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

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.

A Compositional Heterogeneity Analysis of Mitochondrial Phylogenomics in Chalcidoidea Involving Two Newly Sequenced Mitogenomes of Eupelminae (Hymenoptera: Chalcidoidea)

As next-generation sequencing technology becomes more mature and the cost of sequencing continues to fall, researchers are increasingly using mitochondrial genomes to explore phylogenetic relationships among different groups. In this study, we sequenced and analyzed the complete mitochondrial genomes of Eupelmus anpingensis and Merostenus sp. We predicted the secondary-structure tRNA genes of these two species and found that 21 of the 22 tRNA genes in Merostenus sp. exhibited typical clover-leaf structures, with trnS1 being the lone exception. In E. anpingensis, we found that, in addition to trnS1, the secondary structure of trnE was also incomplete, with only DHU arms and anticodon loop remaining. In addition, we found that compositional heterogeneity and variable rates of evolution are prevalent in Chalcidoidea. Under the homogeneity model, a Eupelmidae + Encyrtidae sister group relationship was proposed. Different datasets based on the heterogeneity model produced different tree topologies, but all tree topologies contained Chalcididae and Trichogrammatidae in the basal position of the tree. This is the first study to consider the phylogenetic relationships of Chalcidoidea by comparing a heterogeneity model with a homogeneity model.

The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications

Platygaster robiniae is economically important as a highly specific parasitoid of the invasive pest Obolodiplosis robiniae which was introduced into the Euro-Asia region in the last decade. Despite being a critical and specific parasitoid of the invasive pest O. robiniae and its use as an effective biocontrol agent, the absence of sequence information from P. robiniae have limited its genetic applications for pest management in forests. Mitochondrial (mt) genomes generally contain abundant nucleotide information and thus are helpful for understanding species history. Here, we sequenced the complete mt genome of P. robiniae using next generation sequencing, and annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 702 bp noncoding region. Comparative analysis indicated that this mt genome has a normal A + T content and codons use, however possessed both the expected and unique rearrangements. Ten tRNAs at four gene blocks COII-ATP8, COIII-ND3, ND3-ND5 and the A + T-rich region-ND2 were rearranged, including gene shuffles, transpositions and inversions. Notably, two genes tRNA^Ser(UCN) and tRNA^Leu(CUN) had undergone long-range inversions, which is the first record of this rearrangement type in the superfamily Platygastroidea. The D-loops of both tRNA^Ile and tRNA^Leu(CUN) were absent from the tRNA secondary structure, which has not been reported from hymenopteran previously. Phylogenetic analysis based with the maximum likelihood and Bayesian methods showed that P. robiniae grouped with other species of Platygastridae, and that the superfamily Platygastridea is sister to the other Proctotrupomorpha superfamilies. Our tree strongly supports the monophyly of the five superfamilies of Proctotrupomorpha. This study discovered some unique characters of P. robiniae, and contributes to our understanding of genome rearrangements in the order Hymenoptera.

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Assemble the complete mitochondria genome of the obligate parasitoid (Platygaster robiniae) of Obolodiplosis robiniae.

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Discover some unique tRNA secondary structures.

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Discover some unique rearrangements of Platygaster robiniae and Platygastroidea.

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The abundance rearrangements in the order Hymenoptera.

Characterization and Phylogenetic Analysis of the Complete Mitochondrial Genomes of Two Tiny Necrophagous Phorid Flies, Metopina sagittata and Puliciphora borinquenensis (Diptera: Phoridae)

The mitochondrial genome is frequently used for species identification and phylogenetic studies. In this study, we first sequenced and annotated the complete mitochondrial genomes of two phorid species that are forensically important in buried or enclosed environments: Metopina sagittata (Liu) and Puliciphora borinquenensis (Wheeler). The complete mitochondrial genome sequences of M. sagittata and P. borinquenensis were 15,640 bp with an A+T content of 75.97% and 15,429 bp with an A+T content of 75.38%, respectively. Their circular genomes both contained 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region located between rrnS and trnI which was 808 bp for M. sagittata and 746 bp for P. borinquenensis. All the PCGs of both species started with ATN codons except for cox1 which used TTG codon. In addition to the common stop codon TAA and TAG, the incomplete stop codon T was used in two PCGs (cox1 and nad4) of M. sagittata and five PCGs (cox1, cox2, cox3, nad5, and nad4) of P. borinquenensis. There were 3 and 10 mismatched base pairs in the tRNA secondary structures from M. sagittata and P. borinquenensis, respectively. Both maximum likelihood and Bayesian inference analyses indicated that Platypezidae and Phoridae are sister taxa. M. sagittata is closely related to P. borinquenensis within the subfamily Metopininae. This work enhances the databases of Phoridae genomes and contributes to the further study of species identification and phylogenetics of this family.

The complete mitogenome of Curculiochinensis (Chevrolat, 1878) (Coleoptera: Curculionidae: Curculioninae)

The mitogenome of Curculiochinensis (Chevrolat, 1878) was sequenced and annotated to better identify C.chinensis and related species. The mitogenome is 18,680 bp in length, includes the 37 typical mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes and 22 transfer RNA genes) and two control regions (total length: 3,879 bp). Mitogenome organisation, nucleotide composition and codon usage are similar to the previously sequenced Curculio mitogenomes. All 13 protein-coding genes use ATN or TTG as start codon and end with TAA/G or incomplete stop codons (single T-). Twenty-one transfer RNA genes have the typical clover-leaf structure, while the dihydrouridine (DHU) arm of trnS1 is missing. In Curculio mitogenomes, the size of the control region is highly variable. Both ML and BI analyses, based on the 13 PCGs and two rRNAs from six species of Curculioninae, strongly supported the monophyly of Curculio. In Curculio, the relationships amongst included species were inferred as ((C.chinensis + Curculio. sp.) + (Curculiodavidi + Curculioelephas)), with C.chinensis and C. sp. forming a clade (BS = 100; PP = 1).

The First Mitogenomes of the Subfamily Odontiinae (Lepidoptera, Crambidae) and Phylogenetic Analysis of Pyraloidea

Simple Summary

The Odontiinae is a small group in the Pyraloidea comprised of 388 species in 88 genera, but externally, these moths are diverse, including heterogeneous maculation and a size range from 9 to 50 mm in total wingspan. The monophyly of Pyraloidea and the two families (Pyralidae and Crambidae) is well supported by phylogenetic analyses based on morphology and molecular data of multiple nuclear genes. However, only a few mito-phylogenetic analyses have been conducted and no mitogenome of Odontiinae species has been reported. Three complete mitogenomes of odontiine species were sequenced and analyzed for the first time herein. The results showed that Odontiinae mitogenomes shared similar genomic characters with other Pyraloidea. The phylogenetic analyses based on 13 PCGs of mitogenomes confirmed the monophyly of Odontiinae and its position within Crambidae.

Abstract

The complete mitochondrial genomes of three species of Odontiinae were newly sequenced: Dausara latiterminalis Yoshiyasu, Heortia vitessoides (Moore), and Pseudonoorda nigropunctalis (Hampson). These circular and double-stranded mitogenomes vary from 15,084 bp to 15,237 bp in size, 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. Most PCGs are initiated with an ATN codon and terminated by a codon of TAR. All tRNAs could be folded into the clover-leaf structure with the exception of trnS1 (AGN), in which the dihydrouridine (DHU) arm formed a simple loop, and the motif ‘ATAG’ and ‘ATTTA’ in the A + T-rich region was also founded. The phylogenomic analyses covering Odontiinae + 11 subfamilies of Pyraloidea were conducted. Similar topologies were generated from both Bayesian inference (BI) and maximum likelihood (ML) analyses based on the nucleotide and amino acid sequence data. There was some discrepancy in the sister-group relationship of Odontiinae and Glaphyriinae, and the relationships among the subfamilies in the ‘CAMMSS clade’ of the Crambidae. The results of this study suggest that mitogenomic data are useful for resolving the deep-level relationships of Pyraloidea and the topologies generated from amino acid data might be more realistic and reliable. Moreover, more mitogenomic taxon sampling and larger scale analyses with more genes or a combination of mitogenomic and nuclear genes are needed to reconstruct a comprehensive framework of the pyraloid phylogeny.

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.

The first divergence time estimation of the subfamily Stenogastrinae (Hymenoptera: Vespidae) based on mitochondrial phylogenomics

In this study, the mitochondrial genomes of three Stenogastrinae species, Eustenogaster scitula, Liostenogaster nitidipennis and Parishnogaster mellyi were sequenced and annotated, and a total of 16 vespid mtgenomes are comparatively analyzed. Our results indicate that codon usage bias is mainly dominated by mutational pressure, and affected only slightly by natural selection. Selective pressure analysis of protein-coding genes (PCGs) shows that the highest evolutionary rate is present in NADH complex I, and the lowest in cox1. Compared with the reported mtgenomes of other Vespidae, in Stenogastrinae, trnH is shifted to a new position. Phylogenetic analyses are performed using Bayesian method and Maximum Parsimony. Phylogenetic analysis further confirms that the Stenogastrinae is the sister group of all remaining Vespidae. Divergence time of Stenogastrinae from other Vespidae is estimated at ~ 166 Mya. Our results also support that eusociality evolved twice in the family Vespidae.

The complete mitochondrial genomes of two sibling species of camellia weevils (Coleoptera: Curculionidae) and patterns of Curculionini speciation

Complete mitochondrial genomes contain large and diverse datasets for species delineation. To better understand the divergence of the two morphologically indistinguishable weevil species in Curculionini, we first sequenced and compared their complete mitochondrial genomes. The complete mitochondrial genomes of Curculio chinensis and Curculio sp. were 19,713 bp with an A + T content of 76.61% and 19,216 bp with an A + T content of 76.85%, respectively. All 37 of the typical mitochondrial genes were determined in both species. The 13 protein sequences of the two species shared high homology (about 90%) except for ATP8 (73.08%). The differences in secondary structure of ATP8 were the number of possible proteins and nucleic acid binding sites. There were 22 and 15 mismatched base-pairs in the tRNA secondary structures from C. chinensis and Curculio sp., respectively. Maximum Likelihood and Bayesian analyses indicated that Curculio sp. is a novel species closely related to C. chinensis. The divergence time estimation suggests that Cryptorhynchinae and Curculionini lines diverged in the Cenozoic Period, while C. chinensis and Curculio sp. diverged at 6.7079 (95% CI 5-13) Mya. This study demonstrates the utility of using complete mitochondrial gene sets for phylogenetic analysis and enhances our understanding of the genetic basis for the evolution of the Curculionini.

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))))).

The complete mitochondrial genome of Orancistrocerusaterrimusaterrimus and comparative analysis in the family Vespidae (Hymenoptera, Vespidae, Eumeninae)

To date, only one mitochondrial genome (mitogenome) in the Eumeninae has been reported in the world and this is the first report in China. The mitogenome of O.a.aterrimus is 17 972 bp long, and contains 38 genes, including 13 protein coding genes (PCGs), 23 tRNA genes, two rRNA genes, a long non-coding region (NCR), and a control region (CR). The mitogenome has 79.43% A + T content, its 13 PCGs use ATN as the initiation codon except for cox1 using TTG, and nine genes used complete translation termination TAA and four genes have incomplete stop codon T (cox2, cox3, nad4, and cytb). Twenty-two of 23 tRNAs can form the typical cloverleaf secondary structure except for trnS1. The CR is 1 078 bp long with 84.69% A+T content, comprising 28 bp tandem repeat sequences and 13 bp T-strech. There are two gene rearrangements which are an extra trnM2 located between trnQ and nad2 and the trnL2 in the upstream of nad1. Within all rearrangements of these mitogenomes reported in the family Vespidae, the translocation between trnS1 and trnE genes only appears in Vespinae, and the translocation of trnY in Polistinae and Vespinae. The absent codons of 13 PCGs in Polistinae are more than those both in Vespinae and Eumeninae in the family Vespidae. The study reports the complete mitogenome of O.a.aterrimus, compares the characteristics and construct phylogenetic relationships of the mitogenomes in the family Vespidae.

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

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

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

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

Complete mitochondrial genome of the soybean leaffolder, Omiodes indicata (Lepidoptera: Pyraloidea: Crambidae), and phylogenetic analysis for Pyraloidea

Complete mitochondrial genome (mitogenome) of the Omiodes indicata was sequenced and characterized. The circular mitogenome is 15,367bp long, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A+T-rich region. Nucleotide composition is highly biased toward A+T nucleotides (81.6%). All 13 PCGs initiate with canonical start codon (ATN), except for cox1 that initiates with CGA. All tRNAs have a typical clover-leaf structure, except for trnS1 (AGN) in which the base pairs of the dihydrouridine (DHU) arm are reduced. In O. indicata, the motifs "ATGATAA" and "ATACTAA" between atp8 and atp6, trnS2 and nad1, respectively, and the motifs "ATAG" and "ATTTA" in the A+T-rich region can be identified. Comparative phylogenetic analyses based on four datasets show that the dataset including all coding positions of 13 PCGs exhibit the highest informativeness in resolving higher phylogeny of Pyraloidea. Bayesian inference (BI) and maximum likelihood (ML) analyses yield generally well-supported phylogenetic relationships among the eleven pyraloid subfamilies involved. However, the relationships among the five subfamilies (Acentropinae, Crambinae, Glaphyriinae, Schoenobiinae and Scopariinae) in ML analysis are ambiguous, which might be resolved by ample sampling in future mitogenome-based phylogenetic studies.