers of positions with different amino acid residues encoded by the protein-coding genes implied the separate species status of each member of each of the two pairs of ground crickets. The mt genome sequences of D. fascipes nigrofasciatus and P. taprobanensis will contribute to phylogenetic and taxonomic studies of the Trigonidiidae.

Mitogenome of Xya pfaendleri (Orthoptera: Caelifera): Its comparative description and phylogenetic position within Tridactylidea

We report the comparative examination of the complete mitochondrial genome of the pygmy mole cricket Xya pfaendleri (Orthoptera: Caelifera: Tridactylidae). The mitogenome consists of 13 protein-coding regions, 22 tRNAs, two rRNAs, and one control region, following the gene order of the ancestral pancrustacean mitogenome. The length of the mitogenome in Xya pfaendleri is 15352 bp. The start and stop codons of the protein-coding genes exhibit the general pattern observed in orthopterans. The data indicate that the pattern of gene overlapping/intergenic sequences exhibits a significant phylogenetic signal. A phylogenetic tree inferred using 12 mitogenomes (seven belonging to Tridactylidea, three to Acrididea, and two to Ensifera) confirms the sister group relationship of Acrididea and Tridactylidea. The relationship among the families of Tridactylidea is Cylindrachetidae + (Ripipterygidae + Tridactylidae). The mitogenome sequences of Xya and Tridactylus constitute a single clade, sharing a last common ancestor 94 million years ago, and rendering the first genus paraphyletic. The present preliminary data suggest that we still have much to learn about the evolution and diversity of Tridactylidea.

Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs

A wide range of scientific fields, such as forensics, anthropology, medicine, and molecular evolution, benefits from the analysis of mitogenomic data. With the development of new sequencing technologies, the amount of mitochondrial sequence data to be analyzed has increased exponentially over the last few years. The accurate annotation of mitochondrial DNA is a prerequisite for any mitogenomic comparative analysis. To sustain with the growth of the available mitochondrial sequence data, highly efficient automatic computational methods are, hence, needed. Automatic annotation methods are typically based on databases that contain information about already annotated (and often pre-curated) mitogenomes of different species. However, the existing approaches have several shortcomings: 1) they do not scale well with the size of the database; 2) they do not allow for a fast (and easy) update of the database; and 3) they can only be applied to a relatively small taxonomic subset of all species. Here, we present a novel approach that does not have any of these aforementioned shortcomings, (1), (2), and (3). The reference database of mitogenomes is represented as a richly annotated de Bruijn graph. To generate gene predictions for a new user-supplied mitogenome, the method utilizes a clustering routine that uses the mapping information of the provided sequence to this graph. The method is implemented in a software package called DeGeCI (De Bruijn graph Gene Cluster Identification). For a large set of mitogenomes, for which expert-curated annotations are available, DeGeCI generates gene predictions of high conformity. In a comparative evaluation with MITOS2, a state-of-the-art annotation tool for mitochondrial genomes, DeGeCI shows better database scalability while still matching MITOS2 in terms of result quality and providing a fully automated means to update the underlying database. Moreover, unlike MITOS2, DeGeCI can be run in parallel on several processors to make use of modern multi-processor systems.

Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction

Compared to nuclear genomes, mitochondrial genomes (mitogenomes) are small and usually code for only a few dozen genes. Still, identifying genes and their structure can be challenging and time-consuming. Even automated tools for mitochondrial genome annotation often require manual analysis and curation by skilled experts. The most difficult steps are (i) the structural modelling of intron-containing genes; (ii) the identification and delineation of Group I and II introns; and (iii) the identification of moderately conserved, non-coding RNA (ncRNA) genes specifying 5S rRNAs, tmRNAs and RNase P RNAs. Additional challenges arise through genetic code evolution which can redefine the translational identity of both start and stop codons, thus obscuring protein-coding genes. Further, RNA editing can render gene identification difficult, if not impossible, without additional RNA sequence data. Current automated mito- and plastid-genome annotators are limited as they are typically tailored to specific eukaryotic groups. The MFannot annotator we developed is unique in its applicability to a broad taxonomic scope, its accuracy in gene model inference, and its capabilities in intron identification and classification. The pipeline leverages curated profile Hidden Markov Models (HMMs), covariance (CMs) and ERPIN models to better capture evolutionarily conserved signatures in the primary sequence (HMMs and CMs) as well as secondary structure (CMs and ERPIN). Here we formally describe MFannot, which has been available as a web-accessible service (https://megasun.bch.umontreal.ca/apps/mfannot/) to the research community for nearly 16 years. Further, we report its performance on particularly intron-rich mitogenomes and describe ongoing and future developments.

New Insights into the Origin and Evolution of Mysmenid Spiders (Araneae, Mysmenidae) Based on the First Four Complete Mitochondrial Genomes

The mitochondrial genome (mitogenome) is recognized as an effective molecular marker for studying molecular evolution and phylogeny. The family Mysmenidae is a group of widely distributed and covert-living spiders, of which the mitogenomic information is largely unclear. In this study, we obtained the first four complete mitogenomes of mysmenid spiders (one aboveground species: Trogloneta yuensis, and three cave-dwelling species: T. yunnanense, Yamaneta kehen and Y. paquini). Comparative analyses revealed that their lengths ranged from 13,771 bp (T. yuensis) to 14,223 bp (Y. kehen), containing a standard set of 37 genes and an A + T-rich region with the same gene orientation as other spider species. The mitogenomic size of T. yunnanense was more similar to that of Yamaneta mitogenomes than that of T. yuensis, which might indicate the convergent evolution of cave spiders. High variability was detected between the genera Trogloneta and Yamaneta. The A + T content, the amino acid frequency of protein-coding genes (PCGs) and the secondary structures of tRNAs showed large differences. Yamaneta kehen and Y. paquini contained almost identical truncated tRNAs, and their intergenic spacers and overlaps exhibited high uniformity. The two Yamaneta species also possessed a higher similarity of start/stop codons for PCGs than the two Trogloneta species. In selective pressure analysis, compared to Yamaneta, Trogloneta had much higher Ka/Ks values, which implies that selection pressure may be affected by habitat changes. In our study, the phylogenetic analysis based on the combination of 13 PCGs and two rRNAs showed that Mysmenidae is a sister clade to the family Tetragnathidae. Our data and findings will contribute to the better understanding of the origin and evolution of mysmenid spiders.

The Complete Mitogenomes of Three Grasshopper Species with Special Notes on the Phylogenetic Positions of Some Related Genera

Clarifying phylogenetic position and reconstructing robust phylogeny of groups using various evidences are an eternal theme for taxonomy and systematics. In this study, the complete mitogenomes of Longzhouacris mirabilis, Ranacris albicornis, and Conophyma zhaosuensis were sequenced using next-generation sequencing (NGS), and the characteristics of the mitogenomes are presented briefly. The mitogenomes of the three species are all circular molecules with total lengths of 16,164 bp, 15,720 bp, and 16,190 bp, respectively. The gene structures and orders, as well as the characteristics of the mitogenomes, are similar to those of other published mitogenomes in Caelifera. The phylogeny of the main subfamilies of Acrididae with prosternal process was reconstructed using a selected dataset of mitogenome sequences under maximum likelihood (ML) and Bayesian inference (BI) frameworks. The results showed that the genus Emeiacris consistently fell into the subfamily Melanoplinae rather than Oxyinae, and the genus Choroedocus had the closest relationship with Shirackiacris of the subfamily Eyprepocnemidinae in both phylogenetic trees deduced from mitogenome protein coding genes (PCGs). This finding is entirely consistent with the morphological characters, which indicate that Emeiacris belongs to Melanoplinae and Choroedocus belongs to Eyprepocnemidinae. In addition, the genera Conophymacris and Xiangelilacris, as well as Ranacris and Menglacris, are two pairs of the closest relatives, but their phylogenetic positions need further study to clarify.

Phylogeny and Integrative Taxonomy of the Genera Gymnaetoides and Pseudotachycines (Orthoptera: Rhaphidophoridae)

The genera Gymnaetoides and Pseudotachycines are endemic to China and are morphologically homogeneous. The few available diagnostic characters make species identification particularly challenging. Species cannot be classified according to the given generic diagnosis, and phylogenetic analyses have not been reported. Here, we reconstruct the phylogeny using Bayesian inference and maximum likelihood and employ four approaches to delimit species. The results suggest that both Gymnaetoides and Pseudotachycines are paraphyletic. Therefore, we revise their taxonomy based on the combination of morphological characters and molecular data. A new genus Homotachycines Zhu & Shi gen. nov. is erected, and six new combinations are proposed. Species delimitation identifies 15 new species and one new subspecies: Gymnaetoides huangshanensis, G. petalus, G. yangmingensis, G. lushanensis, Pseudotachycines procerus, P. procerus guizhouensis, P. zhengi, P. nephrus, P. sagittus, P. fengyangshanensis, Homotachycines triangulus, H. quadratus, H. baokangensis, H. fusus, H. concavus, and H. qinlingensis sp. nov. Moreover, we find that the shapes of the dorsal lateral lobes and the dorsal median lobe of the male genitalia are also important characters for identifying these genera and that the shapes of the dorsal and lateral sclerites of the male genitalia are suitable for the classifications of species.

Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS)

Mitochondrial genomes (mtgenome) represent an important source of information for addressing fundamental evolutionary, phylogeographic, systematic, and ecological questions in marine organisms. In the last two decades the advent of high-throughput next-generation sequencing (NGS) has provided an unprecedented possibility to access large amount of genomic data and, as such, there has been a rapid growth in mtgenome resources and studies. In particular, NGS strategies represent a great advantage for investigating nonmodel marine organisms for which no or limited genomic resources are available. Here, we describe a routinely used standardized protocol to obtain mtgenome of nonmodel marine organisms by NGS. The protocol is composed of five main steps, including DNA extraction, DNA fragmentation, library preparation, high-throughput sequencing, and bioinformatic analyses. Each of the first three steps is followed by size/quality and concentration validations. The advantages of the described protocol rely on the assumption that no a priori information on mtgenome of the studied organism is needed and on its versatility as researchers may choose several kits for DNA extraction and library preparation and adopt different methods for DNA fragmentation depending on their needs, experience, and suppliers.

Phylogenetic Position of the Genus Alulacris (Orthoptera: Acrididae: Melanoplinae: Podismini) Revealed by Complete Mitogenome Evidence

Whole mitogenomes are a useful data source for a wide variety of research goals due to the vastly cheaper sequencing cost and the far less demanding high-quality templates. The mitogenome has demonstrated great potential in resolving phylogenetic questions in Orthoptera at different taxonomic scales as well as exploring patterns of molecular and morphological character evolutions. In this study, the complete mitogenome of Alulacrisshilinensis (Zheng, 1977) was sequenced using next-generation sequencing, the characteristics of the mitogenome are presented briefly, and the phylogeny of the Melanoplinae and Catantopinae was reconstructed using a selected dataset of mitogenome sequences under maximum likelihood and Bayesian inference frameworks. The results show that the genus was consistently assigned to the subfamily Melanoplinae rather than Catantopinae in all phylogenetic trees deduced from different datasets under different frameworks, and this finding is entirely consistent with its morphological characters. Therefore, it is more appropriate to place the genus Alulacris in Melanoplinae rather than in Catantopinae.

Mitogenome of Coprophanaeus ensifer and phylogenetic analysis of the Scarabaeidae family (Coleoptera)

Several studies about the phylogenetic relationships of the Scarabaeinae subfamily (Coleoptera: Scarabaeidae) have been performed, but some phylogenetic uncertainties persist including the relationship and monophyly of different tribes and some genera. The aim of this study was to characterize the mitogenome of Coprophanaeus ensifer in order to establish its position within the Scarabaeidae family and to contribute to the resolution of some phylogenetic uncertainties. The mitogenome was sequenced on the Illumina HiSeq 4000, assembled using the Mitobim software and annotated in MITOS WebServer. The phylogenetic trees were reconstructed by Bayesian inference. The C. ensifer mitogenome is a molecule of 14,964 bp that contains the number and organization of the genes similar to those of most Coleoptera species. Phylogenetic reconstruction suggests monophyly of the tribe Phanaeini and supports the hypothesis that Coprini is a sister group of Phanaeini. The results also revealed the position of the tribe Oniticellini which is grouped with Onthophagini and Onitini. The geographic distribution of these species that form the most ancestral clade suggests with Scarabaeinae originated in Africa.

Phylogenetic position of the genera Caryandoides, Paratoacris, Fer and Longchuanacris (Orthoptera:Acrididae) revealed by complete mitogenome sequences

Many taxa in the Acrididae have controversial phylogenetic positions. A typical example of such controversies is the phylogenetic positions of the genera Caryandoides, Paratoacris, Fer and Longchuanacris, as well as some other related taxa, which were placed in Oxyinae by some authors, but were considered members of the subfamily Catantopinae by others. In this study, the complete mitogenomes of nine species were sequenced using next-generation sequencing, the characteristics of the newly sequenced mitogenomes are presented briefly, and the phylogeny of the Oxyinae and Catantopinae are reconstructed using a selected dataset of mitogenome sequences under maximum likelihood and Bayesian inference frameworks. The results show that the four controversial genera were consistently assigned to the subfamily Oxyinae rather than Catantopinae in all phylogenetic trees deduced from different datasets under different frameworks, and this finding is entirely consistent with their morphological characters. Therefore, it is more appropriate to place them in Oxyinae rather than Catantopinae. In addition, the results from our analysis also confirm the membership of the genus Apalacris in Coptacrinae rather than Catantopinae, and indicate the uncertainty in the phylogenetic position of the genus Traulia, and a more in-depth study is necessary to resolve the relationship of Traulia with other catantopine groups or Coptacrinae.

Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae)

In this study, the whole mitochondrial genomes (mitogenomes) from four species were sequenced. The complete mitochondrial genomes of Sinopodisma pieli, S. houshana, S. qinlingensis, and S. wulingshanensis are 15,857 bp, 15,818 bp, 15,843 bp, and 15,872 bp in size, respectively. The 13 protein-coding genes (PCGs) begin with typical ATN codons, except for COXI in S. qinlingensis, which begins with ACC. The highest A+T content in all the sequenced orthopteran mitogenomes is 76.8% (S. qinlingensis), followed by 76.5% (S. wulingshanensis), 76.4% (S. pieli) and 76.4% (S. houshana) (measured on the major strand). The long polythymine stretches (T-stretch) in the A+T-rich region of the four species are not adjacent to the trnI locus but are inside the stem-loop sequences on the major strand. Moreover, several repeated elements are found in the A+T-rich region of the four species. Phylogenetic analysis based on 53 mitochondrial genomes using Bayesian Inference (BI) and Maximum Likelihood (ML) revealed that Melanoplinae (Podismini) was a monophyletic group; however, the monophyly of Sinopodisma was not supported. These data will provide important information for a better understanding of the phylogenetic relationship of Melanoplinae.

MtOrt: an empirical mitochondrial amino acid substitution model for evolutionary studies of Orthoptera insects

BACKGROUND

Amino acid substitution models play an important role in inferring phylogenies from proteins. Although different amino acid substitution models have been proposed, only a few were estimated from mitochondrial protein sequences for specific taxa such as the mtArt model for Arthropoda. The increasing of mitochondrial genome data from broad Orthoptera taxa provides an opportunity to estimate the Orthoptera-specific mitochondrial amino acid empirical model.

RESULTS

We sequenced complete mitochondrial genomes of 54 Orthoptera species, and estimated an amino acid substitution model (named mtOrt) by maximum likelihood method based on the 283 complete mitochondrial genomes available currently. The results indicated that there are obvious differences between mtOrt and the existing models, and the new model can better fit the Orthoptera mitochondrial protein datasets. Moreover, topologies of trees constructed using mtOrt and existing models are frequently different. MtOrt does indeed have an impact on likelihood improvement as well as tree topologies. The comparisons between the topologies of trees constructed using mtOrt and existing models show that the new model outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein data.

CONCLUSIONS

The new mitochondrial amino acid substitution model of Orthoptera shows obvious differences from the existing models, and outperforms the existing models in inferring phylogenies from Orthoptera mitochondrial protein sequences.

OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.

Mitochondrial genome characterization of the family Trigonidiidae (Orthoptera) reveals novel structural features and nad1 transcript ends

The Trigonidiidae, a family of crickets, comprises 981 valid species with only one mitochondrial genome (mitogenome) sequenced to date. To explore mitogenome features of Trigonidiidae, six mitogenomes from its two subfamilies (Nemobiinae and Trigonidiinae) were determined. Two types of gene rearrangements involving a trnN-trnS1-trnE inversion and a trnV shuffling were shared by Trigonidiidae. A long intergenic spacer was observed between trnQ and trnM in Trigonidiinae (210-369 bp) and Nemobiinae (80-216 bp), which was capable of forming extensive stem-loop secondary structures in Trigonidiinae but not in Nemobiinae. The anticodon of trnS1 was TCT in Trigonidiinae, rather than GCT in Nemobiinae and other related subfamilies. There was no overlap between nad4 and nad4l in Dianemobius, as opposed to a conserved 7-bp overlap commonly found in insects. Furthermore, combined comparative analysis and transcript verification revealed that nad1 transcripts ended with a U, corresponding to the T immediately preceding a conserved motif GAGAC in the superfamily Grylloidea, plus poly-A tails. The resultant UAA served as a stop codon for species lacking full stop codons upstream of the motif. Our findings gain novel understanding of mitogenome structural diversity and provide insight into accurate mitogenome annotation.

MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization

Mitochondrial genome (mitogenome) plays important roles in evolutionary and ecological studies. It becomes routine to utilize multiple genes on mitogenome or the entire mitogenomes to investigate phylogeny and biodiversity of focal groups with the onset of High Throughput Sequencing (HTS) technologies. We developed a mitogenome toolkit MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads. We evaluated its performance using a total of 50 samples of which mitogenomes are publicly available. The results showed that MitoZ can recover more full-length mitogenomes with higher accuracy compared to the other available mitogenome assemblers. Overall, MitoZ provides a one-click solution to construct the annotated mitogenome from HTS raw data and will facilitate large scale ecological and evolutionary studies. MitoZ is free open source software distributed under GPLv3 license and available at https://github.com/linzhi2013/MitoZ.

OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes

Organellar (plastid and mitochondrial) genomes play an important role in resolving phylogenetic relationships, and next-generation sequencing technologies have led to a burst in their availability. The ongoing massive sequencing efforts require software tools for routine assembly and annotation of organellar genomes as well as their display as physical maps. OrganellarGenomeDRAW (OGDRAW) has become the standard tool to draw graphical maps of plastid and mitochondrial genomes. Here, we present a new version of OGDRAW equipped with a new front end. Besides several new features, OGDRAW now has access to a local copy of the organelle genome database of the NCBI RefSeq project. Together with batch processing of (multi-)GenBank files, this enables the user to easily visualize large sets of organellar genomes spanning entire taxonomic clades. The new OGDRAW server can be accessed at https://chlorobox.mpimp-golm.mpg.de/OGDraw.html.

The phylogeny and evolutionary timescale of stoneflies (Insecta: Plecoptera) inferred from mitochondrial genomes

Phylogenetic analysis based on mitochondrial genomic data from 25 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera (stoneflies). The monophyly of both currently recognized suborders was strongly supported, concordant with previous molecular analyses of Plecoptera. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae + Diamphipnoidae and Austroperlidae + Gripopterygidae; consistent with relationships proposed based on morphology. The largely northern hemisphere suborder Arctoperlaria also divided into two groups, Euholognatha and Systellognatha, each composed of the five families traditionally assigned to each infraorder (the placement Scopuridae by mt genome data remains untested at this time). Within Euholognatha, strong support for the clade Nemouridae + Notonemouridae confirmed the northern origin of the currently southern hemisphere restricted Notonemouridae. Other family level relationships within the Arctoperlaria differ from those recovered by previous morphology and molecular based analyses. A fossil-calibrated divergence estimation suggests the formation of two suborders dates back to the Jurassic (181 Ma), with subsequent diversification of most stonefly families during the Cretaceous. This result confirms the hypothesis that initial divergence between the suborders was driven by the breakup of the supercontinent Pangaea into Laurasia and Gondwanaland (commencing 200 Ma and complete by 150 Ma).

Comparative analysis of mitochondrial genomes of the superfamily Grylloidea (Insecta, Orthoptera) reveals phylogenetic distribution of gene rearrangements

To further characterize mitochondrial genome (mitogenome) features of the superfamily Grylloidea (Insecta, Orthoptera), mitogenomes of Cacoplistes rogenhoferi and Meloimorpha japonica representing the family Mogoplistidae and three Ornebius species of Phalangopsidae were sequenced. A repeat-containing control region (CR) and 37 genes were present in these mitogenomes. Unusual start codons (TCG, CCG, and CTG) of cox1 and, in Ornebius, a partial stop codon (T) of nad1 followed by a 15-17-bp intergenic spacer were proposed based on transcript information and sequence alignments. The mitogenome-based phylogenetic trees suggest strongly the familial relationships as (((Phalangopsidae + Gryllidae) + Trigonidiidae) + Mogoplistidae). The exclusive occurrence of the trnE-trnS1-trnN rearrangement in Phalangopsidae, Gryllidae, and Trigonidiidae is suggestive of its appearance in the common ancestor of these families after the separation of Mogoplistidae. The trnV transposition in O. bimaculatus and formerly sequenced Trigonidium sjostedti (Trigonidiidae) indicates a potential consequence of parallel evolution. This study offers novel insights into mitogenome evolution, especially gene rearrangements, of Grylloidea.

Complete mitochodrial genome of the crab spider Ebrechtella tricuspidata (Araneae: Thomisidae): A novel tRNA rearrangement and phylogenetic implications for Araneae

Mitochondrial genomes are widely used for phylogenetic and phylogeographic analyses among arthropods, but there is a lack of sufficient mitochondrial genome sequence data for spiders. Herein, we sequenced and characterized the complete mitochondrial genome of a crab spider Ebrechtella tricuspidata (Araneae: Thomisidae). The circular mitochondrial genome is 14,352 bp long, including a standard set of 37 genes and an A + T-rich region. Nucleotide composition is highly biased toward A + T nucleotides (77.3%). A novel gene order rearrangement is detected by a tRNA (trnL1) translocation. Tandem repeats are not identified in the A + T-rich region. Most of the tRNAs are greatly reduced in size and cannot be folded into typical cloverleaf-shaped secondary structures. The phylogenetic analysis confirms that the mitochondrial genome sequences are useful in resolving higher-level relationship of Araneae. Overall, our data present in this study will elevate our knowledge on the architecture and evolution of spider mitochondrial genome.

Mitochondrial genomes of three Tetrigoidea species and phylogeny of Tetrigoidea

The mitochondrial genomes (mitogenomes) of Formosatettix qinlingensis, Coptotettix longjiangensis and Thoradonta obtusilobata (Orthoptera: Caelifera: Tetrigoidea) were sequenced in this study, and almost the entire mitogenomes of these species were determined. The mitogenome sequences obtained for the three species were 15,180, 14,495 and 14,538 bp in length, respectively, and each sequence included 13 protein-coding genes (PCGs), partial sequences of rRNA genes (rRNAs), tRNA genes (tRNAs) and a A + T-rich region. The order and orientation of the gene arrangement pattern were identical to that of most Tetrigoidea species. Some conserved spacer sequences between trnS(UCN) and nad1 were useful to identify Tetrigoidea and Acridoidea. The Ka/Ks value of atp8 between Trachytettix bufo and other four Tetrigoidea species indicated that some varied sites in this gene might be related with the evolution of T. bufo. The three Tetrigoidea species were compared with other Caelifera. At the superfamily level, conserved sequences were observed in intergenic spacers, which can be used for superfamily level identification between Tetrigoidea and Acridoidea. Furthermore, a phylogenomic analysis was conducted based on the concatenated data sets from mitogenome sequences of 24 species of Orthoptera in the superorders Caelifera and Ensifera. Both maximum likelihood and bayesian inference analyses strongly supported Acridoidea and Tetrigoidea as forming monophyletic groups. The relationships among six Tetrigoidea species were (((((Tetrix japonica, Alulatettix yunnanensis), Formosatettix qinlingensis), Coptotettix longjiangensis), Trachytettix bufo), Thoradonta obtusilobata).

The Complete Mitogenome of the Wood-Feeding Cockroach Cryptocercus meridianus (Blattodea: Cryptocercidae) and Its Phylogenetic Relationship among Cockroach Families

In this study, the complete mitochondrial genome of Cryptocercus meridianus was sequenced. The circular mitochondrial genome is 15,322 bp in size and contains 13 protein-coding genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes, and one D-loop region. We compare the mitogenome of C. meridianus with that of C. relictus and C. kyebangensis. The base composition of the whole genome was 45.20%, 9.74%, 16.06%, and 29.00% for A, G, C, and T, respectively; it shows a high AT content (74.2%), similar to the mitogenomes of C. relictus and C. kyebangensis. The protein-coding genes are initiated with typical mitochondrial start codons except for cox1 with TTG. The gene order of the C. meridianus mitogenome differs from the typical insect pattern for the translocation of tRNA-Ser^AGN, while the mitogenomes of the other two Cryptocercus species, C. relictus and C. kyebangensis, are consistent with the typical insect pattern. There are two very long non-coding intergenic regions lying on both sides of the rearranged gene tRNA-Ser^AGN. The phylogenetic relationships were constructed based on the nucleotide sequence of 13 protein-coding genes and two ribosomal RNA genes. The mitogenome of C. meridianus is the first representative of the order Blattodea that demonstrates rearrangement, and it will contribute to the further study of the phylogeny and evolution of the genus Cryptocercus and related taxa.

C. Costa M, A. Andow D, Paula DP. Mitogenome sequence accuracy using different elucidation methods

Mitogenome sequences are highly desired because they are used in several biological disciplines. Their elucidation has been facilitated through the development of massive parallel sequencing, accelerating their deposition in public databases. However, sequencing, assembly and annotation methods might induce variability in their quality, raising concerns about the accuracy of the sequences that have been deposited in public databases. In this work we show that different sequencing methods (number of species pooled in a library, insert size and platform) and assembly and annotation methods generated variable completeness and similarity of the resulting mitogenome sequences, using three species of predaceous ladybird beetles as models. The identity of the sequences varied considerably depending on the method used and ranged from 38.19 to 90.1% for Cycloneda sanguinea, 72.85 to 91.06% for Harmonia axyridis and 41.15 to 93.60% for Hippodamia convergens. Dissimilarities were frequently found in the non-coding A+T rich region, but were also common in coding regions, and were not associated with low coverage. Mitogenome completeness and sequence identity were affected by the sequencing and assembly/annotation methods, and high within-species variation was also found for other mitogenome depositions in GenBank. This indicates a need for methods to confirm sequence accuracy, and guidelines for verifying mitogenomes should be discussed and developed by the scientific community.

Characterization of the complete mitogenomes of two Neoscona spiders (Araneae: Araneidae) and its phylogenetic implications

The complete mitogenomes of two orb-weaving spiders Neoscona doenitzi and Neoscona nautica were determined and a comparative mitogenomic analysis was performed to depict evolutionary trends of spider mitogenomes. The circular mitogenomes are 14,161bp with A+T content of 74.6% in N. doenitzi and 14,049bp with A+T content of 78.8% in N. nautica, respectively. Both mitogenomes contain a standard set of 37 genes typically presented in metazoans. Gene content and orientation are identical to all previously sequenced spider mitogenomes, while gene order is rearranged by tRNAs translocation when compared with the putative ancestral gene arrangement pattern presented by Limulus polyphemus. A comparative mitogenomic analysis reveals that the nucleotide composition bias is obviously divergent between spiders in suborder Opisthothelae and Mesothelae. The loss of D-arm in the trnS(UCN) among all of Opisthothelae spiders highly suggested that this common feature is a synapomorphy for entire suborder Opisthothelae. Moreover, the trnS(AGN) in araneoids preferred to use TCT as an anticodon rather than the typical anticodon GCT. Phylogenetic analysis based on the 13 protein-coding gene sequences consistently yields trees that nest the two Neoscona spiders within Araneidae and recover superfamily Araneoidea as a monophyletic group. The molecular information acquired from the results of this study should be very useful for future research on mitogenomic evolution and genetic diversities in spiders.

The thorax of the cave cricket Troglophilus neglectus: anatomical adaptations in an ancient wingless insect lineage (Orthoptera: Rhaphidophoridae)

BACKGROUND

Secondary winglessness is a common phenomenon found among neopteran insects. With an estimated age of at least 140 million years, the cave crickets (Rhaphidophoridae) form the oldest exclusively wingless lineage within the long-horned grasshoppers (Ensifera). With respect to their morphology, cave crickets are generally considered to represent a `primitive' group of Ensifera, for which no apomorphic character has been reported so far.

RESULTS

We present the first detailed investigation and description of the thoracic skeletal and muscular anatomy of the East Mediterranean cave cricket Troglophilus neglectus (Ensifera: Rhaphidophoridae). T. neglectus possesses sternopleural muscles that are not yet reported from other neopteran insects. Cave crickets in general exhibit some unique features with respect to their thoracic skeletal anatomy: an externally reduced prospinasternum, a narrow median sclerite situated between the meso- and metathorax, a star-shaped prospina, and a triramous metafurca. The thoracic muscle equipment of T. neglectus compared to that of the bush cricket Conocephalus maculatus (Ensifera: Tettigoniidae) and the house cricket Acheta domesticus (Ensifera: Gryllidae) reveals a number of potentially synapomorphic characters between these lineages.

CONCLUSIONS

Based on the observed morphology we favor a closer relationship of Rhaphidophoridae to Tettigoniidae rather than to Gryllidae. In addition, the comparison of the thoracic morphology of T. neglectus to that of other wingless Polyneoptera allows reliable conclusions about anatomical adaptations correlated with secondary winglessness. The anatomy in apterous Ensifera, viz. the reduction of discrete direct and indirect flight muscles as well as the strengthening of specific leg muscles, largely resembles the condition found in wingless stick insects (Euphasmatodea), but is strikingly different from that of other related wingless insects, e.g. heel walkers (Mantophasmatodea), ice crawlers (Grylloblattodea), and certain grasshoppers (Caelifera). The composition of direct flight muscles largely follows similar patterns in winged respectively wingless species within major polyneopteran lineages, but it is highly heterogeneous between those lineages.

Climate oscillations, glacial refugia, and dispersal ability: factors influencing the genetic structure of the least salmonfly, Pteronarcella badia (Plecoptera), in Western North America

Background

Phylogeographic studies of aquatic insects provide valuable insights into mechanisms that shape the genetic structure of communities, yet studies that include broad geographic areas are uncommon for this group. We conducted a broad scale phylogeographic analysis of the least salmonfly Pteronarcella badia (Plecoptera) across western North America. We tested hypotheses related to mode of dispersal and the influence of historic climate oscillations on population genetic structure. In order to generate a larger mitochondrial data set, we used 454 sequencing to reconstruct the complete mitochondrial genome in the early stages of the project.

Results

Our analysis revealed high levels of population structure with several deeply divergent clades present across the sample area. Evidence from five mitochondrial genes and one nuclear locus identified a potentially cryptic lineage in the Pacific Northwest. Gene flow estimates and geographic clade distributions suggest that overland flight during the winged adult stage is an important dispersal mechanism for this taxon. We found evidence of multiple glacial refugia across the species distribution and signs of secondary contact within and among major clades.

Conclusions

This study provides a basis for future studies of aquatic insect phylogeography at the inter-basin scale in western North America. Our findings add to an understanding of the role of historical climate isolations in shaping assemblages of aquatic insects in this region. We identified several geographic areas that may have historical importance for other aquatic organisms with similar distributions and dispersal strategies as P. badia. This work adds to the ever-growing list of studies that highlight the potential of next-generation DNA sequencing in a phylogenetic context to improve molecular data sets from understudied groups.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0553-4) contains supplementary material, which is available to authorized users.

Rampant nuclear insertion of mtDNA across diverse lineages within Orthoptera (Insecta)

Nuclear mitochondrial pseudogenes (numts) are non-functional fragments of mtDNA inserted into the nuclear genome. Numts are prevalent across eukaryotes and a positive correlation is known to exist between the number of numts and the genome size. Most numt surveys have relied on model organisms with fully sequenced nuclear genomes, but such analyses have limited utilities for making a generalization about the patterns of numt accumulation for any given clade. Among insects, the order Orthoptera is known to have the largest nuclear genome and it is also reported to include several species with a large number of numts. In this study, we use Orthoptera as a case study to document the diversity and abundance of numts by generating numts of three mitochondrial loci across 28 orthopteran families, representing the phylogenetic diversity of the order. We discover that numts are rampant in all lineages, but there is no discernable and consistent pattern of numt accumulation among different lineages. Likewise, we do not find any evidence that a certain mitochondrial gene is more prone to nuclear insertion than others. We also find that numt insertion must have occurred continuously and frequently throughout the diversification of Orthoptera. Although most numts are the result of recent nuclear insertion, we find evidence of very ancient numt insertion shared by highly divergent families dating back to the Jurassic period. Finally, we discuss several factors contributing to the extreme prevalence of numts in Orthoptera and highlight the importance of exploring the utility of numts in evolutionary studies.

The complete mitogenome of Arcyptera coreana (Insecta: Orthoptera: Acrididae)

The complete mitogenome of Arcyptera coreana (Insecta: Orthoptera: Acrididae) is determined to be 15,783 bp in length, consisting of 37 typical mitochondrial genes and an AT-rich region. Its gene order and orientation are identical to those of most other grasshoppers. All protein-coding genes (PCGs) are initiated by typical ATN codons, except for cox1 gene with the unusual TTA as its start codon. Eleven genes use complete termination codon (TAA), whereas the cox2 and nad5 genes end with a single T. Except for trnS(AGN), all tRNA genes display typical secondary cloverleaf structures as those of other insects. The two rRNA genes (rrnL and rrnS) are 1,309 bp and 792 bp, respectively. The 946-bp long AT-rich region contains several features common to those of other Caelifera insects, such as the stem-loop secondary structure and the motif "TATTTwATryAyAAA".

The first mitochondrial genome for the superfamily Hagloidea and implications for its systematic status in Ensifera

Hagloidea Handlirsch, 1906 was an ancient group of Ensifera, that was much more diverse in the past extending at least into the Triassic, apparently diminishing in diversity through the Cretaceous, and now only represented by a few extant species. In this paper, we report the complete mitochondrial genome (mitogenome) of Tarragoilus diuturnus Gorochov, 2001, representing the first mitogenome of the superfamily Hagloidea. The size of the entire mitogenome of T. diuturnus is 16144 bp, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The order and orientation of the gene arrangement pattern is identical to that of D. yakuba and most ensiferans species. A phylogenomic analysis was carried out based on the concatenated dataset of 13 PCGs and 2 rRNA genes from mitogenome sequences of 15 ensiferan species, comprising four superfamilies Grylloidea, Tettigonioidae, Rhaphidophoroidea and Hagloidea. Both maximum likelihood and Bayesian inference analyses strongly support Hagloidea T. diuturnus and Rhaphidophoroidea Troglophilus neglectus as forming a monophyletic group, sister to the Tettigonioidea. The relationships among four superfamilies of Ensifera were (Grylloidea, (Tettigonioidea, (Hagloidea, Rhaphidophoroidea))).

The phylogeny of the Orthoptera (Insecta) as deduced from mitogenomic gene sequences

Background

The phylogeny of the Orthoptera was analyzed based on 6 datasets from 47 orthopteran mitochondrial genomes (mitogenomes). The phylogenetic signals in the mitogenomes were rigorously examined under analytical regimens of maximum likelihood (ML) and Bayesian inference (BI), along with how gene types and different partitioning schemes influenced the phylogenetic reconstruction within the Orthoptera. The monophyly of the Orthoptera and its two suborders (Caelifera and Ensifera) was consistently recovered in the analyses based on most of the datasets we selected, regardless of the optimality criteria.

Results

When the seven NADH dehydrogenase subunits were concatenated into a single alignment (NADH) and were analyzed; a near-identical topology to the traditional morphological analysis was recovered, especially for BI_NADH. In both the concatenated cytochrome oxidase (COX) subunits and COX + cytochrome b (Cyt b) datasets, the small extent of sequence divergence seemed to be helpful for resolving relationships among major Orthoptera lineages (between suborders or among superfamilies). The conserved and variable domains of ribosomal (r)RNAs performed poorly when respectively analyzed but provided signals at some taxonomic levels.

Conclusions

Our findings suggest that the best phylogenetic inferences can be made when moderately divergent nucleotide data from mitogenomes are analyzed, and that the NADH dataset was suited for studying orthopteran phylogenetic relationships at different taxonomic levels, which may have been due to the larger amount of DNA sequence data and the larger number of phylogenetically informative sites.

The complete mitochondrial genome of Xya japonica (Haan, 1842) (Orthoptera: Tridactyloidea)

The complete mitochondrial genome of Xya japonica (Haan, 1842), which was collected from Hebei province of China, is reported here. It is 15,352 bp in length and contains 71.2% AT. All X. japonica protein-coding sequences start with a typical ATN codon except for the cytochrome oxidase subunit I (cox1), which start with CCG. The usual termination codon TAA and TAG were found from 13 protein-coding genes. All tRNA genes have the typical clover leaf structure, excluding trnS(AGN) that lacks the dihydrouracil arm. The sizes of the large and small ribosomal RNA genes are 1289 and 747 bp, respectively. The AT content of the A + T-rich region is 75.0%. The orientation and gene order of the X. japonica mitogenome is identical to Ellipes minuta and Gryllotalpa orientalis, there is no phenomenon of "DK rearrangement" which has been wide reported in Caelifera.

Mitochondrial genomes of two Sinochlora species (Orthoptera): novel genome rearrangements and recognition sequence of replication origin

Background

Orthoptera, the largest polyneopteran insect order, contains 2 suborders and 235 subfamilies. Orthoptera mitochondrial genomes (mitogenomes) follow the ancestral insect gene order, with the exception of a trnD-trnK rearrangement in Acridomorphs and rare tRNA inversions. A question still remains regarding whether a long thymine-nucleotide stretch (T-stretch) involved in the recognition of the replication origin exists in the control region (CR) of Orthoptera mitochondrial DNA (mtDNA). Herein, we completed the sequencing of whole mitogenomes of two congeners (Sinochlora longifissa and S. retrolateralis), which possess overlapping distribution areas. Additionally, we performed comparative mitogenomic analysis to depict evolutionary trends of Orthoptera mitogenomes.

Results

Both Sinochlora mitogenomes possess 37 genes and one CR, a common gene orientation, normal structures of transfer RNA and ribosomal RNA genes, rather low A+T bias, and significant C skew in the majority strand (J-strand), resembling all the other sequenced ensiferans. Both mitogenomes are characterized by (1) a large size resulting from multiple copies of an approximately 175 bp GC-rich tandem repeat within CR; (2) a novel gene order (rrnS-trnI-trnM-nad2-CR-trnQ-trnW), compared to the ancestral order (rrnS-CR-trnI-trnQ-trnM-nad2-trnW); and (3) redundant trnS(UCN) pseudogenes located between trnS(UCN) and nad1. Multiple independent duplication events followed by random and/or non-random loss occurred during Sinochlora mtDNA evolution. The Orthoptera mtDNA recognition sequence of the replication origin may be one of two kinds: a long T-stretch situated in or adjacent to a possible stem-loop structure or a variant of a long T-stretch located within a potential stem-loop structure.

Conclusions

The unique Sinochlora mitogenomes reveal that the mtDNA architecture within Orthoptera is more variable than previously thought, enriching our knowledge on mitogenomic genetic diversities. The novel genome rearrangements shed light on mtDNA evolutionary patterns. The two kinds of recognition sequences of replication origin suggest that the regulatory sequences involved in the replication initiation process of mtDNA have diverged through Orthoptera evolution.

The mitochondrial genome of the quiet-calling katydids, Xizicus fascipes (Orthoptera: Tettigoniidae: Meconematinae)

To help determine whether the typical arthropod arrangement was a synapomorphy for the whole Tettigoniidae, we sequenced the mitochondrial genome (mitogenome) of the quiet-calling katydids, Xizicus fascipes (Orthoptera: Tettigoniidae: Meconematinae). The 16,166-bp nucleotide sequences of X. fascipes mitogenome contains the typical gene content, gene order, base composition, and codon usage found in arthropod mitogenomes. As a whole, the X. fascipes mitogenome contains a lower A+T content (70.2%) found in the complete orthopteran mitogenomes determined to date. All protein-coding genes started with a typical ATN codon. Ten of the 13 protein-coding genes have a complete termination codon, but the remaining three genes (COIII, ND5 and ND4) terminate with incomplete T. All tRNAs have the typical clover-leaf structure of mitogenome tRNA, except for tRNA(Ser(AGN)), in which lengthened anticodon stem (9 bp) with a bulged nuleotide in the middle, an unusual T-stem (6 bp in constrast to the normal 5 bp), a mini DHU arm (2 bp) and no connector nucleotides. In the A+T-rich region, two (TA)n conserved blocks that were previously described in Ensifera and two 150-bp tandem repeats plus a partial copy of the composed at 61 bp of the beginning were present. Phylogenetic analysis found: i) the monophyly of Conocephalinae was interrupted by Elimaea cheni from Phaneropterinae; and ii) Meconematinae was the most basal group among these five subfamilies.

The complete mitochondrial genomes of three grasshoppers, Asiotmethis zacharjini, Filchnerella helanshanensis and Pseudotmethis rubimarginis (Orthoptera: Pamphagidae)

The complete mitogenomes of Asiotmethis zacharjini, Filchnerella helanshanensis and Pseudotmethis rubimarginis are 15,660 bp, 15,657 bp and 15,661 bp in size, respectively. All three mitogenomes contain a standard set of 13 protein - coding genes, 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A+T-rich region in the same order as those of the other analysed caeliferan species, including the rearrangement of trnAsp and trnLys. The putative initiation codon for the cox1 gene in the three species is CCG. The long polythymine stretch (T-stretch) in the A+T-rich region of the three species is not adjacent to the trnIle but inside the stem-loop sequence in the majority strand. The mitogenomes of F. helanshanensis and P. rubimarginis have higher overall similarities. The characterization of the three mitogenomes will enrich our knowledge on the Pamphagidae mitogenome. The phylogenetic analyses indicated that within the Caelifera, Pyrgomorphoidea is a sister group to Acridoidea. The species from the Pamphagidae form a monophyletic group, as is the case for Acrididae. Furthermore, the two families cluster as sister groups, supporting the monophyly of Acridoidea. The relationships among eight acridid subfamilies were (Cyrtacanthacridinae+(Calliptaminae+(Catantopinae+(Oxyinae+(Melanopline+(Acridinae+(Oedipodinae+Gomphocerinae).

Conveniently pre-tagged and pre-packaged: extended molecular identification and metagenomics using complete metazoan mitochondrial genomes

BACKGROUND

Researchers sorely need markers and approaches for biodiversity exploration (both specimen linked and metagenomics) using the full potential of next generation sequencing technologies (NGST). Currently, most studies rely on expensive multiple tagging, PCR primer universality and/or the use of few markers, sometimes with insufficient variability.

METHODOLOGY/PRINCIPAL FINDINGS

We propose a novel approach for the isolation and sequencing of a universal, useful and popular marker across distant, non-model metazoans: the complete mitochondrial genome. It relies on the properties of metazoan mitogenomes for enrichment, on careful choice of the organisms to multiplex, as well as on the wide collection of accumulated mitochondrial reference datasets for post-sequencing sorting and identification instead of individual tagging. Multiple divergent organisms can be sequenced simultaneously, and their complete mitogenome obtained at a very low cost. We provide in silico testing of dataset assembly for a selected set of example datasets.

CONCLUSIONS/SIGNIFICANCE

This approach generates large mitogenome datasets. These sequences are useful for phylogenetics, molecular identification and molecular ecology studies, and are compatible with all existing projects or available datasets based on mitochondrial sequences, such as the Barcode of Life project. Our method can yield sequences both from identified samples and metagenomic samples. The use of the same datasets for both kinds of studies makes for a powerful approach, especially since the datasets have a high variability even at species level, and would be a useful complement to the less variable 18S rDNA currently prevailing in metagenomic studies.

MITOS: improved de novo metazoan mitochondrial genome annotation

About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de.

Complete mitochondrial genome of the free-living earwig, Challia fletcheri (Dermaptera: Pygidicranidae) and phylogeny of Polyneoptera

The insect order Dermaptera, belonging to Polyneoptera, includes ∼2,000 extant species, but no dermapteran mitochondrial genome has been sequenced. We sequenced the complete mitochondrial genome of the free-living earwig, Challia fletcheri, compared its genomic features to other available mitochondrial sequences from polyneopterous insects. In addition, the Dermaptera, together with the other known polyneopteran mitochondrial genome sequences (protein coding, ribosomal RNA, and transfer RNA genes), were employed to understand the phylogeny of Polyneoptera, one of the least resolved insect phylogenies, with emphasis on the placement of Dermaptera. The complete mitochondrial genome of C. fletcheri presents the following several unusual features: the longest size in insects is 20,456 bp; it harbors the largest tandem repeat units (TRU) among insects; it displays T- and G-skewness on the major strand and A- and C-skewness on the minor strand, which is a reversal of the general pattern found in most insect mitochondrial genomes, and it possesses a unique gene arrangement characterized by a series of gene translocations and/or inversions. The reversal pattern of skewness is explained in terms of inversion of replication origin. All phylogenetic analyses consistently placed Dermaptera as the sister to Plecoptera, leaving them as the most basal lineage of Polyneoptera or sister to Ephemeroptera, and placed Odonata consistently as the most basal lineage of the Pterygota.

Accelerated evolution of mitochondrial but not nuclear genomes of Hymenoptera: new evidence from crabronid wasps

Mitochondrial genes in animals are especially useful as molecular markers for the reconstruction of phylogenies among closely related taxa, due to the generally high substitution rates. Several insect orders, notably Hymenoptera and Phthiraptera, show exceptionally high rates of mitochondrial molecular evolution, which has been attributed to the parasitic lifestyle of current or ancestral members of these taxa. Parasitism has been hypothesized to entail frequent population bottlenecks that increase rates of molecular evolution by reducing the efficiency of purifying selection. This effect should result in elevated substitution rates of both nuclear and mitochondrial genes, but to date no extensive comparative study has tested this hypothesis in insects. Here we report the mitochondrial genome of a crabronid wasp, the European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae), and we use it to compare evolutionary rates among the four largest holometabolous insect orders (Coleoptera, Diptera, Hymenoptera, Lepidoptera) based on phylogenies reconstructed with whole mitochondrial genomes as well as four single-copy nuclear genes (18S rRNA, arginine kinase, wingless, phosphoenolpyruvate carboxykinase). The mt-genome of P. triangulum is 16,029 bp in size with a mean A+T content of 83.6%, and it encodes the 37 genes typically found in arthropod mt genomes (13 protein-coding, 22 tRNA, and two rRNA genes). Five translocations of tRNA genes were discovered relative to the putative ancestral genome arrangement in insects, and the unusual start codon TTG was predicted for cox2. Phylogenetic analyses revealed significantly longer branches leading to the apocritan Hymenoptera as well as the Orussoidea, to a lesser extent the Cephoidea, and, possibly, the Tenthredinoidea than any of the other holometabolous insect orders for all mitochondrial but none of the four nuclear genes tested. Thus, our results suggest that the ancestral parasitic lifestyle of Apocrita is unlikely to be the major cause for the elevated substitution rates observed in hymenopteran mitochondrial genomes.