Evolutionary dynamics of the mitochondrial genome in the evaniomorpha (hymenoptera)—a group with an intermediate rate of gene rearrangement

Phylogenetic incongruence in an Asiatic species complex of the genus Caryodaphnopsis (Lauraceae)

BACKGROUND

Caryodaphnopsis, a group of tropical trees (ca. 20 spp.) in the family Lauraceae, has an amphi-Pacific disjunct distribution: ten species are distributed in Southeast Asia, while eight species are restricted to tropical rainforests in South America. Previously, phylogenetic analyses using two nuclear markers resolved the relationships among the five species from Latin America. However, the phylogenetic relationships between the species in Asia remain poorly known.

RESULTS

Here, we first determined the complete mitochondrial genome (mitogenome), plastome, and the nuclear ribosomal cistron (nrDNA) sequences of C. henryi with lengths of 1,168,029 bp, 154,938 bp, and 6495 bp, respectively. We found 2233 repeats and 368 potential SSRs in the mitogenome of C. henryi and 50 homologous DNA fragments between its mitogenome and plastome. Gene synteny analysis revealed a mass of rearrangements in the mitogenomes of Magnolia biondii, Hernandia nymphaeifolia, and C. henryi and only six conserved clustered genes among them. In order to reconstruct relationships for the ten Caryodaphnopsis species in Asia, we created three datasets: one for the mitogenome (coding genes and ten intergenic regions), another for the plastome (whole genome), and the other for the nuclear ribosomal cistron. All of the 22 Caryodaphnopsis individuals were divided into four, five, and six different clades in the phylogenies based on mitogenome, plastome, and nrDNA datasets, respectively.

CONCLUSIONS

The study showed phylogenetic conflicts within and between nuclear and organellar genome data of Caryodaphnopsis species. The sympatric Caryodaphnopsis species in Hekou and Malipo SW China may be related to the incomplete lineage sorting, chloroplast capture, and/or hybridization, which mixed the species as a complex in their evolutionary history.

Characterization of the Mitogenome of the Genus Dendrocerus Ratzeburg (Hymenoptera: Megaspilidae) with the Specific Designed Primers

In Hymenoptera, the monophyly of Evaniomorpha has been the focus of debate among different scholars. In this study, we sequenced two mitochondrial genomes of Dendrocerus (Hymenoptera: Megaspilidae) to analyze the mitochondrial genomic features of Dendrocerus and provide new molecular data for phylogenetic studies of Evaniomorpha. The mitogenome sizes of D. bellus and D. anisodontus were 15,445 bp and 15,373 bp, respectively, with the trnG of D. bellus missing. The nucleotide composition was significantly biased toward adenine and thymine, with A + T contents of 81.2% (D. bellus) and 82.4% (D. anisodontus). Using Ceraphron sp. (Ceraphronidae) as reference, the Ka/Ks values of NAD4L and NAD6 in D. anisodontus were both greater than one, indicating that non-synonymous mutations are favored by Darwinian selection, which is rare in other hymenopteran species. Compared with Ceraphon sp. gene order, nine operations were identified in D. anisodontus, including four reversals, four TDRLs (tandem duplication random losses) and one transposition, or four reversals and five TDRLs. Phylogenetic analysis of 40 mitochondrial genomes showed that Evaniomorpha was not a monophyletic group, which was also supported by the PBD values. Ceraphronoidea is a monophyletic group and is a sister to Aulacidae + Gasteruptiidae. Based on the conserved region of the newly sequenced mitochondrial genomes, a pair of specific primers MegaF/MegaR was designed for sequencing the COX1 genes in Megaspilidae and a 60% rate of success was achieved in the genus Dendrocerus.

De novo assembly of the complete mitochondrial genome of Mycetophylax simplex Emery, 1888 through organelle targeting revels no substantial expansion of gene spacers, but rather some slightly shorter genes

Mitochondria play a key role in cell biology and have their own genome, residing in a highly oxidative environment that induces faster changes than the nuclear genome. Because of this, mitochondrial markers have been exploited to reconstruct phylogenetic and phylogeographic relationships in studies of adaptation and molecular evolution. In this study, we determined the complete mitogenome of the fungus-farming ant Mycetophylax simplex (Hymenoptera, Formicidae) and conducted a comparative analysis among 29 myrmicine ant mitogenomes. Mycetophylax simplex is an endemic ant that inhabits sand dunes along the southern Atlantic coast. Specifically, the species occur in the ecosystem known as "restinga", within the Atlantic Forest biome. Due to habitat degradation, land use and decline of restinga habitats, the species is considered locally extinct in extremely urban beaches and is listed as vulnerable on the Brazilian Red List (ICMBio). We employed a mitochondrion-targeting approach to obtain the complete mitogenome through high-throughput DNA sequencing technology. This method allowed us to determine the mitogenome with high performance, coverage and low cost. The circular mitogenome has a length of 16,367 base pairs enclosing 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) along with one control region (CR). All the protein-coding genes begin with a typical ATN codon and end with the canonical stop codons. All tRNAs formed the fully paired acceptor stems and fold into the typical cloverleaf-shaped secondary structures. The gene order is consistent with the shared Myrmicinae structure, and the A + T content of the majority strand is 81.51%. Long intergenic spacers were not found but some gene are slightly shorter. The phylogenetic relationships based on concatenated nucleotide and amino acid sequences of the 13 protein-coding genes, using Maximum Likelihood and Bayesian Inference methods, indicated that mitogenome sequences were useful in resolving higher-level relationship within Formicidae.

The complete mitochondrial genome and gene rearrangements in a gall wasp species, Dryocosmus liui (Hymenoptera: Cynipoidea: Cynipidae)

Mitochondrial genomes (mitogenomes) have been widely used in comparative and evolutionary genomics, molecular evolution, phylogenetics, and population genetics, but very limited information is available for the family Cynipidae. In this report, we describe the mitogenome of Dryocosmus liui Pang, Su et Zhu, providing the first complete mitogenomic data for a cynipid gall wasp species. The mitogenome of D. liui is 16,819 bp in length, and contains the typical set of 37 genes. Two control regions were detected, with the second being a perfect inverted repeat of the major portion of the first. Gene rearrangements were found in transfer RNA (tRNA) genes, protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes, compared with the putative ancestral mitogenome. Similar to two other Cynipidae species with mitogenome data available, D. liui has a novel tRNA gene cluster trnL1-trnI-trnL2-trnW-trnM-trnQ between nad1 and nad2. Phylogenetic analysis based on sequences of PCGs and rRNA genes with D. liui included obtained topologies identical to previous studies supporting the a relationship of (Cynipoidea , (Platygastroidea, Proctotrupoidea)) within the monophyletic Proctotrupomorpha and (Cynipidae, Figitidae), Ibaliidae) within the Cynipoidea.

Mitochondrial genome rearrangements and phylogenomics of the Hymenoptera (Insecta) using an expanded taxon sample

The order Hymenoptera is one of the most species-rich insect orders, with more than 150,000 described extant species. Many hymenopteran insects have very different mitochondrial genome (mitogenome) organizations compared to the putative ancestral organization of insects. In this study, we sequenced 18 mitogenomes of representatives in the order Hymenoptera to increase taxonomic sampling. A total of 475 species were used in phylogenetic analyses, including 18 new mitogenomes and 457 existing mitogenomes. Using a site-heterogeneous model, Bayesian's inference from amino acid data yielded more resolved relationships among Hymenoptera than maximum-likelihood analysis and coalescent-based species analyses. The monophyly of Symphyta was not supported. The Xyeloidea was the earliest branching clade in the Hymenoptera. The Orussoidea was closely related to Apocrita. Within Apocrita, the Parasitoida was non-monophyletic. The monophyly of most Parasitoida superfamilies received strong support. The Proctotrupomorpha clade was supported in Bayesian's analysis. The Apoidea was monophyletic when excluding Ampulex compressa from consideration. The superfamilies Vespoidea and Chrysidoidea were found to be non-monophyletic. Comparisons of mitochondrial gene order revealed a higher frequency of gene rearrangement among lineages with a parasitoid lifestyle, particularly prominent in Chalcidoidea. The degree of gene rearrangement ranked second in specific taxa of Cynipoidea and Ichneumonoidea.

Evolution of Gene Arrangements in the Mitogenomes of Ensifera and Characterization of the Complete Mitogenome of Schizodactylus jimo

Gene arrangement (relative location of genes) is another evolutionary marker of the mitogenome that can provide extensive information on the evolutionary mechanism. To explore the evolution of gene arrangements in the mitogenome of diversified Ensifera, we sequenced the mitogenome of the unique dune cricket species found in China and used it for phylogenetic analysis, in combination with 84 known Ensiferan mitogenomes. The mitogenome of Schizodactylus jimo is a 16,428-bp circular molecule that contains 37 genes. We identified eight types of gene arrangement in the 85 ensiferan mitogenomes. The gene location changes (i.e., gene translocation and duplication) were in three gene blocks: I-Q-M-ND2, rrnl-rns-V, and ND3-A-R-N-S-E-F. From the phylogenetic tree, we found that Schizodactylus jimo and most other species share a typical and ancient gene arrangement type (Type I), while Grylloidea has two types (Types II and III), and the other five types are rare and scattered in the phylogenetic tree. We deduced that the tandem replication–random loss model is the evolutionary mechanism of gene arrangements in Ensifera. Selection pressure analysis revealed that purifying selection dominated the evolution of the ensiferan mitochondrial genome. This study suggests that most gene rearrangements in the ensiferan mitogenome are rare accidental events.

Novel gene rearrangement pattern in mitochondrial genome of Ooencyrtusplautus Huang & Noyes, 1994: new gene order in Encyrtidae (Hymenoptera, Chalcidoidea)

Studies of mitochondrial genomes have a wide range of applications in phylogeny, population genetics, and evolutionary biology. In this study, we sequenced and analyzed the mitochondrial genome of Ooencyrtusplautus Huang & Noyes, 1994 (Hymenoptera, Encyrtidae). The nearly complete mitogenome of O.plautus was 15,730 bp in size, including 13 PCGs (protein-coding genes), 22 tRNAs, 2 rRNAs, and a nearly complete control region. The nucleotide composition was significantly biased toward adenine and thymine, with an A + T content of 84.6%. We used the reference sequence of Chouioiacunea and calculated the Ka/Ks ratio for each set of PCGs. The highest value of the Ka/Ks ratio within 13 PCGs was found in nad2 with 1.1, suggesting that they were subjected to positive selection. This phenomenon was first discovered in Encyrtidae. Compared with other encyrtid mitogenomes, a translocation of trnW was found in O.plautus, which was the first of its kind to be reported in Encyrtidae. Comparing with ancestral arrangement pattern, wasps reflect extensive gene rearrangements. Although these insects have a high frequency of gene rearrangement, species from the same family and genus tend to have similar gene sequences. As the number of sequenced mitochondrial genomes in Chalcidoidea increases, we summarize some of the rules of gene rearrangement in Chalcidoidea, that is four gene clusters with frequent gene rearrangements. Ten mitogenomes were included to reconstruct the phylogenetic trees of Encyrtidae based on both 13 PCGs (nucleotides of protein coding genes) and AA matrix (amino acids of protein coding genes) using the maximum likelihood and Bayesian inference methods. The phylogenetic tree reconstructed by Bayesian inference based on AA data set showed that Aenasiusarizonensis and Metaphycuseriococci formed a clade representing Tetracneminae. The remaining six species formed a monophyletic clade representing Encyrtinae. In Encyrtinae, Encyrtus forms a monophyletic clade as a sister group to the clade formed by O.plautus and Diaphorencyrtusaligarhensis. Encyrtussasakii and Encyrtusrhodooccisiae were most closely related species in this monophyletic clade. In addition, gene rearrangements can provide a valuable information for molecular phylogenetic reconstruction. These results enhance our understanding of phylogenetic relationships among Encyrtidae.

The mitochondrial genome of Chelonus formosanus (Hymenoptera: Braconidae) with novel gene orders and phylogenetic implications

Chelonus formosanus Sonan is an important egg-larval parasitoid of noctuid moths and a potential candidate for understanding interactions between host and parasitoid mediated by polydnavirues (PDVs). We sequenced and annotated the mitochondrial genome of C. formosanus, which is 15,466 bp in length and possesses 38 mitochondrial genes. However, unlike most animal mitochondrial genomes, it contains one extra trnF gene. There are five transfer RNA (tRNA) rearrangement events compared with the ancestral gene order, which is a novel rearrangement type in Hymenoptera for all published mitogenomes so far. Phylogenetic trees supported C. formosanus from the subfamily Cheloninae was closely related to the subfamily Cardiochilinae and Microgastrinae.

Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a 'hot-spot group' of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

Comparative mitogenomics and phylogenetics of the stinging wasps (Hymenoptera: Aculeata)

The stinging wasps (Hymenoptera: Aculeata) include diverse groups such as vespid wasps, ants and bees. Phylogenetic relationships among major lineages of stinging wasps have been inferred from molecular and morphological data. However, the genomic features of the mitochondrial genomes and their phylogenetic utility remain to be explored. In this study, we determined 23 mitochondrial genomes from the Aculeata. Four Mutillidae species showed relatively low A + T content compared to other species of the Aculeata (69.7%-77.4%). Eleven out of 44 species, mainly from the Chrysididae and the Pompilidae, showed reversals of GC skews. Gene rearrangements occurred across the species. Patterns of tRNA rearrangement were conserved in some groups, including the Chrysididae, Bethylidae, Pompilidae, Scolioidea and Vespoidea. Rearrangement of protein-coding genes were found in 12 out of 44 species of the Aculeata, including all four species from the Chrysididae, both species from the Bethylidae, one species from the Dryinidae, all three Scolioidea species and two Apoidea species. Phylogenetic inference showed a long branch in species with unusual genomic features, such as in the Mutillidae and Bethylidae. By excluding these species, we found paraphyly of the Chrysidoidea and a sister group relationship between the Formicoidea and Vespoidea. These results improve our understanding of the evolution of mitochondrial genomes in the Aculeata and, in general, the evolution across this subclade.

Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication

Large intergenic spacers and tRNA gene duplications have been reported in several insect groups, although little is known about mitogenomes of mayflies. Here, we determined complete mitogenomes of ten heptageniid species and systemically analyzed their mitogenomic features. Both a conserved intergenic spacer (IGS) and trnM duplication were detected in those mitogenomes. The IGS, which was observed in heptageniids, could be further folded into a stable stem-loop structure. The tRNA gene duplication was found in almost all analyzed mitogenomes, and a unique gene block trnI-trnM-trnQ-trnM-ND2 was also discovered. Our analysis demonstrates that the heptageniid gene arrangement pattern can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on the nucleotide and amino acid sequence data recovered the genus Epeorus as monophyletic with strong support. Our results provide a better understanding of mitogenomic evolution in Heptageniidae, as well as novel molecular markers for species identification of mayflies.

Novel gene rearrangement pattern in the mitochondrial genomes of Torleya mikhaili and Cincticostella fusca (Ephemeroptera: Ephemerellidae)

The mayfly family Ephemerellidae (Insecta: Ephemeroptera) is distributed around the world and has very high species diversity. However, its evolution pattern of mitogenome and phylogenetic relationships within Ephemeroptera remain unclear. In this study, the complete mitochondrial genomes (mitogenomes) of Torleya mikhaili (15,042 bp) and Cincticostella fusca (15,135 bp) were firstly determined and analyzed. Two ephemerellid mitogenomes shared similar gene organization with 37 typical genes as well as a putative control region. Compared with other reported mitogenomes of mayflies, the unique gene order (I'-CR-Q-M) was found in these two mitogenomes. Although the observed rearrangement pattern is novel within ephemeropteran mitogenomes, it could be explained presumably by the mechanisms of tandem duplication-random loss and recombination. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on four nucleotide datasets placed three ephemerellid species together. Furthermore, the phylogenetic relationships of the three genera were recovered as ((Ephemerella + Cincticostella) + Torleya).

Evolution of tRNA gene rearrangement in the mitochondrial genome of ichneumonoid wasps (Hymenoptera: Ichneumonoidea)

Gene rearrangements in the mitochondrial genome (mt genome) are common in certain insect groups and can be an informative character for phylogenetic reconstruction. However, knowledge of the mechanism and biases of gene rearrangement in insect mt genomes is still limited. With an accelerated rate of gene rearrangements, Hymenoptera is an important group for mt genome rearrangements diversity and for understanding the gene rearrangement evolution in mt genomes. Here, we sequenced the complete mt genome of Aphidius gifuensis and analyzed the evolution of tRNA gene rearrangements in the mt genomes of ichneumonoid wasps. Two control regions were detected in A. gifuensis and most of the tRNA rearrangement events occurred around these control regions. tRNA gene rearrangements occurred in almost all of the sequenced mt genomes of Ichneumonoidea and the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was the main hot spot of gene rearrangement. Mapped over the backbone phylogeny of Ichneumonoidea, we found that the inversion and translocation of both trnI and trnM is likely a synapomorphic rearrangement in Braconidae. Our study also demonstrated that the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was important for inferring the gene rearrangement dynamics in Ichneumonoidea.

Novel gene rearrangement in the mitochondrial genome of Pachyneuron aphidis (Hymenoptera: Pteromalidae)

Species in Hymenoptera usually show exceptionally high rates of mitochondrial molecular evolution and dramatic gene rearrangements, which has been attributed to their parasitic lifestyle. However, mitochondrial genome (mitogenome) of chalcidoid wasps is still poorly understood and the evolution of gene rearrangements is still unclear. In this study, the nearly complete mitogenome of Pachyneuron aphidis, a chalcidoid wasp mainly hyperparasitizes the Aphidius gifuensis, was sequenced using a next-generation sequencing strategy. This genome is 15,137 bp in length, including 13 PCGs, 22 tRNAs, two rRNAs and a partial control region. Alignment with other Chalcidoidea mitogenomes revealed a novel inversion in the srRNA-trnV gene cluster in P. aphidis, which is the first of its kind to be reported in Chalcidoidea. Breakpoint distances analysis showed the high value of chalcidoid wasps compare to the ancestral arrangement pattern, which reflected as extensive gene rearrangements. Despite the high frequency of gene rearrangements in these insects, analyses of gene rearrangement and phylogenetic trees showed that species from the same family and the genus tent to have similar gene orders, and the conserved gene blocks (ND3-trnG, srRNA-trnV and COIII-ATP6-ATP8-trnD-trnK-COII-trnL2-COI) can usually be identified, especially at the family level of chalcidoid wasps.

High and Variable Rates of Repeat-Mediated Mitochondrial Genome Rearrangement in a Genus of Plants

For 30 years, it has been clear that angiosperm mitochondrial genomes evolve rapidly in sequence arrangement (i.e., synteny), yet absolute rates of rearrangement have not been measured in any plant group, nor is it known how much these rates vary. To investigate these issues, we sequenced and reconstructed the rearrangement history of seven mitochondrial genomes in Monsonia (Geraniaceae). We show that rearrangements (occurring mostly as inversions) not only take place at generally high rates in these genomes but also uncover significant variation in rearrangement rates. For example, the hyperactive mitochondrial genome of Monsonia ciliata has accumulated at least 30 rearrangements over the last million years, whereas the branch leading to M. ciliata and its sister species has sustained rearrangement at a rate that is at least ten times lower. Furthermore, our analysis of published data shows that rates of mitochondrial genome rearrangement in seed plants vary by at least 600-fold. We find that sites of rearrangement are highly preferentially located in very close proximity to repeated sequences in Monsonia. This provides strong support for the hypothesis that rearrangement in angiosperm mitochondrial genomes occurs largely through repeat-mediated recombination. Because there is little variation in the amount of repeat sequence among Monsonia genomes, the variable rates of rearrangement in Monsonia probably reflect variable rates of mitochondrial recombination itself. Finally, we show that mitochondrial synonymous substitutions occur in a clock-like manner in Monsonia; rates of mitochondrial substitutions and rearrangements are therefore highly uncoupled in this group.

The first mitogenomes of the superfamily Pamphilioidea (Hymenoptera: Symphyta): Mitogenome architecture and phylogenetic inference

The Pamphilioidea represents a small superfamily of the phytophagous suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genomes (mitogenomes) of three pamphilioid species: Chinolyda flagellicornis (Pamphiliidae), Megalodontes spiraeae and M. cephalotes (Megalodontesidae) were newly sequenced using next generation sequencing and comparatively analysed with the previously reported symphytan mitogenomes. A positive AT skew (0.013) and a negative GC skew (-0.194) were found in pamphilioid mitogenome, and a deviation from strand asymmetry was also observed in the PCGs encoded on both strands. Several gene rearrangement events were observed in four tRNA gene clusters (WCY, IQM, ARNS1EF and TP clusters), which have not been reported from symphytan mitogenomes to date. As the most parsimonious explanation, compared with the inferred insect ancestral mitogenome architecture, the occurrence of gene rearrangements in pamphilioid mitogenomes requires totally five evolutionary steps, including four transpositions and one inversion. The predicted secondary structures of tRNAs, rrnS and rrnL genes are mostly consistent with reported hymenopteran species. Phylogenetic analyses recovered the monophyly of superfamily Pamphilioidea and indicated the relationship Tenthredinoidea + (Pamphilioidea + (Cephoidea + (Orussoidea + Apocrita))) with strong nodal supports.

Information from the mitochondrial genomes of two egg parasitoids, Gonatocerus sp. and Telenomus sp., reveals a controversial phylogenetic relationship between Mymaridae and Scelionidae

The taxonomic status and phylogenetic affinities of Mymaridae and Scelionidae are controversial, based on similarities between these families in the characteristics of adults, larvae, and eggs. In this study, we sequenced the mitochondrial (mt) genomes of representatives from these two families and found that the derived secondary structure of tRNA-Arg was the same in each family due to the absence of the D-stem. The segment of "cox1 trnL₂cox2 trnK trnD atp8 atp6 cox3" in Gonatocerus sp. (Mymaridae) is conserved and distinct from those of four other species of Chalcidoidea but similar to that in Proctotrupoidea and Platygastroidea. However, phylogenetic analysis indicated that Gonatocerus sp. was sister group to other species of Chalcidoidea. Comparisons based on complete gene orders may be more useful in a phylogenetic and systematic context, as different branches may exhibit partially homoplastic gene orders.

The first two mitochondrial genomes of the family Aphelinidae with novel gene orders and phylogenetic implications

Chalcidoidea is one of the most diverse group in Hymenoptera by possessing striking mitochondrial gene arrangement. By using next generation sequencing method, the first two nearly complete mitochondrial genomes in the family Aphelinidae (Insecta, Hymenopetra, Chalcidoidea) were obtained in this study. Almost all previously sequenced mitochondrial genome of Chalcidoidea species have a large inversion including six genes (atp6-atp8-trnD-trnK-cox2-trnL2-cox1) as compared with ancestral mitochondrial genome, but these two Encarsia mitochondrial genomes had a large inversion including nine genes (nad3-trnG-atp6-atp8-trnD-trnK-cox2-trnL2-cox1), which was only congruent with the species in the genus Nasonia. Moreover, we found that one shuffling changes (trnD and trnK) happened in the species E. obtusiclava but not in another species E. formosa within the same genus, of which such shuffling within the same genus at this region was only detected in Polisters within Insecta. Phylogenetic analysis displayed that different data matrix (13PCG+ 2 rRNA or 13 PCG) and inference methods (BI or ML) indicate the identical topology with high nodal supports that Aphelinidae formed a sister group with (Trichogrammatidae + Aganoidae) and the monophyly of Pteramalidae. Our results also indicated the validity of assembling and feasibility of next-generation technology to obtain the mitochondrial genomes of parasitic Hymenoptera.

Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae)

Animal mitochondrial genomes usually exhibit conserved gene arrangement across major lineages, while those in the Hymenoptera are known to possess frequent rearrangements, as are those of several other orders of insects. Here, we sequenced two complete mitochondrial genomes of Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). In total, 37 mitochondrial genes were identified in both species. The same gene arrangement pattern was found in the two species, with extensive gene rearrangement compared with the ancestral insect mitochondrial genome. Most tRNA genes and all protein-coding genes were encoded on the minority strand. In total, 15 tRNA genes and seven protein-coding genes were rearranged. The rearrangements of cox1 and nad2 as well as most tRNA genes were novel. Phylogenetic analysis based on nucleotide sequences of protein-coding genes and on gene arrangement patterns produced identical topologies that support the relationship of (Agaonidae + Pteromalidae) + Trichogrammatidae in Chalcidoidea. CREx analysis revealed eight rearrangement operations occurred from presumed ancestral gene order of Chalcidoidea to form the derived gene order of Trichogramma. Our study shows that gene rearrangement information in Chalcidoidea can potentially contribute to the phylogeny of Chalcidoidea when more mitochondrial genome sequences are available.

Extensive mitochondrial heteroplasmy in the neotropical ants of the Ectatomma ruidum complex (Formicidae: Ectatomminae)

We assembled mitogenomes from 21 ant workers assigned to four morphospecies (E. ruidum spp. 1-4) and putative hybrids of the Ectatomma ruidum complex (E. ruidum spp. 2x3), and to E. tuberculatum using NGS data. Mitogenomes from specimens of E. ruidum spp. 3, 4 and 2 × 3 had a high proportion of polymorphic sites. We investigated whether polymorphisms in mitogenomes are due to nuclear mt paralogues (numts) or due to the presence of more than one mitogenome within an individual (heteroplasmy). We did not find loss of function signals in polymorphic protein-coding genes, and observed strong evidence for purifying selection in two haplotype-phased genes, which indicate the presence of two functional mitochondrial genomes coexisting within individuals instead of numts. Heteroplasmy due to hybrid paternal leakage is not supported by phylogenetic analyses. Our results reveal the presence of a fast-evolving secondary mitochondrial lineage of uncertain origin in the E. ruidum complex.

More evolution underground: Accelerated mitochondrial substitution rate in Australian burrowing freshwater crayfishes (Decapoda: Parastacidae)

To further understand the evolutionary history and mitogenomic features of Australia's highly distinctive freshwater crayfish fauna, we utilized a recently described rapid mitogenome sequencing pipeline to generate 24 new crayfish mitogenomes including a diversity of burrowing crayfish species and the first for Astacopsis gouldi, the world's largest freshwater invertebrate. Whole mitogenome-based phylogeny estimates using both Bayesian and Maximum Likelihood methods substantially strengthen existing hypotheses for systematic relationships among Australian freshwater crayfish with evidence of pervasive diversifying selection and accelerated mitochondrial substitution rate among the members of the clade representing strongly burrowing crayfish that may reflect selection pressures for increased energy requirement for adaptation to terrestrial environment and a burrowing lifestyle. Further, gene rearrangements are prevalent in the burrowing crayfish mitogenomes involving both tRNA and protein coding genes. In addition, duplicated control regions were observed in two closely related Engaeus species, together with evidence for concerted evolution. This study significantly adds to the understanding of Australian freshwater crayfish evolutionary relationships and suggests a link between mitogenome evolution and adaptation to terrestrial environments and a burrowing lifestyle in freshwater crayfish.

Complete mitochondrial genome of the lappet moth, Kunugia undans (Lepidoptera: Lasiocampidae): genomic comparisons among macroheteroceran superfamilies

The mitochondrial genome (mitogenome) characteristics of the monotypic Lasiocampoidea are largely unknown, because only limited number of mitogenomes is available from this superfamily. In this study, we sequenced the complete mitogenome of the lappet moth, Kunugia undans (Lepidoptera: Lasiocampidae) and compared it to those of Lasiocampoidea and macroheteroceran superfamilies (59 species in six superfamilies). The 15,570-bp K. undans genome had one additional trnR that was located between trnA and trnN loci and this feature was unique in Macroheterocera, including Lasiocampoidea. Considering that the two trnR copies are located in tandem with proper secondary structures and identical anticodons, a gene duplication event might be responsible for the presence of the two tRNAs. Nearly all macroheteroceran species, excluding Lasiocampoidea, have a spacer sequence (1-34 bp) at the trnS2 and ND1 junction, but most lasiocampid species, including K. undans, have an overlap at the trnS2 and ND1 junction, which represents a different genomic feature in Lasiocampoidea. Nevertheless, a TTAGTAT motif, which is typically detected in Macroheterocera at the trnS2 and ND1 junction, was also detected in all Lasiocampoidea. In summary, the general mitogenome characteristics of Lasiocampoidea did not differ greatly from the remaining macroheteroceran superfamilies, but it did exhibit some unique features.

Nearly complete mitogenome of hairy sawfly, Corynis lateralis (Brullé, 1832) (Hymenoptera: Cimbicidae): rearrangements in the IQM and ARNS1EF gene clusters

The Cimbicidae is a small family of the primitive and relatively less diverse suborder Symphyta (Hymenoptera). Here, nearly complete mitochondrial genome (mitogenome) of hairy sawfly, Corynis lateralis (Hymenoptera: Cimbicidae) was sequenced using next generation sequencing and comparatively analysed with the mitogenome of Trichiosoma anthracinum. The sequenced length of C. lateralis mitogenome was 14,899 bp with an A+T content of 80.60%. All protein coding genes (PCGs) are initiated by ATN codons and all are terminated with TAR or T- stop codon. All tRNA genes preferred usual anticodons. Compared with the inferred insect ancestral mitogenome, two tRNA rearrangements were observed in the IQM and ARNS1EF gene clusters, representing a new event not previously reported in Symphyta. An illicit priming of replication and/or intra/inter-mitochondrial recombination and TDRL seem to be responsible mechanisms for the rearrangement events in these gene clusters. Phylogenetic analyses confirmed the position of Corynis within Cimbicidae and recovered a relationship of Tenthredinoidea + (Cephoidea + Orussoidea) in Symphyta.

Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda)

BACKGROUND

Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information.

METHODS

Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements.

RESULTS

We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens, and Caridina cf. nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders.

DISCUSSION

Our findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.

The Complete Mitochondrial Genome of Aleurocanthus camelliae: Insights into Gene Arrangement and Genome Organization within the Family Aleyrodidae

There are numerous gene rearrangements and transfer RNA gene absences existing in mitochondrial (mt) genomes of Aleyrodidae species. To understand how mt genomes evolved in the family Aleyrodidae, we have sequenced the complete mt genome of Aleurocanthus camelliae and comparatively analyzed all reported whitefly mt genomes. The mt genome of A. camelliae is 15,188 bp long, and consists of 13 protein-coding genes, two rRNA genes, 21 tRNA genes and a putative control region (GenBank: KU761949). The tRNA gene, trnI, has not been observed in this genome. The mt genome has a unique gene order and shares most gene boundaries with Tetraleurodes acaciae. Nineteen of 21 tRNA genes have the conventional cloverleaf shaped secondary structure and two (trnS₁ and trnS₂) lack the dihydrouridine (DHU) arm. Using ARWEN and homologous sequence alignment, we have identified five tRNA genes and revised the annotation for three whitefly mt genomes. This result suggests that most absent genes exist in the genomes and have not been identified, due to be lack of technology and inference sequence. The phylogenetic relationships among 11 whiteflies and Drosophila melanogaster were inferred by maximum likelihood and Bayesian inference methods. Aleurocanthus camelliae and T. acaciae form a sister group, and all three Bemisia tabaci and two Bemisia afer strains gather together. These results are identical to the relationships inferred from gene order. We inferred that gene rearrangement plays an important role in the mt genome evolved from whiteflies.

Next-Generation Sequencing of Two Mitochondrial Genomes from Family Pompilidae (Hymenoptera: Vespoidea) Reveal Novel Patterns of Gene Arrangement

Animal mitochondrial genomes have provided large and diverse datasets for evolutionary studies. Here, the first two representative mitochondrial genomes from the family Pompilidae (Hymenoptera: Vespoidea) were determined using next-generation sequencing. The sequenced region of these two mitochondrial genomes from the species Auplopus sp. and Agenioideus sp. was 16,746 bp long with an A + T content of 83.12% and 16,596 bp long with an A + T content of 78.64%, respectively. In both species, all of the 37 typical mitochondrial genes were determined. The secondary structure of tRNA genes and rRNA genes were predicted and compared with those of other insects. Atypical trnS1 using abnormal anticodons TCT and lacking D-stem pairings was identified. There were 49 helices belonging to six domains in rrnL and 30 helices belonging to three domains in rrns present. Compared with the ancestral organization, four and two tRNA genes were rearranged in mitochondrial genomes of Auplopus and Agenioideus, respectively. In both species, trnM was shuffled upstream of the trnI-trnQ-trnM cluster, and trnA was translocated from the cluster trnA-trnR-trnN-trnS1-trnE-trnF to the region between nad1 and trnL1, which is novel to the Vespoidea. In Auplopus, the tRNA cluster trnW-trnC-trnY was shuffled to trnW-trnY-trnC. Phylogenetic analysis within Vespoidea revealed that Pompilidae and Mutillidae formed a sister lineage, and then sistered Formicidae. The genomes presented in this study have enriched the knowledge base of molecular markers, which is valuable in respect to studies about the gene rearrangement mechanism, genomic evolutionary processes and phylogeny of Hymenoptera.

Progress, pitfalls and parallel universes: a history of insect phylogenetics

The phylogeny of insects has been both extensively studied and vigorously debated for over a century. A relatively accurate deep phylogeny had been produced by 1904. It was not substantially improved in topology until recently when phylogenomics settled many long-standing controversies. Intervening advances came instead through methodological improvement. Early molecular phylogenetic studies (1985-2005), dominated by a few genes, provided datasets that were too small to resolve controversial phylogenetic problems. Adding to the lack of consensus, this period was characterized by a polarization of philosophies, with individuals belonging to either parsimony or maximum-likelihood camps; each largely ignoring the insights of the other. The result was an unfortunate detour in which the few perceived phylogenetic revolutions published by both sides of the philosophical divide were probably erroneous. The size of datasets has been growing exponentially since the mid-1980s accompanied by a wave of confidence that all relationships will soon be known. However, large datasets create new challenges, and a large number of genes does not guarantee reliable results. If history is a guide, then the quality of conclusions will be determined by an improved understanding of both molecular and morphological evolution, and not simply the number of genes analysed.

Mitochondrial genomes of praying mantises (Dictyoptera, Mantodea): rearrangement, duplication, and reassignment of tRNA genes

Insect mitochondrial genomes (mitogenomes) contain a conserved set of 37 genes for an extensive diversity of lineages. Previously reported dictyopteran mitogenomes share this conserved mitochondrial gene arrangement, although surprisingly little is known about the mitogenome of Mantodea. We sequenced eight mantodean mitogenomes including the first representatives of two families: Hymenopodidae and Liturgusidae. Only two of these genomes retain the typical insect gene arrangement. In three Liturgusidae species, the trnM genes have translocated. Four species of mantis (Creobroter gemmata, Mantis religiosa, Statilia sp., and Theopompa sp.-HN) have multiple identical tandem duplication of trnR, and Statilia sp. additionally includes five extra duplicate trnW. These extra trnR and trnW in Statilia sp. are erratically arranged and form another novel gene order. Interestingly, the extra trnW is converted from trnR by the process of point mutation at anticodon, which is the first case of tRNA reassignment for an insect. Furthermore, no significant differences were observed amongst mantodean mitogenomes with variable copies of tRNA according to comparative analysis of codon usage. Combined with phylogenetic analysis, the characteristics of tRNA only possess limited phylogenetic information in this research. Nevertheless, these features of gene rearrangement, duplication, and reassignment provide valuable information toward understanding mitogenome evolution in insects.

The Whole Genome Assembly and Comparative Genomic Research of Thellungiella parvula (Extremophile Crucifer) Mitochondrion

The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile species Thellungiella parvula (T. parvula) have been determined with the lengths of 255,773 bp. T. parvula mt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome of T. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes' evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species, T. parvula is related to Arabidopsis thaliana whose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.

Complete mitochondrial genome of Camponotus atrox (Hymenoptera: Formicidae): a new tRNA arrangement in Hymenoptera

We sequenced the complete mitochondrial (mt) genome of Camponotus atrox (Hymenoptera: Formicidae), which is only distributed in Korea. The genome was 16 540 bp in size and contained typical sets of genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs). The C. atrox A+T-rich region, at 1402 bp, was the longest of all sequenced ant genomes and was composed of an identical tandem repeat consisting of six 100-bp copies and one 96-bp copy. A total of 315 bp of intergenic spacer sequence was spread over 23 regions. An alignment of the spacer sequences in ants was largely feasible among congeneric species, and there was substantial sequence divergence, indicating their potential use as molecular markers for congeneric species. The A/T contents at the first and second codon positions of protein-coding genes (PCGs) were similar for ant species, including C. atrox (73.9% vs. 72.3%, on average). With increased taxon sampling among hymenopteran superfamilies, differences in the divergence rates (i.e., the non-synonymous substitution rates) between the suborders Symphyta and Apocrita were detected, consistent with previous results. The C. atrox mt genome had a unique gene arrangement, trnI-trnM-trnQ, at the A+T-rich region and ND2 junction (underline indicates inverted gene). This may have originated from a tandem duplication of trnM-trnI, resulting in trnM-trnI-trnM-trnI-trnQ, and the subsequent loss of the first trnM and second trnI, resulting in trnI-trnM-trnQ.

Mitochondrial genome of Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae)

The mitochondrial genome of the parasitic wasp Megaphragma amalphitanum is published in this paper. The mitochondrial DNA (mtDNA) is 15 041 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. The overall base composition of the genome in descending order was 45.67% A, 8.71% C, 39.63% T and 5.99% G, with a significant AT bias of 85.30%.

The complete mitogenomes of Calameuta filiformis (Eversmann, 1847) and Calameuta idolon (Rossi, 1794) (Hymenoptera: Cephidae): The remarkable features of the elongated A+T rich region in Cephini

Two complete mitogenomes of the stem borers, Calameuta filiformis and Calameuta idolon, and the complete A+T-rich region of Trachelus iudaicus (Hymenoptera: Cephidae), are reported. The mitogenomes of these species are the longest reported from hymenopterans to date. A remarkable increase in length of the A+T-rich region, the longest for Hymenoptera, was found and compared across the tribe Cephini. The presence of the tRNA- and rRNA-like sequences were reported in the A+T-rich region of sawflies and they were suggested to play a role in replication and/or transcription. The long and short tandem repeats were orderly located in both sides of the A+T-rich region producing stable secondary structures. We suggest that the short tandem repeats are likely to function as a replication fork barrier.

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.

The Complete Mitochondrial Genome of Corizus tetraspilus (Hemiptera: Rhopalidae) and Phylogenetic Analysis of Pentatomomorpha

Insect mitochondrial genome (mitogenome) are the most extensively used genetic information for molecular evolution, phylogenetics and population genetics. Pentatomomorpha (>14,000 species) is the second largest infraorder of Heteroptera and of great economic importance. To better understand the diversity and phylogeny within Pentatomomorpha, we sequenced and annotated the complete mitogenome of Corizus tetraspilus (Hemiptera: Rhopalidae), an important pest of alfalfa in China. We analyzed the main features of the C. tetraspilus mitogenome, and provided a comparative analysis with four other Coreoidea species. Our results reveal that gene content, gene arrangement, nucleotide composition, codon usage, rRNA structures and sequences of mitochondrial transcription termination factor are conserved in Coreoidea. Comparative analysis shows that different protein-coding genes have been subject to different evolutionary rates correlated with the G+C content. All the transfer RNA genes found in Coreoidea have the typical clover leaf secondary structure, except for trnS1 (AGN) which lacks the dihydrouridine (DHU) arm and possesses a unusual anticodon stem (9 bp vs. the normal 5 bp). The control regions (CRs) among Coreoidea are highly variable in size, of which the CR of C. tetraspilus is the smallest (440 bp), making the C. tetraspilus mitogenome the smallest (14,989 bp) within all completely sequenced Coreoidea mitogenomes. No conserved motifs are found in the CRs of Coreoidea. In addition, the A+T content (60.68%) of the CR of C. tetraspilus is much lower than that of the entire mitogenome (74.88%), and is lowest among Coreoidea. Phylogenetic analyses based on mitogenomic data support the monophyly of each superfamily within Pentatomomorpha, and recognize a phylogenetic relationship of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))).

Two nearly complete mitogenomes of wheat stem borers, Cephus pygmeus (L.) and Cephus sareptanus Dovnar-Zapolskij (Hymenoptera: Cephidae): an unusual elongation of rrnS gene

Two nearly complete mitochondrial genomes (mitogenomes) of wheat stem borers, Cephus pygmeus and Cephus sareptanus (Hymenoptera: Cephidae), were sequenced, characterised and compared with the previously known mitogenome of Cephus cinctus. The gene orders are mostly conserved, except for translocation of trnM and swapped position of trnI and trnQ. An A+T bias was found, but a deviation from strand asymmetry was also detected on the J strand. All protein coding genes (PCGs) are initiated by ATN codons, except for nad1, nad2 and atp8, and all are terminated with TAA, TA- or T- as a stop codon. The predicted secondary structures of rrnS and rrnL genes are mostly consistent with reported hymenopteran species. However, an unusual elongation in rrnS, not know elsewhere in the order, was discovered in Cephus species. Three autonomous sequences detected in domains I and II are mainly responsible for the length expansions.

Higher-level phylogeny of the Hymenoptera inferred from mitochondrial genomes

Higher-level hymenopteran relationships remain unresolved in both morphological and molecular analyses. In this study, we present the most comprehensive analyses of hymenopteran relationships based on 48 mitochondrial (mt) genomes. One complete and two nearly complete mt genomes representing three hymenopteran superfamilies were newly sequenced. We assessed the influence of inclusion/exclusion of 3rd codon positions, alignment approaches, partition schemes and phylogenetic approaches on topology and nodal support within the Hymenoptera. The results showed that the topologies were sensitive to the variation of dataset and analytical approach. However, some robust and highly supported relationships were recovered: the Ichneumonomorpha was monophyletic; the Trigonalyoidea+Megalyroidea and the Diaprioidea+Chalcidoidea were consistently recovered; the Cynipoidea was generally recovered as the sister group to the Diaprioidea+Chalcidoidea. In addition, the monophyletic Aculeata and Proctotrupomorpha were recovered in some analyses. Several gene rearrangements were detected in each of the three newly sequenced mt genomes. Specifically, the Ibalia leucospoides mt genome harbors a large inversion of a gene block from trnE to trnS2. Inverted, duplicated A+T rich regions were detected in the Ibalia leucospoides mt genome, which probably played an important role during the formation of the large gene block inversion via recombination.