Multiple Lines of Evidence from Mitochondrial Genomes Resolve Phylogenetic Relationships of Parasitic Wasps in Braconidae

The first two complete mitochondrial genomes for the genus Anagyrus (Hymenoptera, Encyrtidae) and their phylogenetic implications

Anagyrus, a genus of Encyrtidae (Hymenoptera, Chalcidoidea), represents a successful group of parasitoid insects that attack various mealybug pests of agricultural and forestry plants. Until now, only 20 complete mitochondrial genomes have been sequenced, including those in this study. To enrich the diversity of mitochondrial genomes in Encyrtidae and to gain insights into their phylogenetic relationships, the mitochondrial genomes of two species of Anagyrus were sequenced, and the mitochondrial genomes of these species were compared and analyzed. Encyrtid mitochondrial genomes exhibit similarities in nucleotide composition, gene organization, and control region patterns. Comparative analysis of protein-coding genes revealed varying molecular evolutionary rates among different genes, with six genes (ATP8, ND2, ND4L, ND6, ND4 and ND5) showing higher rates than others. A phylogenetic analysis based on mitochondrial genome sequences supports the monophyly of Encyrtidae; however, the two subfamilies, Encyrtinae and Tetracneminae, are non-monophyletic. This study provides valuable insights into the phylogenetic relationships within the Encyrtidae and underscores the utility of mitochondrial genomes in the systematics of this family.

A Mysterious Asian Firefly Genus, Oculogryphus Jeng, Engel & Yang (Coleoptera, Lampyridae): The First Complete Mitochondrial Genome and Its Phylogenetic Implications

The firefly genus Oculogryphus Jeng, Engel & Yang, 2007 is a rare-species group endemic to Asia. Since its establishment, its position has been controversial but never rigorously tested. To address this perplexing issue, we are the first to present the complete mitochondrial sequence of Oculogryphus, using the material of O. chenghoiyanae Yiu & Jeng, 2018 determined through a comprehensive morphological identification. Our analyses demonstrate that its mitogenome exhibits similar characteristics to that of Stenocladius, including a rearranged gene order between trnC and trnW, and a long intergenic spacer (702 bp) between the two rearranged genes, within which six remnants (29 bp) of trnW were identified. Further, we incorporated this sequence into phylogenetic analyses of Lampyridae based on different molecular markers and datasets using ML and BI analyses. The results consistently place Oculogryphus within the same clade as Stenocladius in all topologies, and the gene rearrangement is a synapomorphy for this clade. It suggests that Oculogryphus should be classified together with Stenocladius in the subfamily Ototretinae at the moment. This study provides molecular evidence confirming the close relationship between Oculogryphus and Stenocladius and discovers a new phylogenetic marker helpful in clarifying the monophyly of Ototretinae, which also sheds a new light on firefly evolution.

Mitogenome architecture supports the non-monophyly of the cosmopolitan parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) recovered by nuclear and mitochondrial phylogenomics

Mitochondrial DNA gene organisation is an important source of phylogenetic information for various metazoan taxa at different evolutionary timescales, though this has not been broadly tested for all insect groups nor within a phylogenetic context. The cosmopolitan subfamily Doryctinae is a highly diverse group of braconid wasps mainly represented by ectoparasitoids of xylophagous beetle larvae. Previous molecular studies based on Sanger and genome-wide (ultraconserved elements, UCE; and mitochondrial genomes) sequence data have recovered a non-monophyletic Doryctinae, though the relationships involved have always been weakly supported. We characterised doryctine mitogenomes and conducted separate phylogenetic analyses based on mitogenome and UCE sequence data of ~100 representative doryctine genera to assess the monophyly and higher-level classification of the subfamily. We identified rearrangements of mitochondrial transfer RNAs (tRNAs) that support a non-monophyletic Doryctinae consisting of two separate non-related clades with strong geographic structure ('New World' and 'Old World' clades). This geographic structure was also consistently supported by the phylogenetic analyses preformed with mitogenome and UCE sequence data. These results highlight the utility of the mitogenome gene rearrangements as a potential source of phylogenetic information at different evolutionary timescales.

The complete mitochondrial genome of Aphidius colemani (Hymenoptera: Braconidae: Aphidiinae)

The genome-level features are crucial genetic resources for species identification and phylogenetic analysis. Here, the complete mitochondrial genome of Aphidius colemani Viereck 1912 (Hymenoptera: Braconidae: Aphidiinae) was sequenced, determined and analyzed. The circular genome is 16,372 bp in length with an overall base composition of 38.9% for A, 46.2% for T, 6.7% for C, and 8.2% for G. The mitochondrial genome of A. colemani contained 13 protein-coding genes that initiated by the ATN codon, 22 transfer RNA genes, two ribosomal RNA genes (rRNAs), and a control region (CR). It shared the same gene arrangement patterns that occurred in two tRNA clusters of trnI-trnQ-trnM and trnW-trnC-trnY with Aphidius gifuensis. Phylogenetic analyses using Bayesian inference and Maximum-likelihood methods supported that the two species of Aphidiinae formed a clade and sister to other subfamilies of Braconidae.

Characterization of the complete mitochondrial genome of the longhorn beetle, Batocerahorsfieldi (Coleoptera, Cerambycidae) and its phylogenetic analysis with suitable longhorn beetles

Mitochondrial genome analysis is an important tool for studying insect phylogenetics. The longhorn beetle, Batocerahorsfieldi, is a significant pest in timber, economic and protection forests. This study determined the mitochondrial genome of B.horsfieldi and compared it with the mitochondrial genomes of other Cerambycidae with the aim of exploring the phylogenetic status of the pest and the evolutionary relationships among some Cerambycidae subgroups. The complete mitochondrial genome of B.horsfieldi was sequenced by the Illumina HiSeq platform. The mitochondrial genome was aligned and compared with the existing mitochondrial genomes of Batoceralineolata and B.rubus in GenBank (MF521888, MW629558, OM161963, respectively). The secondary structure of transfer RNA (tRNA) was predicted using tRNAScan-SE server v.1.21 and MITOS WebSever. Thirteen protein-coding genes (PCGs) and two ribosomal RNA gene sequences of 21 longhorn beetles, including B.horsfieldi, plus two outgroups, Dryopsernesti (Dryopidae) and Heterocerusparallelus (Heteroceridae), were analyzed. The phylogenetic tree was constructed using maximum likelihood and Bayesian inference methods. In this study, we successfully obtained the complete mitochondrial genome of B.horsfieldi for the first time, which is 15 425 bp in length. It contains 37 genes and an A + T-rich region, arranged in the same order as the recognized ancestor of longhorn beetles. The genome of B.horsfieldi is composed of 33.12% A bases, 41.64% T bases, 12.08% C bases, and 13.16% G bases. The structure, nucleotide composition, and codon usage of the new mitochondrial genome are not significantly different from other longhorn mitochondrial genomes. Phylogenetic analyses revealed that Cerambycidae formed a highly supported single clade, and Vesperidae was either clustered with Cerambycidae or formed a separate clade. Interestingly, B.horsfieldi, B.rubus and B.lineolata were clustered with Monochamus and Anoplophora species in both analyses, with high node support. Additionally, the VesperidaeSpiniphilusspinicornis and Vesperussanzi and the 19 Cerambycidae species formed a sister clade in the Bayesian analysis. Our results have produced new complete mitogenomic data, which will provide information for future phylogenetic and taxonomic research, and provide a foundation for future relevant research.

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genome of Aythya marila

Aythya marila is a large diving duck belonging to the family Anatidae. However, the phylogenetic relationship among these Aythya species remains unclear due to the presence of extensive interspecific hybridization events within the Aythya genus. Here, we sequenced and annotated the complete mitochondrial genome of A. marila, which contained 22 tRNAs, 13 protein-coding genes (PCGs), 2 ribosomal RNAs, and 1 D-loop, with a length of 16,617 bp. The sizes of the PCGs ranged from 297 to 1824 bp and were all, except for ND6, located on the heavy chain (H). ATG and TAA were the most common start and termination codons of the 13 PCGs, respectively. The fastest- and slowest-evolving genes were ATP8 and COI, respectively. Codon usage analysis indicated that CUA, AUC, GCC, UUC, CUC, and ACC were the six most frequent codons. The nucleotide diversity values indicated a high level of genetic diversity in A. marila. F_ST analysis suggested a widespread gene exchange between A. baeri and A. nyroca. Moreover, phylogenetic reconstructions using the mitochondrial genomes of all available Anatidae species showed that, in addition to A. marila, four major clades among the Anatidae (Dendrocygninae, Oxyurinae, Anserinae, and Anatinae) were closely related to A. fuligula. Overall, this study provides valuable information on the evolution of A. marila and new insights into the phylogeny of Anatidae.

The mitochondrial genome of Binodoxys acalephae (Hymenoptera: Braconidae) with unique gene rearrangement and phylogenetic implications

BACKGROUND

Species in the subfamily Aphidiinae from the Braconidae of Hymenoptera are endoparasitic wasps that exclusively utilize aphids as hosts. Some Aphidiinae species are widely used as biological agents. However, there were only one species with determined complete mitochondrial genome from this subfamily.

METHODS AND RESULTS

In this study, we sequenced and annotated the mitochondrial genome (mitogenome) of Binodoxys acalephae, which was 15,116 bp in size and contained 37 genes. The start codon of 13 protein-coding genes was ATN, and the complete stop codon TAA and TAG was widely assigned to 11 protein-coding genes. The lrRNA contains 43 stem-loop structures, and srRNA contains 25 stem-loop structures. Translocation and inversion of tRNA genes was found to be dominant in B. acalephae. In contrast to Aphidius gifuensis from the same subfamily Aphidiinae, inverted tRNALeu1 was translocated to the gene cluster between tRNALeu2 and COX2, and the control region between tRNAIle and tRNAMet was deleted in the mitogenome of B. acalephae. Within Braconidae, gene clusters tRNATrp-tRNACys-tRNATyr and CR-tRNAIle-tRNAGln-tRNAMet were hotspots for gene rearrangement. Phylogenetic analysis showed that both Bayesian and maximum-likelihood methods recovered the monophyly of Aphidiinae and suggested that Aphidiinae formed sister clades with the remaining subfamilies. The phylogenetic analyses of nine subfamilies supported the monophyly of Cyclostomes and Noncyclostomes in Braconidae.

CONCLUSION

The arrangement of mitochondrial genes and the phylogenetic relationships among nine Braconidae subfamilies were constructed better to understand the diversity and evolution of Aphidiinae mitogenomes.

Comparative mitogenomes reveal diverse and novel gene rearrangements in the genus Meteorus (Hymenoptera: Braconidae)

Meteorus Haliday, 1835 is a cosmopolitan genus within Braconidae (Hymenoptera). They are koinobiont endoparasitoids of Coleoptera or Lepidoptera larvae. Only one mitogenome of this genus was available. Here, we sequenced and annotated three mitogenomes of Meteorus species, and found that the tRNA gene rearrangements in these mitogenomes were rich and diverse. Compared with the ancestral organization, only seven tRNAs (trnW, trnY, trnL2, trnH, trnT, trnP and trnV) were conserved and trnG had its own unique location in the four mitogenomes. This dramatic tRNA rearrangement was not observed in mitogenomes of other insect groups before. In addition, the tRNA cluster (trnA-trnR-trnN-trnS1-trnE-trnF) between nad3 and nad5 was rearranged into two patterns, i.e., trnE-trnA-trnR-trnN-trnS1 and trnA-trnR-trnS1-trnE-trnF-trnN. The phylogenetic results showed that the Meteorus species formed a clade within the subfamily Euphorinae, and were close to Zele (Hymenoptera, Braconidae, Euphorinae). In the Meteorus, two clades were reconstructed: M. sp. USNM and Meteorus pulchricornis forming one clade while the remaining two species forming another clade. This phylogenetic relationship also matched the tRNA rearrangement patterns. The diverse and phylogenetic signal of tRNA rearrangements within one genus provided insights into tRNA rearrangements of the mitochondrial genome at genus/species levels in insects.

Heat tolerance variation reveals vulnerability of tropical herbivore-parasitoid interactions to climate change

Assessing the heat tolerance (CTmax) of organisms is central to understand the impact of climate change on biodiversity. While both environment and evolutionary history affect CTmax, it remains unclear how these factors and their interplay influence ecological interactions, communities and ecosystems under climate change. We collected and reared caterpillars and parasitoids from canopy and ground layers in different seasons in a tropical rainforest. We tested the CTmax and Thermal Safety Margins (TSM) of these food webs with implications for how species interactions could shift under climate change. We identified strong influence of phylogeny in herbivore-parasitoid community heat tolerance. The TSM of all insects were narrower in the canopy and parasitoids had lower heat tolerance compared to their hosts. Our CTmax-based simulation showed higher herbivore-parasitoid food web instability under climate change than previously assumed, highlighting the vulnerability of parasitoids and related herbivore control in tropical rainforests, particularly in the forest canopy.

The Mitochondrial Genomes of Two Parasitoid Wasps Protapanteles immunis and Parapanteles hyposidrae (Hymenoptera: Braconidae) with Phylogenetic Implications and Novel Gene Rearrangements

Parapanteles hypsidrae (Wilkinson, 1928) and Protapanteles immunis (Haliday, 1834) are the most important parasitic wasps of Ectropis grisescens Warren and Ectropis obliqua (Prout). We sequenced and annotated the mitochondrial genomes of Pa. hyposidrae and Pr. immunis, which are 17,063 bp and 16,397 bp in length, respectively, and possess 37 mitochondrial genes. We discovered two novel types of gene rearrangement, the local inversion of nad4L in Pa. hyposidrae and the remote inversion of the block cox3-nad3-nad5-nad4 in Pr. immunis, within the mitogenomes of Braconidae. The phylogenetic analysis supported the subfamily Microgastrinae is a monophyletic group, but the tribes Apantelini and Cotesiini within this subfamily are paraphyletic groups.

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.

Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica

Asobara japonica is an endoparasitic wasp that parasitizes Drosophila flies. It synthesizes various toxic components in the venom gland and injects them into host larvae during oviposition. To identify and characterize these toxic components for enabling parasitism, we performed the whole-genome sequencing (WGS) and devised a protocol for RNA interference (RNAi) with A. japonica. Because it has a parthenogenetic lineage due to Wolbachia infection, we generated a clonal strain from a single wasp to obtain highly homogenous genomic DNA. The WGS analysis revealed that the estimated genome size was 322 Mb with a heterozygosity of 0.132%. We also performed RNA-seq analyses for gene annotation. Based on the qualified WGS platform, we cloned ebony-Aj, which encodes the enzyme N-β-alanyl dopamine synthetase, which is involved in melanin production. The microinjection of double-stranded RNA (dsRNA) targeting ebony-Aj led to body colour changes in adult wasps, phenocopying ebony-Dm mutants. Furthermore, we identified putative venom genes as a target of RNAi, confirming that dsRNA injection-based RNAi specifically suppressed the expression of the target gene in wasp adults. Taken together, our results provide a powerful genetic toolkit for studying the molecular mechanisms of parasitism.

Novel Gene Rearrangements in the Mitochondrial Genomes of Cynipoid Wasps (Hymenoptera: Cynipoidea)

Cynipoidea is a medium-sized superfamily of Hymenoptera with diverse lifestyles. In this study, 16 mitochondrial genomes were newly sequenced, 11 of which were the first obtained mitochondrial genomes in the family Liopteridae and four subfamilies (Anacharitinae, Aspicerinae, Figitinae, and Parnipinae) of Figitidae. All of the newly sequenced mitogenomes have unique rearrangement types within Cynipoidea, whereas some gene patterns are conserved in several groups. nad5-nad4-nad4L-nad6-cytb was remotely inverted and two rRNA genes were translocated to nad3 downstream in Ibaliidae and three subfamilies (Anacharitinae, Eucoilinae, and Parnipinae within Figitidae); two rRNA genes in Aspicerinae, Figitinae, and Liopteridae were remotely inverted to the cytb-nad1 junction; rrnL-rrnS was translocated to the cytb-nad1 junction in Cynipidae. Phylogenetic inference suggested that Figitidae was a polyphyletic group, while the Ibaliidae nested deep within Cynipoidea and was a sister-group to the Figitidae. These results will improve our understanding of the gene rearrangement of the mitogenomes and the phylogenetic relationships in the Cynipoidea.

Comparative Mitogenomics of True Frogs (Ranidae, Anura), and Its Implications for the Phylogeny and Evolutionary History of Rana

Simple Summary

The true frogs of the genus Rana are a complex and diverse group. Many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana were not well understood. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.

Abstract

The true frogs of the genus Rana are a complex and diverse group, containing approximately 60 species with wide distribution across Eurasia and the Americas. Recently, many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana was not well understood and might be limited by the absence of mitogenome information. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis, containing 22 tRNAs, 13 protein-coding genes, two ribosomal RNAs, and a non-coding region, with 17,502 bp and 18,006 bp in length, respectively. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. The mitochondrial gene arrangement was not related to species diversification, and several independent shifts happened in evolutionary history. Climate fluctuation and environmental change may have played an essential role in species diversification in Rana. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.

Five new mitogenomes sequences of Calidridine sandpipers (Aves: Charadriiformes) and comparative mitogenomics of genus Calidris

Background

The genus Calidris (Charadriiformes, Scolopacidae) includes shorebirds known as dunlin, knots, and sanderlings. The relationships between species nested within Calidris, including Eurynorynchus, Limicola and Aphriza, are not well-resolved.

Methods

Samples were collected from Xiaoyangkou, Rudong County, Jiangsu Province, China. Mitogenomes were sequenced using the Illumina Novaseq 6000 platform for PE 2 × 150 bp sequencing, and then checked for PCR products. Protein-coding genes were determined using an Open Reading Frame Finder. tRNAscan-SE, MITOS, and ARWEN were used to confirm tRNA and rRNA annotations. Bioinformatic analyses were conducted using DnaSP 5.1 and MEGA X. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses.

Results

We sequenced and annotated the mitogenome of five species and obtained four complete mitogenomes and one nearly complete mitogenome. Circular mitogenomes displayed moderate size variation, with a mean length of 16,747 bp, ranging from 16,642 to 16,791 bp. The mitogenome encoded a control region and a typical set of 37 genes containing two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. There were four start codons, four stop codons, and one incomplete stop codon (T-). The nucleotide composition was consistently AT-biased. The average uncorrected pairwise distances revealed heterogeneity in the evolutionary rate for each gene; the COIII had a slow evolutionary rate, whereas the ATP8 gene had a fast rate. dN/dS analysis indicated that the protein-coding genes were under purifying selection. The genetic distances between species showed that the greatest genetic distance was between Eurynorhynchus pygmeus and Limicola falcinellus (22.5%), and the shortest was between E. pygmeus and Calidris ruficollis (12.8%). Phylogenetic trees revealed that Calidris is not a monophyletic genus, as species from the genera Eurynorynchus and Limicola were nested within Calidris. The molecular data obtained in this study are valuable for research on the taxonomy, population genetics, and evolution of birds in the genus Calidris.

Mitochondrial phylogenomics and mitogenome organization in the parasitoid wasp family Braconidae (Hymenoptera: Ichneumonoidea)

BACKGROUND

Mitochondrial (mt) nucleotide sequence data has been by far the most common tool employed to investigate evolutionary relationships. While often considered to be more useful for shallow evolutionary scales, mt genomes have been increasingly shown also to contain valuable phylogenetic information about deep relationships. Further, mt genome organization provides another important source of phylogenetic information and gene reorganizations which are known to be relatively frequent within the insect order Hymenoptera. Here we used a dense taxon sampling comprising 148 mt genomes (132 newly generated) collectively representing members of most of the currently recognised subfamilies of the parasitoid wasp family Braconidae, which is one of the largest radiations of hymenopterans. We employed this data to investigate the evolutionary relationships within the family and to assess the phylogenetic informativeness of previously known and newly discovered mt gene rearrangements.

RESULTS

Most subfamilial relationships and their composition obtained were similar to those recovered in a previous phylogenomic study, such as the restoration of Trachypetinae and the recognition of Apozyginae and Proteropinae as valid braconid subfamilies. We confirmed and detected phylogenetic signal in previously known as well as novel mt gene rearrangements, including mt rearrangements within the cyclostome subfamilies Doryctinae and Rogadinae.

CONCLUSIONS

Our results showed that both the mt genome DNA sequence data and gene organization contain valuable phylogenetic signal to elucidate the evolution within Braconidae at different taxonomic levels. This study serves as a basis for further investigation of mt gene rearrangements at different taxonomic scales within the family.

Highly diversified mitochondrial genomes provide new evidence for interordinal relationships in the Arachnida

Arachnida is an exceptionally diverse class in the Arthropoda, consisting of 20 orders and playing crucial roles in the terrestrial ecosystems. However, their interordinal relationships have been debated for over a century. Rearranged or highly rearranged mitochondrial genomes (mitogenomes) were consistently found in this class, but their various extent in different lineages and efficiency for resolving arachnid phylogenies are unclear. Here, we reconstructed phylogenetic trees using mitogenome sequences of 290 arachnid species to decipher interordinal relationships as well as diversification through time. Our results recovered monophyly of ten orders (i.e. Amblypygi, Araneae, Ixodida, Mesostigmata, Opiliones, Pseudoscorpiones, Ricinulei, Sarcoptiformes, Scorpiones and Solifugae), while rejecting monophyly of the Trombidiformes due to the unstable position of the Eriophyoidea. The monophyly of Acari (subclass) was rejected, possibly due to the long-branch attraction of the Pseudoscorpiones. The monophyly of Arachnida was further rejected because the Xiphosura nested within arachnid orders with unstable positions. Mitogenomes that are highly rearranged in mites but less rearranged or conserved in the remaining lineages point to their exceptional diversification in mite orders; however, shared derived mitochondrial (mt) gene clusters were found within superfamilies rather than interorders, confusing phylogenetic signals in arachnid interordinal relationships. Molecular dating results show that arachnid orders have ancient origins, ranging from the Ordovician to the Carboniferous, yet have significantly diversified since the Cretaceous in orders Araneae, Mesostigmata, Sarcoptiformes, and Trombidiformes. By summarizing previously resolved key positions of some orders, we propose a plausible arachnid tree of life. Our results underline a more precise framework for interordinal phylogeny in the Arachnida and provide new insights into their ancient evolution.

Comparative Mitochondrial Genomics of 104 Darwin Wasps (Hymenoptera: Ichneumonidae) and Its Implication for Phylogeny

Simple Summary

Nearly a hundred mitochondrial genomes of ichneumonid wasps are newly reported. Comparative mitogenomics of 104 mitochondrial genomes representing 33 subfamilies of Ichneumonidae, as well as its implications for phylogeny, were studied. We found that the mitochondrial genomes of ichneumonid wasps were highly conserved in their base composition and had low evolutionary rates, but were diverse in gene order. There are 38 types of gene rearrangement events in 104 ichneumonid mitochondrial genomes, of which 30 novel rearrangement types (R3-6, R8-R10, R12-R15, R17-R18, R20-R35 and R38) and a hot spot rearrangement around R1, with a shuffled tRNA cluster trnW-trnY-trnC and trnI-trnQ-trnM, were detected. The relationships among these subfamilies are firstly discussed based on mitochondrial genomes at a large scale. We suggest five subfamily groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively.

Abstract

Ichneumonidae is one of the largest families of insects with a mega-diversity of specialized morphological and biological characteristics. We newly sequenced 92 mitochondrial genomes of ichneumonid wasps and found that they have a conserved base composition and a lower evolutionary rate than that of other families of parasitic Hymenoptera. There are 38 types of gene order in the ichneumonid mitochondrial genome, with 30 novel types identified in 104 ichneumonids. We also found that the rearrangement events occur more frequently in Ophioniformes than in Ichneumoniformes and Pimpliformes. Furthermore, the higher Ophioniformes and their relative lineages shared the transposition of trnL2 to trnI-trnQ-trnM tRNA cluster. We confirmed five higher-level groupings of Ichneumonidae: Brachycyrtiformes, Ichneumoniformes, Ophioniformes, Pimpliformes and Xoridiformes. Two formerly unplaced subfamilies, Eucerotinae and Microleptinae, were placed in Brachycyrtiformes and Ichneumoniformes, respectively. The results will improve our understanding of the diversity and evolution of Ichneumonidae.

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.

Discriminating lineages of Batrachochytrium dendrobatidis using quantitative PCR

The ability to detect and monitor infectious disease in a phylogenetically informative manner is critical for their management. Phylogenetically informative diagnostic tests enable patterns of pathogen introduction or changes in the distribution of genotypes to be measured, enabling research into the ecology of the pathogen. Batrachochytrium dendrobatidis (Bd), a causative agent of chytridiomycosis in amphibian populations, emerged worldwide in the 21st century and is composed of six lineages which are display varying levels of virulence in their hosts. Research into the distribution, ecology and pathogenicity of these lineages has been hampered by an inability to type lineage efficiently. Here, we describe a lineage‐specific TaqMan qPCR assay that differentiates the two lineages of Bd most commonly associated with chytridiomycosis: BdGPL and BdCAPE. We demonstrate how this assay can be used for the surveillance of wild populations of amphibians in Southern Africa using skin swabs, tissue samples and cultured isolates.

see also the Perspective by Claudio Azat

Mitochondrial genomes of eight Scelimeninae species (Orthoptera) and their phylogenetic implications within Tetrigoidea

Scelimeninae is a key member of the pygmy grasshopper community, and an important ecological indicator. No mitochondrial genomes of Scelimeninae have been reported to date, and the monophyly of Scelimeninae and its phylogenetic relationship within Tetrigidae is still unclear. We sequenced and analyzed eight nearly complete mitochondrial genomes representing eight genera of Scelimeninae. These mitogenomes ranged in size from 13,112 to 16,380 bp and the order of tRNA genes between COII and ATP8 was reversed compared with the ancestral order of insects. The protein-coding genes (PCGs) of tetrigid species mainly with the typical ATN codons and most terminated with complete (TAA or TAG) stop codons. Analyses of pairwise genetic distances showed that ATP8 was the least conserved gene within Tetrigidae, while COI was the most conserved. The longest intergenic spacer (IGS) region in the mitogenomes was always found between tRNASer(UCN) and ND1. Additionally, tandem repeat units were identified in the longest IGS of three mitogenomes. Maximum likelihood (ML) and Bayesian Inference (BI) analyses based on the two datasets supported the monophyly of Tetriginae. Scelimeninae was classified as a non-monophyletic subfamily.

The complete mitochondrial genome of Leptopilina syphax (Hymenoptera: Figitidae)

Leptopilina syphax (Hymenoptera: Figitidae) is a newly recorded species of parasitic wasp, and it attacks the larval stage of Drosophilidae, mainly the Drosophila species. Few works have been done in the basic study of L. syphax, including the data of mitochondrial genome. In this study, the complete mitochondrial genome of L. syphax (GeneBank accession number: MT649407) was sequenced using Illumina HiSeq X Ten system. The mitochondrial genome is 15,882bp long and comprises 13 protein-coding genes, 2 ribosomal RNA genes and 22 transfer RNA genes. Meanwhile, 26 genes are in majority strand, and the remaining 11 genes are in minority strand. The overall base composition is 41.7% for A, 6.0% for G, 13.6% for C, and 38.7% for T, with an A + T content of 80.4%, respectively. We also performed a phylogenetic analysis with other known mitochondrial genomes of some parasitic wasps. The results show that L. syphax is closely related to L. boulardi, which is another Drosophila parasitoid.

New Mitochondrial Gene Rearrangement in Psyttalia concolor, P. humilis and P. lounsburyi (Hymenoptera: Braconidae), Three Parasitoid Species of Economic Interest

The family Braconidae consists mostly of specialized parasitoids, some of which hold potential in biocontrol of agricultural pests. Psyttalia concolor, Psyttalia humilis and Psyttalia lounsburyi are parasitoids associated with Bactrocera oleae, a major pest of cultivated olives. The native range of Psyttalia concolor is the Mediterranean, and P. humilis and P. lounsburyi are native to sub-Saharan Africa. This study reports the mitochondrial genomes of the three species, thus laying the foundation for mitogenomic analyses in the genus Psyttalia. Comparative mitogenomics within Braconidae showed a novel gene arrangement in Psyttalia in involving translocation and inversion of transfer RNA genes. The placement of Psyttalia in the subfamily Opiinae was well-supported, and the divergence between Psyttalia and its closest relative (Diachasmimorpha longicaudata) was at ~55 MYA [95% highest posterior density (HPD): 34-83 MYA]. Psyttalia lounsburyi occupied the most basal position among the three Psyttalia, having diverged from the other two species ~11 MYA (95% HPD: 6-17 MYA). Psyttalia concolor and P. humilis were recovered as sister species diverged at ~2 MYA (95% HPD: 1.1-3.6 MYA). This phylogeny combining new sequences and a set of 31 other cyclostomes and non-cyclostomes highlights the importance of a comprehensive taxonomic coverage of Braconidae mitogenomes to overcome the lack of robustness in the placement of several subfamilies.

Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization

Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp's genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.

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.

The mitochondrial genome of an ectoparasitoid wasp, Habrobracon hebetor (Hymenoptera: Braconidae: Braconinae)

In this study, we sequenced the mitogenome of Habrobracon hebetor, and obtained almost complete mitogenome of it. The mitogenome contains 14,629 bp which consists of 13 protein-coding genes (PCGs), 20 transfer RNA genes (trnI and trnM are absent), and 2 ribosomal RNA genes (GenBank accession no. MT558946). Gene rearrangement events occurred in this species, five tRNA genes with changes in positions or/and directions are found. All of 13 PCGs started with ATN. Eight PCGs used the typical stop codon ‘TAA’, five PCGs terminated with incomplete stop codons (T). Phylogenetic analyses within the Cyclostomes were performed based on mitochondrial PCGs.

The complete mitochondrial genome of Trichopria drosophilae (Hymenoptera: Diapriidae)

Trichopria drosophilae (Hymenoptera: Diapriidae) is an important pupal endoparasitoid of Drosophila species, which has been found to be an ideal biocontrol agent to D. suzukii. In this study, the complete mitochondrial genome of T. drosophilae (GeneBank accession number: MN966974) was sequenced using Illumina HiSeq X Ten system. The mitochondrial genome is 16,375 bp long and comprises 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. Among them, 24 genes are in majority strand, while the others are in minority strand. The nucleotide composition of A, G, C, T is 44.9%, 6.4%, 5.6%, 43.2% respectively. We also performed a phylogenetic analysis with other known mitochondrial genomes within four families that have been shown to parasitize drosophilid species. The result shows that T. drosophilae is closely related to Ismarus sp.

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.

Five mitochondrial genomes of black fungus gnats (Sciaridae) and their phylogenetic implications

Sciaridae is a family of great species diversity, distributed worldwide, that includes important agricultural pests of cultivated mushrooms and plants produced in greenhouses. Here we sequenced five nearly complete mitochondrial genomes representing three subfamilies of Sciaridae. The lengths of these mitogenomes range from 13,849 bp to 16,923 bp with 13 protein-coding genes (PCGs), 20-22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (CR). Compared with other dipteran species, rearrangements in Sciaridae are more common. Inversion or transition is observed frequently of trnL2, and in the tRNA clusters trnI-trnQ-trnM, trnW-trnC-trnY, and trnA-trnR-trnN-trnS1-trnE-trnF. Phylogenetic relationships within the family were reconstructed based on these newly sequenced species, combined with the published mitogenomes of related families, and recovered the topology within Sciaroidea as Cecidomyiidae + (Sciaridae + Keroplatidae). Relationships recovered within Sciaridae were Sciarinae + ('Pseudolycoriella group' + Megalosphyinae).

Complete mitochondrial genome of a parasitic wasp Microplitis pallidipes (Hymenoptera: Braconidae: Microgastrinae)

The complete mitochondrial genome of Microplitis pallidipes contains 15931 bp, with an A + T content of 86.5% and consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region (GenBank accession no. MN892396). All of the 22 tRNA genes displayed an usual clover-leaf structure. Gene rearrangement events occurred in this species, there are eight tRNA genes changed their positions or/and directions. 13 PCGs started with ATN. Ten PCGs used the typical stop codon ‘TAA’ and ‘TAG’, three PCGs terminated with incomplete stop codons (TA). Phylogenetic analyses within the microgastroid complex were performed based on mitochondrial protein-coding genes.

The complete mitochondrial genome of stag beetle Lucanus cervus (Coleoptera: Lucanidae) and phylogenetic analysis

Background

The stag beetle Lucanus cervus (Coleoptera: Lucanidae) is widely distributed in Europe. Habitat loss and fragmentation has led to significant reductions in numbers of this species. In this study, we sequenced the complete mitochondrial genome of L. cervus and reconstructed phylogenetic relationships among Lucanidae using complete mitochondrial genome sequences.

Methods

Raw data sequences were generated by the next generation sequencing using Illumina platform from genomic DNA of L. cervus. The mitochondrial genome was assembled by IDBA and annotated by MITOS. The aligned sequences of mitochondrial genes were partitioned using PartitionFinder 2. Phylogenetic relationships among 19 stag beetle species were constructed using Maximum Likelihood (ML) method implemented in IQ-TREE web server and Bayesian method implemented in PhyloBayes MPI 1.5a. Three scarab beetles were used as outgroups.

Results

The complete mitochondrial genome of L. cervus is 20,109 bp in length, comprising 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNAs and a control region. The A + T content is 69.93% for the majority strand. All protein-coding genes start with the typical ATN initiation codons except for cox1, which uses AAT. Phylogenetic analyses based on ML and Bayesian methods shown consistent topologies among Lucanidae.

The complete mt genomes of Lutzia halifaxia, Lt. fuscanus and Culex pallidothorax (Diptera: Culicidae) and comparative analysis of 16 Culex and Lutzia mt genome sequences

BACKGROUND

Despite the medical importance of the genus Culex, the mitochondrial genome (mt genome) characteristics of Culex spp. are not well understood. The phylogeny of the genus and particularly the generic status of the genus Lutzia and the subgenus Culiciomyia remain unclear.

METHODS

The present study sequenced and analyzed the complete mt genomes of Lutzia halifaxia, Lutzia fuscanus and Cx. (Culiciomyia) pallidothorax and assessed the general characteristics and phylogenetics of all known 16 mt genome sequences for species in the genera Culex and Lutzia.

RESULTS

The complete mt genomes of Lt. halifaxia, Lt. fuscanus and Cx. pallidothorax are 15,744, 15,803 and 15,578 bp long, respectively, including 13 PCGs, 22 tRNAs, two tRNAs and a control region (CR). Length variations in the Culex and Lutzia mt genomes involved mainly the CR, and gene arrangements are the same as in other mosquitoes. We identified four types of repeat units in the CR sequences, and the poly-T stretch exists in all of these mt genomes. The repeat units of CR are conserved to different extent and provide information on their evolution. Phylogenetic analyses demonstrated that the Coronator and Sitiens groups are each monophyletic, whereas the monophyletic status of the Pipiens Group was not supported; Cx. pallidothorax is more closely related to the Sitiens and Pipiens groups; and both phylogenetics analysis and repeat unit features in CR show that Lutzia is a characteristic monophyletic entity, which should be an independent genus.

CONCLUSIONS

To our knowledge, this is the first comprehensive review of the mt genome sequences and taxonomic discussion based on the mt genomes of Culex spp. and Lutzia spp. The research provides general information on the mt genome of these two genera, and the phylogenetic and taxonomic status of Lutzia and Culiciomyia.

Mitochondrial genome reorganization provides insights into the relationship between oribatid mites and astigmatid mites (Acari: Sarcoptiformes: Oribatida)

Oribatida s.l. represents one of the most species-rich mite lineages, including two recognized groups: oribatid mites (Oribatida s.s., non-astigmatan oribatids) and astigmatid mites (Astigmata). However, the relationship between these two groups has been debated. Here, we sequenced the complete mitochondrial (mt) genome of one oribatid mite and one astigmatid mite, retrieved complete mt genomes of three oribatid mites, and compared them with two other oribatid mites and 12 astigmatid mites sequenced previously. We find that gene orders in the mt genomes of both oribatid mites and astigmatid mites are rearranged relative to the hypothetical ancestral arrangement of the arthropods. Based on the shared derived gene clusters in each mt genome group, rearranged mt genomes are roughly divided into two groups corresponding to each mite group (oribatid mites or astigmatid mites). Phylogenetic results show that Astigmata nested in Oribatida. The monophyly of Astigmata is recovered, while paraphyly of Oribatida s.s. is observed. Our results show that rearranged gene orders in the mt genomes characterize various lineages of oribatid mites and astigmatid mites, and have potential phylogenetic information for resolving the high-level (cohort or supercohort) phylogeny of Oribatida.

The first mitochondrial genome of the family Epicopeiidae and higher-level phylogeny of Macroheterocera (Lepidoptera: Ditrysia)

The Macroheterocera clade contains most of the Lepidoptera species. However, extensive comparative and phylogenetic analyses of this group using complete mitochondrial genomes (mitogenome) are limited particularly in the context of increasing macroheteroceran mitogenomes reported to date. In this study, complete mitogenome of the Epicopeia hainesii is determined as the first Epicopeiidae species with mitogenome available. The whole mitogenome is circular with 15,395 bp long, and is highly biased toward A + T nucleotides (80.6%) in nucleotide composition. Comparative analyses show that gene content and arrangement of macroheteroceran mitogenomes are generally conservative and are typical of Lepidoptera but exceptions exist. In newly sequenced mitogenome, the motif "ATACTAA" is putatively located at the end of gene nad1, rather than in intergenic sequences between trnS2 and nad1 genes routinely observed in Lepidoptera. Interestingly, multiple phylogenetic analyses recover the six macroheteroceran superfamilies as Mimallonoidea + (Drepanoidea + ((Bombycoidea + Lasiocampoidea) + (Noctuoidea + Geometroidea))), providing supports for a large-scale transcriptomic study rather than various mitogenome- and multiple-gene-based investigations. In addition, our analyses consistently place the Epicopeiidae as sister group with Geometroidea, firstly demonstrating that this family is closer with Geometroidea than Drepanoidea based on mitogenome data.

The first two mitochondrial genomes of wood wasps (Hymenoptera: Symphyta): Novel gene rearrangements and higher-level phylogeny of the basal hymenopterans

The Symphyta has long been recognized as a paraphyletic grade forming the base of the remaining Hymenopteran, and the superfamily relationships within Symphyta remain controversial. Here, the first two representative mitochondrial genomes from the superfamily Siricoidea and Xiphydrioidea (Hymenoptera: Symphyta) are obtained using next-generation sequencing. The complete mitochondrial genome of Xiphydria sp. is 16,482 bp long with an A + T content of 84.18% while the incomplete one of Tremex columba is 16,847 bp long and A + T content is 81.69%. All 37 typical mitochondrial genes are possessed in both species. The secondary structure of tRNAs and rRNAs for both species are successfully predicted. Compared with the ancestral organization, seven and five tRNA genes are rearranged in mitochondrial genomes of Tremex and Xiphydria, respectively, which are the most rearrangement events within Symphyta. The rearrangement patterns in Tremex and Xiphydria present in this study are all novel to the Symphyta. Phylogenetic relationships among the major lineages of Symphyta are reconstructed using mitochondrial genomes. Both maximum likelihood and Bayesian inference analyses highly support Symphyta is a paraphyletic grade, Xyeloidea + (Tenthredinoidea + (Pamphilioidea + (Xiphydrioidea + (Cephoidea + (Orussoidea + Apocrita))))).

Systematics, Phylogeny, and Evolution of Braconid Wasps: 30 Years of Progress

The parasitoid wasp family Braconidae is likely the second-most species-rich family in the animal kingdom. Braconid wasps are widely distributed and often encountered. They constitute one of the principal groups of natural enemies of phytophagous insects, of which many are serious pest species. The enormous biological diversification of braconid wasps has led to many homoplasies, which contributed widely to instabilities in historical classifications. Recent studies using combinations of genetic markers or total mitochondrial genomes allow for better founded groupings and will ultimately lead to a stable classification. We present the current status of the phylogenetics of the Braconidae in a historical perspective and our understanding of the effects on higher classification.

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.

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.

The first mitochondrial genomes for Pyralinae (Pyralidae) and Glaphyriinae (Crambidae), with phylogenetic implications of Pyraloidea

In the present study, we report five complete and one nearly complete mitochondrial genomes of the Pyraloidea including the first representatives from the Pyralinae (Pyralidae) and Glaphyriinae (Crambidae). We also conduct a comparative analysis of mitogenomic features of this group. Our results show that Pyraloidea mitogenomes evolved under a common trend found in lepidopteran mitogenomes and share several typical genomic characters. The extra conserved blocks are identified in the Pyraloidea control region, and diverse missing codons formed another unique trait within Pyraloidea mitogenome. Furthermore, we reconstruct the mitogenomic phylogeny of Pyraloidea and confirm the phylogenetic position of Pyralinae and Glaphyriinae within the Pyraloidea using BI and ML method based on multiple mitochondrial datasets.