The First Two Complete Mitochondrial Genomes for the Subfamily Meligethinae (Coleoptera: Nitidulidae) and Implications for the Higher Phylogeny of Nitidulidae

The phylogenetic status of the family Nitidulidae and its sister group relationship remain controversial. Also, the status of the subfamily Meligethinae is not fully understood, and previous studies have been mainly based on morphology, molecular fragments, and biological habits, rather than the analysis of the complete mitochondrial genome. Up to now, there has been no complete mitochondrial genome report of Meligethinae. In this study, the complete mitochondrial genomes of Meligethinus tschungseni and Brassicogethes affinis (both from China) were provided, and they were compared with the existing complete mitochondrial genomes of Nitidulidae. The phylogenetic analysis among 20 species of Coleoptera was reconstructed via PhyloBayes analysis and Maximum likelihood (ML) analysis, respectively. The results showed that the full lengths of Meligethinus tschungseni and Brassicogethes affinis were 15,783 bp and 16,622 bp, and the AT contents were 77% and 76.7%, respectively. Each complete mitochondrial genome contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and a control region (A + T-rich region). All the PCGs begin with the standard start codon ATN (ATA, ATT, ATG, ATC). All the PCGs terminate with a complete terminal codon, TAA or TAG, except cox1, cox2, nad4, and nad5, which terminate with a single T. Furthermore, all the tRNAs have a typical clover-leaf secondary structure except trnS1, whose DHU arm is missing in both species. The two newly sequenced species have different numbers and lengths of tandem repeat regions in their control regions. Based on the genetic distance and Ka/Ks analysis, nad6 showed a higher variability and faster evolutionary rate. Based on the available complete mitochondrial genomes, the results showed that the four subfamilies (Nitidulinae, Meligethinae, Carpophilinae, Epuraeinae) of Nitidulidae formed a monophyletic group and further supported the sister group relationship of Nitidulidae + Kateretidae. In addition, the taxonomic status of Meligethinae and the sister group relationship between Meligethinae and Nitidulinae (the latter as currently circumscribed) were also preliminarily explored.

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.

The rearranged mitochondrial genome of Podagrion sp. (Hymenoptera: Torymidae), a parasitoid wasp of mantis

The complete sequence of the mitochondrial genome of Podagrion sp. (Hymenoptera: Torymidae) is described. The mitogenome was 15,845 bp in size, and contained typical sets of mitochondrial genes. The base composition of the Podagrion sp. mitogenome was also biased toward A + T bases (81.8%). The mitochondrial genome of Podagrion sp. has a weak AT skew (0.07) and a strong GC skew (-0.26). Podagrion sp. exhibits a novel rearrangement compared with the ancestral order, including six protein-coding genes (nad3, cox3, atp6, atp8, cox2 and cox1), which have inverted to the minor strand from the major strand. The A + T-rich region of Podagrion sp., which is located between trnN and trnI, have five tandem repeats. The apomorphic rearrangements, including the conserved block "cox3-atp6-atp8-cox2-cox1-nad5-nad4-nad4l-nad6-cob" and the special locations of trnV and trnA, were mapped onto the phylogeny of Proctotrupomorpha.

Complete mitochondrial genomes of two blattid cockroaches, Periplaneta australasiae and Neostylopyga rhombifolia, and phylogenetic relationships within the Blattaria

Complete mitochondrial genomes (mitogenomes) of two cockroach species, Periplaneta australasiae and Neostylopyga rhombifolia, 15,605 bp and 15,711 bp in length, respectively, were determined. As reported for other cockroach mitogenomes, the two mitogenomes possessed typical ancestral insect mitogenome gene composition and arrangement. Only several small intergenic spacers were found: one, which was common in all sequenced cockroach mitogenomes except for the genus Cryptocercus, was between tRNA-Ser (UCN) and ND1 and contained a 7bp highly conserved motif (WACTTAA). Three different types of short tandem repeats in the N. rhombifolia control region (CR) were observed. The homologous alignments of these tandem repeats with other six cockroach mitogenome CRs revealed a low similarity. Three conserved sequence blocks (CSB) were detected in both cockroach mitochondrial CRs. CSB1 was specific for blattinine mitogenomes and was highly conserved with 95% similarity, speculating that this block was a possible molecular synapomorphy for this subfamily. CSB3 located nearby downstream of CSB1 and has more variations within blattinine mitogenomes compared with CSB1. The CSB3 was capable of forming stable stem-loop structure with a small T-stretch in the loop portion. We assessed the influence of four datasets and two inference methods on topology within Orthopteroidea. All genes excluding the third codon positions of PCGs could generate more stable topology, and higher posterior probabilities than bootstrap values were presented at some branch nodes. The phylogenetic analysis with different datasets and analytical methods supported the monophyly of Dictyoptera and supported strongly the proposal that Isoptera should be classified as a family (Termitidae) of the Blattaria. Specifically, Shelfordella lateralis was inserted in the clade Periplaneta. Considering the K2P genetic distance, morphological characters, and the phylogenetic trees, we suggested that S. lateralis should be placed in the genus Periplaneta.

Revisiting Coleoptera a + T-rich region: structural conservation, phylogenetic and phylogeographic approaches in mitochondrial control region of bioluminescent Elateridae species (Coleoptera)

The control region (CR) or A + T-rich region in Coleoptera mt genome is poorly characterized, including the Elateroidea bioluminescent species. Here, we provided the first attempt to characterize and compare the structure and organization of the CR of different species within Elateridae. We also revisited some sequenced Coleoptera CR and observed consensus T-stretches, non-conserved sequences near the stem-loop and unusual inner tRNAs-like sequences. All these features are probably involved in the replication start of the mt genome. The phylogenetic relationships in Elateridae bioluminescent groups using partial sequence of CR showed the monophyly of Pyrearinus pumilus group and Pyrearinus as a polyphyletic genus, corroborating our previous results. The wider genetic variation obtained by CR analysis could separate two different lineages that occur within P. termitilluminans populations. In Elateridae, the CR exhibited high polymorphism within and between populations, which was also observed in other Coleoptera species, suggesting that the CR could be described as a suitable molecular marker to be applied in phylogenetic and phylogeographic studies.

Mitochondrial genomes of four katydids (Orthoptera: Phaneropteridae): New gene rearrangements and their phylogenetic implications

Phaneropteridae is a family of Orthoptera that displays an amazing amount of diversity in terms of both forms and species. We sequenced the mitochondrial genomes (mitogenomes) of two bush katydids: Ruidocollaris obscura and Kuwayamaea brachyptera (Phaneropterinae), and two true katydids: Orophyllus montanus and Phyllomimus detersus (Pseudophyllinae), to obtain further insight into the characteristics of the katydid mitogenomes and to investigate the taxonomic status of subfamily Pseudophyllinae and the diversity of gene arrangements among Phaneropteridae. The following general genomic characteristics were observed in the four katydids: a longer length of the mitogenomes (16,007bp-16,667bp) compared with Caelifera, abundant intergenic spacers, and accepted atypical initiation codons (GTG and TTG, found in cox1, nad1 and nad2). A new orientation of the gene arrangement "trnM-trnI-trnQ" was identified in P. detersus, which is the first representative of Polyneoptera found to carry this gene cluster. Large identical fragments (492bp) were detected in control region 1 (CR1) and control region 2 (CR2) of R. obscura. The high similarity of the duplicated CRs is likely due to a recent gene duplication or concerted evolution. Analyses of the duplicated CRs revealed one conserved stem-loop (on the N-strand) located in the identical sequences of both CRs that might be linked to replication initiation. Phylogenetic analyses based on 13 protein-coding genes and 2 ribosomal RNA genes from 20 Ensiferan species yielded the identical topologies between two different methods (maximum likelihood and bayesian inference). The newly sequenced Pseudophyllinae species was placed as the sister group of Phaneropterinae, and Mecopodinae clustered with Pseudophyllinae+Phaneropterinae. Additionally, we speculate that the species in Ruidocollaris and Sinochlora, as well as their closely related genera, may have undergone numerous rearrangement events.

Phylogenetic utility, and variability in structure and content, of complete mitochondrial genomes among genetic lineages of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis 1963 (Atyidae:Decapoda)

The Atyidae are caridean shrimp possessing hair-like setae on their claws and are important contributors to ecological services in tropical and temperate fresh and brackish water ecosystems. Complete mitochondrial genomes have only been reported from five of the 449 species in the family, thus limiting understanding of mitochondrial genome evolution and the phylogenetic utility of complete mitochondrial sequences in the Atyidae. Here, comparative analyses of complete mitochondrial genomes from eight genetic lineages of Halocaridina rubra, an atyid endemic to the anchialine ecosystem of the Hawaiian Archipelago, are presented. Although gene number, order, and orientation were syntenic among genomes, three regions were identified and further quantified where conservation was substantially lower: (1) high length and sequence variability in the tRNA-Lys and tRNA-Asp intergenic region; (2) a 317-bp insertion between the NAD6 and CytB genes confined to a single lineage and representing a partial duplication of CytB; and (3) the putative control region. Phylogenetic analyses utilizing complete mitochondrial sequences provided new insights into relationships among the H. rubra genetic lineages, with the topology of one clade correlating to the geologic sequence of the islands. However, deeper nodes in the phylogeny lacked bootstrap support. Overall, our results from H. rubra suggest intra-specific mitochondrial genomic diversity could be underestimated across the Metazoa since the vast majority of complete genomes are from just a single individual of a species.

Sequence and analysis of mtDNA control region in Cnaphalacrocis medinalis Guenée and Marasmia patnalis Bradley (Lepidoptera: Pyralidae)

Rice leaffolders Cnaphalocrocis medinalis and Marasmia patnalis (Lepidoptera: Pyralidae) are important rice pests and morphologically related with same damage methods. The control region of mitochondrial DNA (mtDNA) in two rice leaffolders C. medinalis and M. patnalis were sequenced and analyzed. The control regions of the two rice leaffolders are located between 12S ribosomal RNA and tRNA_Met, and exhibit conserved structural elements. We identified the poly T stretches, (TA)n block, and stem-loop structure. There are no long tandem repeats found in mtDNA control region in the two rice leaffolders studied. Nevertheless, we did not find the GA-rich block in mtDNA control regions of the two rice leaffolders. The molecular-based phylogenies support the traditional morphologically based view of relationships of Pyralidae within the Ditrysia. The addition of the C. medinalis and M. patnalis mtDNA control regions to the literature promotes the understanding of the molecular evolution of Pyralidae in Ditrysia.

The complete mitochondrial genome of Meloidogyne graminicola (Tylenchina): a unique gene arrangement and its phylogenetic implications

Meloidogyne graminicola is one of the most economically important plant parasitic-nematodes (PPNs). In the present study, we determined the complete mitochondrial (mt) DNA genome sequence of this plant pathogen. Compared with other PPNs genera, this genome (19,589 bp) is only slightly smaller than that of Pratylenchus vulnus (21,656 bp). The nucleotide composition of the whole mtDNA sequence of M. graminicola is significantly biased toward A and T, with T being the most favored nucleotide and C being the least favored. The A+T content of the entire genome is 83.51%. The mt genome of M. graminicola contains 36 genes (lacking atp8) that are transcribed in the same direction. The gene arrangement of the mt genome of M. graminicola is unique. A total of 21 out of 22 tRNAs possess a DHU loop only, while tRNASer(AGN) lacks a DHU loop. The two large noncoding regions (2,031 bp and 5,063 bp) are disrupted by tRNASer(UCN). Phylogenetic analysis based on concatenated amino acid sequences of 12 protein-coding genes support the monophylies of the three orders Rhabditida, Mermithida and Trichinellida, the suborder Rhabditina and the three infraorders Spiruromorpha, Oxyuridomorpha and Ascaridomorpha, but do not support the monophylies of the two suborders Spirurina and Tylenchina, and the three infraorders Rhabditomorpha, Panagrolaimomorpha and Tylenchomorpha. The four Tylenchomorpha species including M. graminicola, P. vulnus, H. glycines and R. similis from the superfamily Tylenchoidea are placed within a well-supported monophyletic clade, but far from the other two Tylenchomorpha species B. xylophilus and B. mucronatus of Aphelenchoidea. In the clade of Tylenchoidea, M. graminicola is sister to P. vulnus, and H. glycines is sister to R. similis, which suggests root-knot nematodes has a closer relationship to Pratylenchidae nematodes than to cyst nematodes.

Pause-melting misalignment: a novel model for the birth and motif indel of tandem repeats in the mitochondrial genome

Background

Tandem repeats (TRs) in the mitochondrial (mt) genome control region have been documented in a wide variety of vertebrate species. The mechanism by which repeated tracts originate and undergo duplication and deletion, however, remains unclear.

Results

We analyzed DNA sequences of mt genome TRs (mtTRs) in the ridged-eye flounder (Pleuronichthys cornutus), and characterized DNA sequences of mtTRs from other vertebrates using the data available in GenBank. Tandem repeats are concentrated in the control regions; however, we found approximately 16.6% of the TRs elsewhere in the mt genome. The flounder mtTRs possess three motif types with hypervariable characteristics at the 3′ end of the control region (CR).

Conclusion

Based on our analysis of this larger dataset of mtTR sequences, we propose a novel model of Pause Melting Misalignment (PMM) to describe the birth and motif indel of tandem repeats. PMM is activated during a pause event in mitochondrial replication in which a dynamic competition between the nascent (N) heavy strand and the displaced (D) heavy strand may lead to the melting of the N-strand from the template (T) light strand. When mispairing occurs during rebinding of the N-strand, one or several motifs can be inserted or deleted in both strands during the next round of mt-replication or repair. This model can explain the characteristics of TRs in available vertebrate mt genomes.

The complete mitochondrial genome of the black mud crab, Scylla serrata (Crustacea: Brachyura: Portunidae) and its phylogenetic position among (pan)crustaceans

The black mud crab, Scylla serrata (Forskål 1775), is the most economically important edible crab in South-East Asia. In the present study, the complete mitochondrial genome of black mud crab, S. serrata, was determined with the sequential polymerase chain reaction and primer walking sequencing. The complete mitochondrial genome was 15,721 bp in length with an A+T content of 69.2 % and contained 37 mitochondrial genes (13 protein coding genes (PCGs), 2 ribosomal RNA genes and 22 transfer RNA genes) and a control region (CR). The analysis of the CR sequence shows that it contains a multitude of repetitive fragments which can fold into hairpin-like or secondary structures and conserved elements as in other arthropods. The gene order of S. serrata mainly retains as the pancrustacean ground pattern, except for a single translocation of trnH. The gene arrangement of S. serrata appears to be a typical feature of portunid crabs. Phylogenetic analyses with concatenated amino acid sequences of 12 PCGs establishes that S. serrata in a well-supported monophyletic Portunidae and is consistent with previous morphological classification. Moreover, the phylogenomic results strongly support monophyletic Pancrustacea (Hexapoda plus "Crustaceans"). Within Pancrustacea, this study identifies Malacostraca + Entomostraca and Branchiopoda as the sister group to Hexapoda, which confirms that "Crustacea" is not monophyletic. Cirripedia + Remipedia appear to be a basal lineage of Pancrustacea. The present study also provides considerable data for the application of both population and phylogenetic studies of other crab species.