Higher tRNA gene duplication in mitogenomes of praying mantises (Dictyoptera, Mantodea) and the phylogeny within Mantodea

The Phylogenetic Relationships of Major Lizard Families Using Mitochondrial Genomes and Selection Pressure Analyses in Anguimorpha

Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism's energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed.

How Does Mitochondrial Protein-Coding Gene Expression in Fejervarya kawamurai (Anura: Dicroglossidae) Respond to Extreme Temperatures?

Unusual climates can lead to extreme temperatures. Fejervarya kawamurai, one of the most prevalent anurans in the paddy fields of tropical and subtropical regions in Asia, is sensitive to climate change. The present study focuses primarily on a single question: how do the 13 mitochondrial protein-coding genes (PCGs) respond to extreme temperature change compared with 25 °C controls? Thirty-eight genes including an extra tRNA-Met gene were identified and sequenced from the mitochondrial genome of F. kawamurai. Evolutionary relationships were assessed within the Dicroglossidae and showed that Dicroglossinae is monophyletic and F. kawamurai is a sister group to the clade of (F. multistriata + F. limnocharis). Transcript levels of mitochondrial genes in liver were also evaluated to assess responses to 24 h exposure to low (2 °C and 4 °C) or high (40 °C) temperatures. Under 2 °C, seven genes showed significant changes in liver transcript levels, among which transcript levels of ATP8, ND1, ND2, ND3, ND4, and Cytb increased, respectively, and ND5 decreased. However, exposure to 4 °C for 24 h was very different in that the expressions of ten mitochondrial protein-coding genes, except ND1, ND3, and Cytb, were significantly downregulated. Among them, the transcript level of ND5 was most significantly downregulated, decreasing by 0.28-fold. Exposure to a hot environment at 40 °C for 24 h resulted in a marked difference in transcript responses with strong upregulation of eight genes, ranging from a 1.52-fold increase in ND4L to a 2.18-fold rise in Cytb transcript levels, although COI and ND5 were reduced to 0.56 and 0.67, respectively, compared with the controls. Overall, these results suggest that at 4 °C, F. kawamurai appears to have entered a hypometabolic state of hibernation, whereas its mitochondrial oxidative phosphorylation was affected at both 2 °C and 40 °C. The majority of mitochondrial PCGs exhibited substantial changes at all three temperatures, indicating that frogs such as F. kawamurai that inhabit tropical or subtropical regions are susceptible to ambient temperature changes and can quickly employ compensating adjustments to proteins involved in the mitochondrial electron transport chain.

Novel Gene Rearrangements in Mitochondrial Genomes of four families of Praying Mantises (Insecta, Mantodea) and Phylogenetic Relationships of Mantodea

The mitochondrial genome (mitogenome) plays an important role in phylogenetic studies of many species. The mitogenomes of many praying mantis groups have been well-studied, but mitogenomes of special mimic praying mantises, especially Acanthopoidea and Galinthiadoidea species, are still sorely lacking in the NCBI database. The present study analyzes five mitogenomes from four species of Acanthopoidea (Angela sp., Callibia diana, Coptopteryx sp., Raptrix fusca) and one of Galinthiadoidea (Galinthias amoena) that were sequenced by the primer-walking method. Among Angela sp. and Coptopteryx sp., three gene rearrangements were detected in ND3-A-R-N-S-E-F and COX1-L2-COX2 gene regions, two of which were novel. In addition, individual tandem repeats were found in control regions of four mitogenomes (Angela sp., C. diana, Coptopteryx sp., G. amoena). For those, plausible explanations were derived from the tandem duplication-random loss (TDRL) model and the slipped-strand mispairing model. One potential motif was found in Acanthopidae that was seen as a synapomorphy. Several conserved block sequences (CBSs) were detected within Acanthopoidea that paved the way for the design of specific primers. Via BI and ML analysis, based on four datasets (PCG12, PCG12R, PCG123, PCG123R), the merged phylogenetic tree within Mantodea was reconstructed. This showed that the monophyly of Acanthopoidea was supported and that the PCG12R dataset was the most suitable for reconstructing the phylogenetic tree within Mantodea.

Exploring the Mitogenomes of Mantodea: New Insights from Structural Diversity and Higher-Level Phylogenomic Analyses

The recently reorganized classification of Mantodea has made significant progress in resolving past homoplasy problems, although some relationships among higher taxa remain uncertain. In the present study, we utilized newly sequenced mitogenomes and nuclear gene sequences of 23 mantid species, along with published data of 53 mantises, to perform familial-sampling structural comparisons of mantodean mitogenomes and phylogenomic studies. Our rstructural analysis revealed generally conserved mitogenome organizations, with a few cases of tRNA gene rearrangements, including the detection of trnL₂ duplication for the first time. In our phylogenetic analysis, we found a high degree of compositional heterogeneity and lineage-specific evolutionary rates among mantodean mitogenomes, which frequently corresponded to several unexpected groupings in the topologies under site-homogeneous models. In contrast, the topologies obtained using the site-heterogeneous mixture model fit the currently accepted phylogeny of Mantodea better. Topology tests and four-cluster likelihood mapping analyses further determined the preferred topologies. Our phylogenetic results confirm the monophyly of superfamilial groups Schizomantodea, Amerimantodea, Heteromantodea, Promantidea, and Mantidea and recover the early-branching relationships as (Mantoidoidea + (Amerimantodea + (Metallyticoidea + Cernomantodea))). Additionally, the results suggest that the long-unresolved phylogenetic position of Majangidae should be placed within Mantidea, close to Mantoidea, rather than within Epaphroditoidea. Our findings contribute to understanding the compositional and structural diversity in mantodean mitogenomes, underscore the importance of evolutionary model selection in phylogenomic studies, and provide new insights into the high-level phylogeny of Mantodea.

Nine Mitochondrial Genomes of Phasmatodea with Two Novel Mitochondrial Gene Rearrangements and Phylogeny

The classification of stick and leaf insects (Order Phasmatodea) is flawed at various taxonomic ranks due to a lack of robust phylogenetic relationships and convergent morphological characteristics. In this study, we sequenced nine new mitogenomes that ranged from 15,011 bp to 17,761 bp in length. In the mitogenome of Carausis sp., we found a translocation of trnR and trnA, which can be explained by the tandem duplication/random loss (TDRL) model. In the Stheneboea repudiosa Brunner von Wattenwyl, 1907, a novel mitochondrial structure of 12S rRNA-CR1-trnI-CR2-trnQ-trnM was found for the first time in Phasmatodea. Due to the low homology of CR1 and CR2, we hypothesized that trnI was inverted through recombination and then translocated into the middle of the control region. Control region repeats were frequently detected in the newly sequenced mitogenomes. To explore phylogenetic relationships in Phasmatodea, mtPCGs from 56 Phasmatodean species (composed of 9 stick insects from this study, 31 GenBank data, and 16 data derived from transcriptome splicing) were used for Bayesian inference (BI), and maximum likelihood (ML) analyses. Both analyses supported the monophyly of Lonchodinae and Necrosciinae, but Lonchodidae was polyphyletic. Phasmatidae was monophyletic, and Clitumninae was paraphyletic. Phyllidae was located at the base of Neophasmatodea and formed a sister group with the remaining Neophasmatodea. Bacillidae and Pseudophasmatidae were recovered as a sister group. Heteroptergidae was monophyletic, and the Heteropteryginae sister to the clade (Obriminae + Dataminae) was supported by BI analysis and ML analysis.

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.

Mitochondrial genomes of 10 Mantidae species and their phylogenetic implications

This article aims to present a phylogenetic evaluation of Mantidae based on a mitochondrial genome (mitogenome) data set. The mitogenome of 10 Mantidae species were sequenced using next-generation sequencing. The length of nine the complete mitogenomes ranged from 15,371 bp in Tenodera aridifolia to 16,063 bp in Hierodula longa. Mantidae mitogenomes have 37 genes and control region with two exceptions: five trnR copies in Statilia maculata, and H. zhangi was incomplete missing trnI, trnQ, trnM and a portion of the control region. There was a large noncoding region (LNC) between trnM and nad2 in H. chinensis, H. longa, H. maculata and Titanodula sp. Most of protein-coding genes (PCGs) used the typical start ATN codon and TAA/TAG stop codons. All tRNAs fold into the typical clover-leaf secondary structure except trnS1 which lacks a dihydrouracil (DHU) arm. Nucleotide diversity and Ka/Ks analysis of 13 PCGs showed that atp8 had the highest variability and fastest evolutionary rate. Phylogenetic relationships among 42 Mantidae species were reconstructed using the 13 PCGs and two rRNA genes using Bayesian Inference (BI) and Maximum Likelihood (ML) methods. Of the seven mantid subfamilies included in this analysis, only four had multiple exemplars, and of those only Mantinae and Vatinae formed monophyletic groups in BI and ML trees. Consistent with previous studies, the monophyly of the Hierudulinae and Tenoderinae were not been supported. The present results imply that it is necessary to combine nuclear molecular markers and external characteristic to understand the phylogenetic relationships within Mantidae.

The Complete Mitochondrial Genomes of Three Sphenomorphinae Species (Squamata: Scincidae) and the Selective Pressure Analysis on Mitochondrial Genomes of Limbless Isopachys gyldenstolpei

In order to adapt to diverse habitats, organisms often evolve corresponding adaptive mechanisms to cope with their survival needs. The species-rich family of Scincidae contains both limbed and limbless species, which differ fundamentally in their locomotor demands, such as relying on the movement of limbs or only body swing to move. Locomotion requires energy, and different types of locomotion have their own energy requirements. Mitochondria are the energy factories of living things, which provide a lot of energy for various physiological activities of organisms. Therefore, mitochondrial genomes could be tools to explore whether the limb loss of skinks are selected by adaptive evolution. Isopachys gyldenstolpei is a typical limbless skink. Here, we report the complete mitochondrial genomes of I. gyldenstolpei, Sphenomorphus indicus, and Tropidophorus hainanus. The latter two species were included as limbed comparator species to the limbless I. gyldenstolpei. The results showed that the full lengths of the mitochondrial genomes of I. gyldenstolpei, S. indicus, and T. hainanus were 17,210, 16,944, and 17,001 bp, respectively. Three mitochondrial genomes have typical circular double-stranded structures similar to other reptiles, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and the control region. Three mitochondrial genomes obtained in this study were combined with fifteen mitochondrially complete genomes of Scincidae in the NCBI database; the phylogenetic relationship between limbless I. gyldenstolpei and limbed skinks (S. indicus and T. hainanus) is discussed. Through BI and ML trees, Sphenomorphinae and Mabuyinae were monophyletic, while the paraphyly of Scincinae was also recovered. The limbless skink I. gyldenstolpei is closer to the species of Tropidophorus, which has formed a sister group with (T. hainanus + T. hangman). In the mitochondrial genome adaptations between limbless I. gyldenstolpei and limbed skinks, one positively selected site was found in the branch-site model analysis, which was located in ND2 (at position 28, BEB value = 0.907). Through analyzing the protein structure and function of the selected site, we found it was distributed in mitochondrial protein complex I. Positive selection of some mitochondrial genes in limbless skinks may be related to the requirement of energy to fit in their locomotion. Further research is still needed to confirm this conclusion though.

Mitochondrial Phylogenomics Suggests Complex Evolutionary Pattern of Pronotal Foliaceous Mimicry in Hierodulinae (Mantodea: Mantidae), with Description of a New Species of Rhombodera Burmeister, 1838 from China

Hierodulinae is a species-rich mantid subfamily, with some species bearing a notable leaf-like pronotum. However, the evolutionary pattern and taxonomic significance of the leaf-like pronotum are largely unknown. Here, we present a phylogenomic analysis of the Hierodulinae genera Rhombodera Burmeister, 1838, and Hierodula Burmeister, 1838 based on mitochondrial genomes. We also describe a new species, namely Rhombodera hyalina sp. nov. from Guangxi, China. Our phylogenetic result, together with the evidence from male genitalia, suggests the division of the Oriental Hierodula and Rhombodera complex into three clades. We find a complex pattern on the evolution of the leaf-like pronotum, which is present in at least five lineages, respectively, of the above three clades.

Novel Mitochondrial Gene Rearrangement and Intergenic Regions Exist in the Mitochondrial Genomes from Four Newly Established Families of Praying Mantises (Insecta: Mantodea)

Simple Summary

Mantodea is regarded as an excellent material to study the gene rearrangements and large non-coding regions (LNCRs) in mitochondrial genomes. Meanwhile, as a result of the convergent evolution and parallelism, the gene rearrangements and LNCRs are specific to some taxonomic groups within Mantodea, which play an important role in phylogenetic relationship research. Nine mitochondrial genomes (mitogenomes) from four newly established families of praying mantises are obtained and annotated. Eight types of gene rearrangements, including four novel types of gene rearrangements in Mantodea, are detected, which can be explained by the tandem replication-random loss (TDRL) model. Moreover, one conserved motif between trnI-trnQ is detected in Toxoderidae. This study shed light on the formation mechanisms of these gene rearrangements and LNCRs in four newly established families of praying mantises.

Abstract

Long non-coding regions (NCRs) and gene rearrangements are commonly seen in mitochondrial genomes of Mantodea and are primarily focused on three regions: CR-I-Q-M-ND2, COX2-K-D-ATP8, and ND3-A-R-N-S-E-F-ND5. In this study, eight complete and one nearly complete mitochondrial genomes of praying mantises were acquired for the purpose of discussing mitochondrial gene rearrangements and phylogenetic relationships within Mantodea, primarily in the newly established families Haaniidae and Gonypetidae. Except for Heterochaeta sp. JZ-2017, novel mitochondrial gene arrangements were detected in Cheddikulama straminea, Sinomiopteryx graham, Pseudovates chlorophaea, Spilomantis occipitalis. Of note is the fact that one type of novel arrangement was detected for the first time in the Cyt b-S2-ND1 region. This could be reliably explained by the tandem replication-random loss (TDRL) model. The long NCR between trnT and trnP was generally found in Iridopteryginae and was similar to the ND4L or ND6 gene. Combined with gene rearrangements and intergenic regions, the monophyly of Haaniidae was supported, whereas the paraphyly of Gonypetidae was recovered. Furthermore, several synapomorphies unique to some clades were detected that conserved block sequences between trnI and trnQ and gaps between trnT and trnP in Toxoderidae and Iridopteryginae, respectively.

The complete mitochondrial genome of Leptomantella tonkinae (Hebard, 1920) (Mantodea: Leptomantellidae) and its phylogeny

The complete mitochondrial (mt) genome of Leptomantella tonkinae (Hebard, 1920) was 15,527 bp in length and contained 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and one control region. The gene arrangement of mt genome of L. tonkinae was identical to the primitive mantis. The overall AT content of the mt genome was 74%. In ML and BI phylogenetic analyses, the monophyly of Leptomantellidae was robustly supported and the clade of Leptomantellidae is a sister clade to the group of (Gonypetidae+(Leptomantellidae+(Amorphoscelidae+Nanomantidae))).

Complete mitochondrial genomes of four species of praying mantises (Dictyoptera, Mantidae) with ribosomal second structure, evolutionary and phylogenetic analyses

Praying mantises are distributed all over the world. Though some Mantodea mitogenomes have been reported, an evolutionary genomic and phylogenetic analysis study lacks the latest taxonomic system. In the present study, four new mitogenomes were sequenced and annotated. Deroplatys truncate, D. lobate, Amorphoscelis chinensis and Macromantis sp. belong to Deroplatyidae, Amorphoscelidae and Photinaidae family, respectively. Our results indicated that the ATP8 gene may be lost in D. truncate and D. lobata mt genome, and four tRNA genes have not been found in D. truncate, D. lobata and Macromantis sp. A dN/dS pair analysis was conducted and it was found that all genes have evolved under purifying selection. Furthermore, we tested the phylogenetic relationships between the eight families of the Mantodea, including 35 species of praying Mantis. Based on the complete mitochondrial genome data, it was also suggested as sister to Deroplatyidae + Mantidae, Metallyticus sp., the only representative of Metallyticidae, is sister to the remaining mantises. Our results support the taxonomic system of Schwarz and Roy and are consistent with previous studies.

The mitochondrial genome of Eurycantha calcarata Lucas, 1869 (Phasmatodea: Lonchodinae) and its phylogeny

The Lonchodinae (Phasmatodea: Phasmatidae) is rich in insect species with more than 330 species of 40 genera. The phylogenetic relationships within Lonchodinae have been under debate. We successfully sequenced the complete mitogenome of Eurycantha calcarata Lucas, 1869 (Phasmatodea: Lonchodinae) with a length of 16,280 bp, which had the same genes and gene arrangements as those of various published papers on stick insects. The whole mitogenome and control region of E. calcarata had a high AT content of 78.2 and 85.9%, respectively. All PCGs used ATN as the start codon, and most PCGs used TAA/TAG as the stop codons excluding COX2 (T), COX3 (TA), and ND5 (TA). To discuss the phylogeny of Lonchodinae, we reconstructed the phylogenetic relationships of 27 species of Phasmatodea including E. calcarata and two species of Embioptera used as outgroups. In BI and ML trees, the monophyly of Lonchodinae and Necrosciinae was well supported, whereas the monophyly of Clitumninae was not recovered. These results indicated that Lonchodinae was a sister clade to Phylliinae and E. calcarata was a sister clade to Phraortes genus.

Comparative Mitogenomes of Two Coreamachilis Species (Microcoryphia: Machilidae) along with Phylogenetic Analyses of Microcoryphia

The order Microcoryphia, commonly known as bristletails, is considered as the most primitive one among living insects. Within this order, two species, Coreamachilis coreanus and C. songi (Machilidae: Machilinae), display the following contrasting reproductive strategies: parthenogenesis occurs in C. coreanus, whereas sexual reproduction is found in C. songi. In the present study, the complete mitogenomes of C. coreanus and C. songi were sequenced to compare their mitogenome structure, analyze relationships within the Microcoryphia, and assess adaptive evolution. The length of the mitogenomes of C. coreanus and C. songi were 15,578 bp and 15,570 bp, respectively, and the gene orders were those of typical insects. A long hairpin structure was found between the ND1 and 16S rRNA genes of both species that seem to be characteristic of Machilinae and Petrobiinae species. Phylogenetic assessment of Coreamachilis was conducted using BI and ML analyses with concatenated nucleotide sequences of the 13 protein-coding genes. The results showed that the monophyly of Machilidae, Machilinae, and Petrobiinae was not supported. The genus Coreamachilis (C. coreanus and C. songi) was a sister clade to Allopsontus helanensis, and then the clade of ((C. coreanus + C. songi) + A. helanensis) was a sister clade to A. baii, which suggests that the monophyly of Allopsontus was not supported. Positive selection analysis of the 13 protein-coding genes failed to reveal any positive selection in C. coreanus or C. songi. The long hairpin structures found in Machilinae and Petrobiinae were highly consistent with the phylogenetic results and could potentially be used as an additional molecular characteristic to further discuss relationships within the Microcoryphia.

Three Complete Mitochondrial Genomes of Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis (Insecta: Phasmatodea) and Their Phylogeny

Insects of the order Phasmatodea are mainly distributed in the tropics and subtropics and are best known for their remarkable camouflage as plants. In this study, we sequenced three complete mitochondrial genomes from three different families: Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis. The lengths of the three mitochondrial genomes were 15,896 bp, 16,869 bp, and 17,005 bp, respectively, and the gene composition and structure of the three stick insects were identical to those of the most recent common ancestor of insects. The phylogenetic relationships among stick insects have been chaotic for a long time. In order to discuss the intra- and inter-ordinal relationship of Phasmatodea, we used the 13 protein-coding genes (PCGs) of 85 species for maximum likelihood (ML) and Bayesian inference (BI) analyses. Results showed that the internal topological structure of Phasmatodea had a few differences in both ML and BI trees and long-branch attraction (LBA) appeared between Embioptera and Zoraptera, which led to a non-monophyletic Phasmatodea. Consequently, after removal of the Embioptera and Zoraptera species, we re-performed ML and BI analyses with the remaining 81 species, which showed identical topology except for the position of Tectarchus ovobessus (Phasmatodea). We recovered the monophyly of Phasmatodea and the sister-group relationship between Phasmatodea and Mantophasmatodea. Our analyses also recovered the monophyly of Heteropterygidae and the paraphyly of Diapheromeridae, Phasmatidae, Lonchodidae, Lonchodinae, and Clitumninae. In this study, Peruphasma schultei (Pseudophasmatidae), Phraortes sp. YW-2014 (Lonchodidae), and species of Diapheromeridae clustered into the clade of Phasmatidae. Within Heteropterygidae, O. guangxiensis was the sister clade to O. mouhotii belonging to Dataminae, and the relationship of (Heteropteryginae + (Dataminae + Obriminae)) was recovered.

Insight into the Phylogenetic Relationships among Three Subfamilies within Heptageniidae (Insecta: Ephemeroptera) along with Low-Temperature Selection Pressure Analyses Using Mitogenomes

We determined 15 complete and two nearly complete mitogenomes of Heptageniidae belonging to three subfamilies (Heptageniinae, Rhithrogeninae, and Ecdyonurinae) and six genera (Afronurus, Epeorus, Leucrocuta, Maccaffertium, Stenacron, and Stenonema). Species of Rhithrogeninae and Ecdyonurinae had the same gene rearrangement of CR-I-M-Q-M-ND2, whereas a novel gene rearrangement of CR-I-M-Q-NCR-ND2 was found in Heptageniinae. Non-coding regions (NCRs) of 25-47 bp located between trnA and trnR were observed in all mayflies of Heptageniidae, which may be a synapomorphy for Heptageniidae. Both the BI and ML phylogenetic analyses supported the monophyly of Heptageniidae and its subfamilies (Heptageniinae, Rhithrogeninae, and Ecdyonurinae). The phylogenetic results combined with gene rearrangements and NCR locations confirmed the relationship of the subfamilies as (Heptageniinae + (Rhithrogeninae + Ecdyonurinae)). To assess the effects of low-temperature stress on Heptageniidae species from Ottawa, Canada, we found 27 positive selection sites in eight protein-coding genes (PCGs) using the branch-site model. The selection pressure analyses suggested that mitochondrial PCGs underwent positive selection to meet the energy requirements under low-temperature stress.

Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations

BACKGROUND

The phylogenetic relationships of Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) remain unresolved. Different researchers have supported one of three hypotheses (Palaeoptera, Chiastomyaria or Metapterygota) based on data from different morphological characters and molecular markers, sometimes even re-assessing the same transcriptomes or mitochondrial genomes. The appropriate choice of outgroups and more taxon sampling is thought to eliminate artificial phylogenetic relationships and obtain an accurate phylogeny. Hence, in the current study, we sequenced 28 mt genomes from Ephemeroptera, Odonata and Plecoptera to further investigate phylogenetic relationships, the probability of each of the three hypotheses, and to examine mt gene arrangements in these species. We selected three different combinations of outgroups to analyze how outgroup choice affected the phylogenetic relationships of Odonata and Ephemeroptera.

METHODS

Mitochondrial genomes from 28 species of mayflies, dragonflies, damselflies and stoneflies were sequenced. We used Bayesian inference (BI) and Maximum likelihood (ML) analyses for each dataset to reconstruct an accurate phylogeny of these winged insect orders. The effect of outgroup choice was assessed by separate analyses using three outgroups combinations: (a) four bristletails and three silverfish as outgroups, (b) five bristletails and three silverfish as outgroups, or (c) five diplurans as outgroups.

RESULTS

Among these sequenced mitogenomes we found the gene arrangement IMQM in Heptageniidae (Ephemeroptera), and an inverted and translocated tRNA-Ile between the 12S RNA gene and the control region in Ephemerellidae (Ephemeroptera). The IMQM gene arrangement in Heptageniidae (Ephemeroptera) can be explained via the tandem-duplication and random loss model, and the transposition and inversion of tRNA-Ile genes in Ephemerellidae can be explained through the recombination and tandem duplication-random loss (TDRL) model. Our phylogenetic analysis strongly supported the Chiastomyaria hypothesis in three different outgroup combinations in BI analyses. The results also show that suitable outgroups are very important to determining phylogenetic relationships in the rapid evolution of insects especially among Ephemeroptera and Odonata. The mt genome is a suitable marker to investigate the phylogeny of inter-order and inter-family relationships of insects but outgroup choice is very important for deriving these relationships among winged insects. Hence, we must carefully choose the correct outgroup in order to discuss the relationships of Ephemeroptera and Odonata.

Novel tRNA gene rearrangements in the mitochondrial genomes of praying mantises (Mantodea: Mantidae): Translocation, duplication and pseudogenization

Gene rearrangements have been found in several mitochondrial genomes of Mantodea, located in the gene blocks CR-I-Q-M-ND2, COX1-K-D-ATP8 and ND3-A-R-N-S-E-F-ND5. We have sequenced one mitogenome of Amelidae (Yersinia mexicana) and six mitogenomes of Mantidae to discuss the mitochondrial gene rearrangement and the phylogenetic relationship within Mantidae. These mitogenomes showed rearrangements of tRNA genes except for Asiadodis yunnanensis and Hierodula zhangi. These novel gene rearrangements of Mantidae were primarily concentrated in the region of CR-I-Q-M-ND2, including gene translocation, duplication and pseudogenization. For the occurrences of these rearrangements, the tandem duplication-random loss (TDRL) model and slipped-strand mispairing model were suitable to explain. Large non-coding regions (LNCRs) located in the region of CR-I-Q-M-ND2 were detected in most Mantidae species, whereas some LNCRs had high similarity to the control region (CR). Both BI and ML phylogenetic analyses supported the monophyly of Mantidae and the paraphyly of Mantinae. The phylogenetic results with the gene order and the location of NCRs acted as forceful evidence that specific gene rearrangements and special LNCRs may be synapomorphies for several groups of mantises.

Mitogenome Analysis of Four Lamiinae Species (Coleoptera: Cerambycidae) and Gene Expression Responses by Monochamus alternatus When Infected with the Parasitic Nematode, Bursaphelenchus mucronatus

We determined the mitochondrial gene sequence of Monochamus alternatus and three other mitogenomes of Lamiinae (Insect: Coleoptera: Cerambycidae) belonging to three genera (Aulaconotus, Apriona and Paraglenea) to enrich the mitochondrial genome database of Lamiinae and further explore the phylogenetic relationships within the subfamily. Phylogenetic trees of the Lamiinae were built using the Bayesian inference (BI) and maximum likelihood (ML) methods and the monophyly of Monochamus, Anoplophora, and Batocera genera was supported. Anoplophora chinensis, An. glabripennis and Aristobia reticulator were closely related, suggesting they may also be potential vectors for the transmission of the pine wood pathogenic nematode (Bursaphelenchus xylophilus) in addition to M. alternatus, a well-known vector of pine wilt disease. There is a special symbiotic relationship between M. alternatus and Bursaphelenchus xylophilus. As the native sympatric sibling species of B. xylophilus, B. mucronatus also has a specific relationship that is often overlooked. The analysis of mitochondrial gene expression aimed to explore the effect of B. mucronatus on the energy metabolism of the respiratory chain of M. alternatus adults. Using RT-qPCR, we determined and analyzed the expression of eight mitochondrial protein-coding genes (COI, COII, COIII, ND1, ND4, ND5, ATP6, and Cty b) between M. alternatus infected by B. mucronatus and M. alternatus without the nematode. Expression of all the eight mitochondrial genes were up-regulated, particularly the ND4 and ND5 gene, which were up-regulated by 4-5-fold (p < 0.01). Since longicorn beetles have immune responses to nematodes, we believe that their relationship should not be viewed as symbiotic, but classed as parasitic.

Six complete mitochondrial genomes of mayflies from three genera of Ephemerellidae (Insecta: Ephemeroptera) with inversion and translocation of trnI rearrangement and their phylogenetic relationships

As a small order of Pterygota (Insecta), Ephemeroptera has almost 3,500 species around the world. Ephemerellidae is a widely distributed common group of Ephemeroptera. However, the relationship among Ephemerellidae, Vietnamellidae and Teloganellidae is still in dispute. In this study, we sequenced six complete mitogenomes of three genera from Ephemerellidae (Insecta: Ephemeroptera): Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018, Serratella sp. Liaoning-2019, Torleya grandipennis and T. tumiforceps. These mitogenomes were employed to reveal controversial phylogenetic relationships among the Ephemeroptera, with emphasis on the phylogenetic relationships among Ephemerellidae. The lengths of the six mayfly mitogenomes ranged from 15,134 bp to 15,703 bp. Four mitogenomes of Ephemerella sp. Yunnan-2018, Serratella zapekinae, Serratella sp. Yunnan-2018 and Serratella sp. Liaoning-2019 had 22 tRNAs including an inversion and translocation of trnI. By contrast, the mitogenomes of T. tumiforceps and T. grandipennis had 24 tRNAs due to an extra two copies of inversion and translocation of trnI. Within the family Ephemerellidae, disparate gene rearrangement occurred in the mitogenomes of different genera: one copy of inversion and translocation trnI in the genera Ephemerella and Serratella, and three repeat copies of inversion and translocation of trnI in the genus Torleya. A large non-coding region (≥200 bp) between trnS1 (AGN) and trnE was detected in T. grandipennis and T. tumiforceps. Among the phylogenetic relationship of the Ephemeroptera, the monophyly of almost all families except Siphlonuridae was supported by BI and ML analyses. The phylogenetic results indicated that Ephemerellidae was the sister clade to Vietnamellidae whereas Teloganellidae was not a sister clade of Ephemerellidae and Vietnamellidae.

The complete mitochondrial genome of Xanthomantis bimaculata (Mantodea: Iridopterygidae) and its phylogeny

The mitochondrial genome sequence of Xanthomantis bimaculata (Mantodea: Iridopterygidae) from Yunnan, China is a circular molecule with the typical insect mitochondrial gene arrangement, which is 15,941 bp in length and contains 22 tRNAs, two rRNAs, 13 protein-coding genes, and one control region. The overall AT content of the mitogenome is 73.12% (A = 37.58%, T = 35.54%, C = 16.54%, G = 10.34%). In BI and ML phylogenetic analyses, X. bimaculata was a sister clade to Sceptuchus simplex. The monophyly of the families Iridopterygidae, Thespidae and Liturgusidae were supported.

Mantidis Oötheca (mantis egg case) original species identification via morphological analysis and DNA barcoding

ETHNOPHARMACOLOGICAL RELEVANCE

Mantidis Oötheca (mantis egg case; sangpiaoxiao) is a medicine from an insect source, which has been widely used in Asian countries. However, misidentification due to a lack of information given variations in the medicinal portion of the ootheca and morphological similarities of the ootheca as an egg chamber.

AIM OF THE STUDY

Thus, this study aims to provide the first comprehensive data for discriminating authentic of Mantidis Oötheca. Here, we provide detailed ootheca morphology and their molecular information to accurately identify Mantidis Oötheca.

MATERIALS AND METHODS

Oothecae of Tenodera angustipennis (Saussure, 1869), Tenodera sinensis (Saussure, 1871), Hierodula patellifera Serville, 1839, and Hierodula sp. were used in the comparative morphological, principal component analysis, and DNA barcoding.

RESULTS

The morphological analyses revealed that the emergence area, outline, angle of distal end, width of air-filled layer, and weight are useful diagnostic characters. Using these quantitative and qualitative characteristics, we developed the effective identification key. Furthermore, our CO1 sequences from all individuals were monophyletic with high bootstrap values at genus and species levels. Moreover, morphological identification using our developed key among all studied individuals agreed with molecular identification results using CO1 barcoding data.

CONCLUSIONS

These multilateral approaches, including morphological, statistical, and DNA barcoding methods are highly reliable identification tools. Moreover, our diagnostic key characteristics and molecular barcoding should aid in the accurate identification, authentication, and quality control of Mantidis Oötheca medicinal materials.

The complete mitochondrial genome of Annamanum lunulatum (Coleoptera: Lamiinae) and its phylogeny

The complete mitochondrial genome of the Annamanum lunulatum is 15,610 bp in length, which contains 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and the A + T-rich region. The arrangement of genes is identical to all know longhorn beetles mitochondrial genomes. The overall AT content of the mitochondrial genome is 75.3%, whereas the AT content of A + T-rich region is 84.3%. In ML and BI phylogenetic analyses, A. lunulatum is a sister clade to Blepephaeus succinctor, and the monophyly of Lamiinae is supported.

The complete mitochondrial genome of Mantis religiosa (Mantodea: Mantidae) from Canada and its phylogeny

The complete mitochondrial genome of Mantis religiosa (Mantodea: Mantidae) from Canada was successfully sequenced. The mitochondrial genome was a circular molecule of 15,521 bp in length, containing 13 protein-coding genes, two rRNA genes, 23 tRNA genes (including an extra tRNAArg gene), and the control region. The AT content of the whole genome was 76.9% and the length of the control region was 636 bp with 81.9% AT content. The structure of the M. religiosa mitochondrial genome from Canada was almost identical to M. religiosa from China and their genetic distance was just 0.017. In Bayesian inference (BI) and maximum likelihood (ML) analyses, we found that M. religiosa was a sister clade to Statilia sp. and the monophyly of the genera Hierodula and Rhombodera was not supported.

Characterization of the complete mitochondrial genome of the praying mantis Mekongomantis quinquespinosa (Mantodea, Mantidae)

The complete mitochondrial genome of the praying mantises Mekongomantis quinquespinosa was characterized in this study. The circular molecule is 15388 bp in length (GenBank accession no. MN267041), containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes. The nucleotide composition is asymmetric (39.0% A, 15.8% C, 9.8% G, 35.4% T), with an overall A + T content of 74.4%. The gene arrangement of M. quinquespinosa is identical to that observed in other Mantidae family praying mantises. Ten reading frame overlaps and seven intergenic regions are found in the mitogenome of M. quinquespinosa. The phylogenetic relationships based on 13 PCGs show that M. quinquespinosa clusters closest to the species of Mantidae.

The complete mitochondrial genomes of five longicorn beetles (Coleoptera: Cerambycidae) and phylogenetic relationships within Cerambycidae

Cerambycidae is one of the most diversified groups within Coleoptera and includes nearly 35,000 known species. The relationships at the subfamily level within Cerambycidae have not been convincingly demonstrated and the gene rearrangement of mitochondrial genomes in Cerambycidae remains unclear due to the low numbers of sequenced mitogenomes. In the present study, we determined five complete mitogenomes of Cerambycidae and investigated the phylogenetic relationship among the subfamilies of Cerambycidae based on mitogenomes. The mitogenomic arrangement of all five species was identical to the ancestral Cerambycidae type without gene rearrangement. Remarkably, however, two large intergenic spacers were detected in the mitogenome of Pterolophia sp. ZJY-2019. The origins of these intergenic spacers could be explained by the slipped-strand mispairing and duplication/random loss models. A conserved motif was found between trnS2 and nad1 gene, which was proposed to be a binding site of a transcription termination peptide. Also, tandem repeat units were identified in the A + T-rich region of all five mitogenomes. The monophyly of Lamiinae and Prioninae was strongly supported by both MrBayes and RAxML analyses based on nucleotide datasets, whereas the Cerambycinae and Lepturinae were recovered as non-monophyletic.

Characterization of the complete mitochondrial genome sequence of Asiadodis yunnanensis (Mantidae: Choeradodinae) and phylogenetic analysis

The complete mitochondrial genome of the praying mantises Asiadodis yunnanensis was characterized in this study. The circular molecule is 15,416 bp in length (GenBank accession no. MN037794), containing 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes. The nucleotide composition is asymmetric (39.5% A, 15.1% C, 9.6% G, 35.8% T), with an overall A + T content of 75.3%. The gene arrangement of A. yunnanensis is identical to that observed in other praying mantises. Seven PCGs are initiated with typical ATN start codons, Four genes (cox1, nad3, nad4L, and nad6) begin with TTN, nad1 begin with GTT, and nad5 use CTT, as initiation codon. Twelve PCGs stop with complete termination codon TAA and TAG, whereas nad5 uses incomplete termination codon (T––). Twenty reading frame overlaps and seven intergenic regions are found in the mitogenome of A. yunnanensis. The phylogenetic relationships based on 13 PCGs show that A. yunnanensis clusters closest to the species of Mantidae.

Data for praying mantis mitochondrial genomes and phylogenetic constructions within Mantodea

In this data article, we provide five datasets of mantis mitochondrial genomes: (1) PCG123: nucleotide sequences of 13 protein-coding genes including all codon positions; (2) PCG123R: nucleotide sequences of two rRNAs and 13 protein-coding genes including all codon positions; (3) PCG12: nucleotide sequences of 13 protein-coding genes without third codon positions; (4) PCG12R: nucleotide sequences of two rRNAs and 13 protein-coding genes without third codon positions, and (5) PCGAA: amino acid sequences of 13 protein-coding genes. These were used to construct phylogenetic relationships within Mantodea and the phylogenetic trees inferred from Bayesian analysis using two data sets (PCG12R, PCGAA) and Maximum Likelihood analysis using four data sets (PCG123, PCG12, PCG12R and PCGAA). We also provide initiation codon, termination codon, amino acid length and nucleotide diversity (Pi) of protein-coding genes among 27 mantises. The whole mitochondrial genomes of 27 praying mantises were submitted to GenBank with the accession numbers KY689112-KY689138.

Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae). The total length of the S. longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr (CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S. longialata mitogenome was as follows: A = 41.0%, T = 33.8%, C = 15.5%, G = 9.7%. Both Bayesian inference and ML analyses strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.

The mitochondrial genome of Caenis sp. (Ephemeroptera: Caenidae) and the phylogeny of Ephemeroptera in Pterygota

The phylogenetic relationship between Ephemeroptera (mayflies) and Odonata (dragonflies and damselflies) remains hotly debated in the insect evolution community. We sequenced the complete mitochondrial genome of Caenis sp. (Ephemeroptera: Caenidae) to discuss the phylogenetic relationship of Palaeoptera. The mitochondrial genome of Caenis sp. is a circular molecule of 15,254 bp in length containing 37 genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs), which showed the typical insect mitochondrial gene arrangement. In BI and ML phylogenetic trees using 71 species of 12 orders, our results support the Ephemeroptera as the basal group of winged insects.

Gene characteristics of the complete mitochondrial genomes of Paratoxodera polyacantha and Toxodera hauseri (Mantodea: Toxoderidae)

The family Toxoderidae (Mantodea) contains an ecologically diverse group of praying mantis species that have in common greatly elongated bodies. In this study, we sequenced and compared the complete mitochondrial genomes of two Toxoderidae species, Paratoxodera polyacantha and Toxodera hauseri, and compared their mitochondrial genome characteristics with another member of the Toxoderidae, Stenotoxodera porioni (KY689118). The lengths of the mitogenomes of T. hauseri and P. polyacantha were 15,616 bp and 15,999 bp, respectively, which is similar to that of S. porioni (15,846 bp). The size of each gene as well as the A+T-rich region and the A+T content of the whole genome were also very similar among the three species as were the protein-coding genes, the A+T content and the codon usages. The mitogenome of T. hauseri had the typical 22 tRNAs, whereas that of P. polyacantha had 26 tRNAs including an extra two copies of trnA-trnR. Intergenic regions of 67 bp and 76 bp were found in T. hauseri and P. polyacantha, respectively, between COX2 and trnK; these can be explained as residues of a tandem duplication/random loss of trnK and trnD. This non-coding region may be synapomorphic for Toxoderidae. In BI and ML analyses, the monophyly of Toxoderidae was supported and P. polyacantha was the sister clade to T. hauseri and S. porioni.