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

Purifying selection drove the adaptation of mitochondrial genes along with correlation of gene rearrangements and evolutionary rates in two subfamilies of Whitefly (Insecta: Hemiptera)

Insect mitochondrial genomes (mitogenomes) are usually represented by a conserved gene order. Whiteflies exhibit gene rearrangement in their mitogenomes; however, understanding how nucleotide substitution rates shape gene rearrangement in whiteflies is unclear due to the limited number of mitogenomes. Additionally, the mechanisms by which selection pressure drives adaptations in mitochondrial genes in the two subfamilies of whiteflies are not yet known. Here, we analyzed 18 whitefly mitogenomes, including one newly generated mitogenome, to compare nucleotide substitution rates, selection pressure, and gene arrangements. The newly generated mitogenome is reported along with reannotation of Pealius mori and comparisons to other whitefly mitogenomes. Comparative studies on nucleotide composition of 18 whiteflies revealed the positive GC skewness, confirming the reversal of strand asymmetry. We found 11 rearranged gene orders within two subfamilies of whiteflies with 8-18 breakpoints of gene rearrangements. Members of the subfamily Aleyrodinae exhibit more complex pathways in the evolution of gene order as compared to the subfamily Aleurodicinae. Our findings also revealed that the increase or reduction of nucleotide substitution rates does not have an impact on any of the gene rearrangement scenarios depicting neutral correlation. Selection pressure analysis revealed that the mitogenomes from members of both the subfamilies Aleurodicinae and Aleyrodinae are characterized by intense purifying selection pressure.

Geometric Morphometrics and Genetic Diversity Analysis of Chalcidoidea (Diglyphus and Pachyneuron) at Various Elevations

Eulophidae and Pteromalidae are parasitic wasps with a global distribution and import for the biological control of pests. They can be distributed in different altitude regions, but their morphological and genetic adaptations to different altitudes are unclear. Here, we collected specimens that belong to Eulophidae and Pteromalidae from various altitudinal gradients, based on integrated taxonomic approaches to determine the species composition, and we analyzed their body shape and size from different altitudes using geometric morphometrics. Then, we performed an analysis of the D. isaea population's haplotype genes to illustrate their genetic diversity. As a result, eight species that belong to two genera, Diglyphus Walker (Eulophidae) and Pachyneuron Walker (Pteromalidae), were identified, including two newly recorded species from China (D. chabrias and D. sabulosus). Through a geometric morphometrics analysis of body shape, we found that a narrow forewing shape and a widened thorax are the significant characteristics of adaptation to high-altitude environments in D. isaea and P. aphidis. Additionally, the body size studies showed a principal relationship between centroid size and altitude; the size of the forewings and thorax increases at higher altitudes. Next, using haplotype analysis, 32 haplotypes were found in seven geographic populations with high genetic diversity of this species. Our research provides preliminary evidence for the morphological and genetic diversity adaptation of parasitic wasps to extreme environments, and these data can provide important references for investigations on the ecological adaptability of parasitic wasps.

Characterization of the complete mitochondrial genome of Spirobolus grahami (Diplopoda: Spirobolidae) with phylogenetic analysis

Diplopoda is one of the most diverse and important groups of soil arthropods, but little research has been done on their phylogenetic relationship and evolution. Here, we sequenced and annotated the complete mitochondrial genomes of Spirobolus grahami. The total mitogenome of S. grahami was typical circular, double-stranded molecules, with 14,875 bp in length, including 13 protein-coding genes, 22 tRNAs, two rRNAs, and one control region. Base composition analysis suggested that the mitochondrial sequences were biased toward A and T, with A + T content of 58.68%. The mitogenomes of S. grahami exhibited negative AT and positive GC skews. Most of the 13 PCGs had ATN as the start codon, except COX1 start with CGA, and most PCGs ended with the T stop codon. The dN/dS values for most PCGs were lower than 1, suggesting that purifying selection was likely the main driver of mitochondrial PCG evolution. Phylogenetic analyses based on 13 PCGs using BI and ML methods support the classification of genus Spirobolus and Tropostreptus. Glomeridesmus spelaeus is distantly related to the other Diplopoda species.

The first two whole mitochondrial genomes for the genus Dactylis species: assembly and comparative genomics analysis

BACKGROUND

Orchardgrass (Dactylis glomerata L.), a perennial forage, has the advantages of rich leaves, high yield, and good quality and is one of the most significant forage for grassland animal husbandry and ecological management in southwest China. Mitochondrial (mt) genome is one of the major genetic systems in plants. Studying the mt genome of the genus Dactylis could provide more genetic information in addition to the nuclear genome project of the genus.

RESULTS

In this study, we sequenced and assembled two mitochondrial genomes of Dactylis species of D. glomerata (597, 281 bp) and D. aschersoniana (613, 769 bp), based on a combination of PacBio and Illumina. The gene content in the mitochondrial genome of D. aschersoniana is almost identical to the mitochondrial genome of D. glomerata, which contains 22-23 protein-coding genes (PCGs), 8 ribosomal RNAs (rRNAs) and 30 transfer RNAs (tRNAs), while D. glomerata lacks the gene encoding the Ribosomal protein (rps1) and D. aschersoniana contains one pseudo gene (atp8). Twenty-three introns were found among eight of the 30 protein-coding genes, and introns of three genes (nad 1, nad2, and nad5) were trans-spliced in Dactylis aschersoniana. Further, our mitochondrial genome characteristics investigation of the genus Dactylis included codon usage, sequences repeats, RNA editing and selective pressure. The results showed that a large number of short repetitive sequences existed in the mitochondrial genome of D. aschersoniana, the size variation of two mitochondrial genomes is due largely to the presence of a large number of short repetitive sequences. We also identified 52-53 large fragments that were transferred from the chloroplast genome to the mitochondrial genome, and found that the similarity was more than 70%. ML and BI methods used in phylogenetic analysis revealed that the evolutionary status of the genus Dactylis.

CONCLUSIONS

Thus, this study reveals the significant rearrangements in the mt genomes of Pooideae species. The sequenced Dactylis mt genome can provide more genetic information and improve our evolutionary understanding of the mt genomes of gramineous plants.

Novel Gene Rearrangement Pattern in Pachycrepoideus vindemmiae Mitochondrial Genome: New Gene Order in Pteromalidae (Hymenoptera: Chalcidoidea)

The mitochondrial genomes of Muscidifurax similadanacus, M. sinesensilla, Nasonia vitripennis, and Pachycrepoideus vindemmiae were sequenced to better understand the structural evolution of Pteromalidae mitogenomes. These newly sequenced mitogenomes all contained 37 genes. Nucleotide composition was AT-biased and the majority of the protein-coding genes exhibited a negative AT skew. All 13 protein-coding genes (PCGs) initiated with the standard start codon of ATN, excepted for nad1 of N. vitripennis, which started with TTG, and terminated with a typical stop codon TAA/TAG or an incomplete stop codon T. All transfer RNA (tRNA) genes were predicted to fold into the typical clover-leaf secondary structures, except for trnS1, which lacks the DHU arm in all species. In P. vindemmiae, trnR and trnQ lack the DHU arm and TΨC arm, respectively. Although most genes evolved under a strong purifying selection, the Ka/Ks value of the atp8 gene of P. vindemmiae was greater than 1, indicating putative positive selection. A novel transposition of trnR in P. vindemmiae was revealed, which was the first of this kind to be reported in Pteromalidae. Two kinds of datasets (PCG12 and AA) and two inference methods (maximum likelihood and Bayesian inference) were used to reconstruct a phylogenetic hypothesis for the newly sequenced mitogenomes of Pteromalidae and those deposited in GenBank. The topologies obtained recovered the monophyly of the three subfamilies included. Pachyneurinae and Pteromalinae were recovered as sister families, and both appeared sister to Sycophaginae. The pairwise breakpoint distances of mitogenome rearrangements were estimated to infer phylogeny among pteromalid species. The topology obtained was not totally congruent with those reconstructed using the ML and BI methods.

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.

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.

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

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

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

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

Characterization of the mitochondrial genomes of Bradysia hygida, Phytosciara flavipes and Trichosia splendens (Diptera: Sciaridae) and novel insights on the control region of sciarid mitogenomes

Sciarids, also called "fungus gnats" are small, almost entirely dark-coloured insects. Sciarid larvae feed on different substrates and can infest agricultural crops and mushroom nurseries, causing economic losses. Of the 2174 Diptera mitogenome sequences currently available in GenBank, only eight are from the Sciaridae family, none of which are complete circular molecules. Here we describe the mitogenome sequences of three sciarid species: Phytosciara flavipes, Trichosia splendens and Bradysia hygida and provide novel insights on the control region of sciarid mitogenomes. The assembled mitogenomes range from 16,062 bp in P. flavipes to 17,095 bp in B. hygida. All 13 protein coding genes, 22 tRNAs and 2 rRNAs characteristic of insect mitogenomes were identified, but the sequence of the control region could not be determined. Experimental results suggest that the B. hygida control region is about 21 kb long resulting in a 37 kb long mitogenome which constitutes the largest insect mitochondrial genome described so far. Phylogenetic analysis using all Bibionomorpha mitogenome sequences available in GenBank strongly supports the Sciaridae monophyly and led to the identification of species and subfamily specific gene rearrangements. Our study extends the knowledge of this large and diverse insect family that includes agricultural pest species.

Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Diospyros oleifera, the first representative from the family Ebenaceae

Plant mitochondrial genomes are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitochondrial genome of any species in Ebenaceae has been reported. In this study, we reported the first mitochondrial genome of an Ebenaceae model plant Diospyros oleifera. The mitogenome was 493,958 bp in length, contained 39 protein-coding genes, 27 transfer RNA genes, and 3 ribosomal RNA genes. The rps2 and rps11 genes were missing in the D. oleifera mt genome, while the rps10 gene was identified. The length of the repetitive sequence in the D. oleifera mt genome was 31 kb, accounting for 6.33%. A clear bias in RNA-editing sites were found in the D. oleifera mt genome. We also detected 28 chloroplast-derived fragments significantly associated with D. oleifera mt genes, indicating intracellular tRNA genes transferred frequently from chloroplasts to mitochondria in D. oleifera. Phylogenetic analysis based on the mt genomes of D. oleifera and 27 other taxa reflected the exact evolutionary and taxonomic status of D. oleifera. Ka/Ks analysis revealed that 95.16% of the protein-coding genes in the D. oleifera mt genome had undergone negative selections. But, the rearrangement of mitochondrial genes has been widely occur among D. oleifera and these observed species. These results will lay the foundation for identifying further evolutionary relationships within Ebenaceae.

Comparative mitochondrial genome analysis and phylogenetic relationship among lepidopteran species

Lepidoptera has rich species including many agricultural pests and economical insects around the world. The mitochondrial genomes (mitogenomes) were utilized to explore the phylogenetic relationships between difference taxonomic levels in Lepidoptera. However, the knowledge of mitogenomic characteristics and phylogenetic position about superfamily-level in this order is unresolved. In this study, we integrated 794 mitogenomes consisting of 37 genes and a noncoding control region, which covered 26 lepidopteran superfamilies from newly sequenced and publicly available genomes for comparative genomic and phylogenetic analysis. In primitive taxon, putative start codon of cox1 gene was ATA or ATT instead of CGA, but stop codon of that showed four types, namely TAA, TAG, TA and T. The 7-bp overlap between atp8 and atp6 presented as "ATGATAA". Moreover, the most frequently utilized amino acids were leucine (UUA) in 13 PCGs. Phylogenetic analysis showed that the main backbone relationship in Lepidoptera was (Hepialoidea + (Nepticuloidea + (Adeloidea + (Tischerioidea + (Tineoidea + (Yponomeutoidea + (Gracillarioidea + (Papilionoidea + ((Zygaenoidea + Tortricoidea) + (Gelechioidea + (Pyraloidea + ((Geometroidea + Noctuoidea) + (Lasiocampoidea + Bombycoidea))))))))))))).

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.

Novel gene rearrangement in the mitochondrial genome of Anastatus fulloi (Hymenoptera Chalcidoidea) and phylogenetic implications for Chalcidoidea

The genus Anastatus comprises a large group of parasitoids, including several biological control agents in agricultural and forest systems. The taxonomy and phylogeny of these species remain controversial. In this study, the mitogenome of A. fulloi Sheng and Wang was sequenced and characterized. The nearly full-length mitogenome of A. fulloi was 15,692 bp, compromising 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes and a control region (CR). The total A + T contents were 83.83%, 82.18%, 87.58%, 87.27%, and 82.13% in the whole mitogenome, 13 PCGs, 22 tRNA genes, 2 rRNA genes, and CR, respectively. The mitogenome presented negative AT skews and positive GC skews, except for the CR. Most PCGs were encoded on the heavy strand, started with ATN codons, and ended with TAA codons. Among the 3736 amino acid-encoding codons, TTA (Leu1), CGA (Arg), TCA (Ser2), and TCT (Ser2) were predominant. Most tRNAs had cloverleaf secondary structures, except trnS1, with the absence of a dihydrouridine (DHU) arm. Compared with mitogenomes of the ancestral insect and another parasitoid within Eupelmidae, large-scale rearrangements were found in the mitogenome of A. fulloi, especially inversions and inverse transpositions of tRNA genes. The gene arrangements of parasitoid mitogenomes within Chalcidoidea were variable. A novel gene arrangement was presented in the mitogenome of A. fulloi. Phylogenetic analyses based on the 13 protein-coding genes of 20 parasitoids indicated that the phylogenetic relationship of 6 superfamilies could be presented as Mymaridae + (Eupelmidae + (Encyrtidae + (Trichogrammatidae + (Pteromalidae + Eulophidae)))). This study presents the first mitogenome of the Anastatus genus and offers insights into the identification, taxonomy, and phylogeny of these parasitoids.

Two Complete Mitogenomes of Chalcididae (Hymenoptera: Chalcidoidea): Genome Description and Phylogenetic Implications

Simple Summary

The Chalcididae are a moderate-sized family of the superfamily Chalcidoidea in Hymenoptera, comprising 1548 species in 87 genera worldwide. Some species are potential natural enemies of pests in agriculture and forestry. Currently, there are still some controversies about the monophyly of Chalcididae and the phylogenetic relationships between Chalcididae and other families in Chalcidoidea. Based on the fact that no mitogenomic phylogenetic analyses of all of the published mitogenomes of Chalcidoidea have been conducted and no complete mitogenome of Chalcididae species has been reported, two newly completed mitochondrial genomes of Chalcididae species (Brachymeria lasus and Haltichella nipponensis) were sequenced and analyzed. The results show that the two chalcidid mitogenomes have quite similar structures and features. In phylogenetic analyses based on 13 PCGs of mitogenomes, the basal position and monophyly of Chalcididae within Chalcidoidea were supported by all trees derived from maximum likelihood (ML) and Bayesian inference (BI) methods.

Abstract

The complete mitochondrial genomes of two species of Chalcididae were newly sequenced: Brachymeria lasus and Haltichella nipponensis. Both circular mitogenomes are 15,147 and 15,334 bp in total length, respectively, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A+T-rich region. The nucleotide composition indicated a strong A/T bias. All PCGs of B. lasus and H. nipponensis began with the start codon ATD, except for B. lasus, which had an abnormal initiation codon TTG in ND1. Most PCGs of the two mitogenomes are terminated by a codon of TAR, and the remaining PCGs by the incomplete stop codon T or TA (ATP6, COX3, and ND4 in both species, with an extra CYTB in B. lasus). Except for trnS1 and trnF, all tRNAs can be folded into a typical clover structure. Both mitogenomes had similar control regions, and two repeat units of 135 bp were found in H. nipponensis. Phylogenetic analyses based on two datasets (PCG123 and PCG12) covering Chalcididae and nine families of Chalcidoidea were conducted using two methods (maximum likelihood and Bayesian inference); all the results support Mymaridae as the sister group of the remaining Chalcidoidea, with Chalcididae as the next successive group. Only analyses of PCG123 generated similar topologies of Mymaridae + (Chalcididae + (Agaonidae + remaining Chalcidoidea)) and provided one relative stable clade as Eulophidae + (Torymidae + (Aphelinidae + Trichogrammatidae)). Our mitogenomic phylogenetic results share one important similarity with earlier molecular phylogenetic efforts: strong support for the monophyly of many families, but a largely unresolved or unstable “backbone” of relationships among families.

The mitochondrial genome of a parasitic wasp, Chouioia cunea Yang (Hymenoptera: Chalcidoidea: Eulophidae) and phylogenetic analysis

Chouioia cunea Yang 1989 is a parasitic wasp and natural enemy of several lepidopteran pests during their pupal stage. In this study, we sequenced and analyzed the mitochondrial genome of C. cunea, and obtained a complete DNA molecule that is 14,930 bp in size with 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) (GenBank accession number MW192646). All the 13 PCGs started with typical ATN (ATA, ATG, and ATT) and terminated with the stop codon TAA or TAG. Phylogenetic analysis showed that C. cunea formed the sister group with Tamarixia radiata, which belongs to the same family.

Characterization of the complete mitochondrial genome of Pentatoma semiannulata (Hemiptera: Pentatomidae)

The Pentatoma semiannulata is an important fruit pest in Chinese agricultural system. In current study, the complete mitochondrial genome of P. semiannulata is determined. This mitogenome is 15,515 bp in size and comprises of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Gene order is identical to that of the putative ancestral arrangement of insects. All protein-coding genes initiate with ATN, except for ATP8, COX1 and NAD1 use GTG or TTG as the start codon, and terminate with TAA with the exception for COX2 which uses a single T residue as the stop codon. All tRNAs, ranging from 62 to 72 bp, have the clover-leaf structure except for tRNA^Ser(AGN). The monophyly of Pentatomidae is highly supported by the phylogenetic tree and P. semiannulata is very close to other herbivorous species of the remaining Pentatomidae species.

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

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

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

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