Complete mitochondrial genome of brown marmorated stink bug Halyomorpha halys (Hemiptera: Pentatomidae), and phylogenetic relationships of hemipteran suborders

Phylogenetic and divergence analysis of Pentatomidae, with a comparison of the mitochondrial genomes of two related species (Hemiptera, Pentatomidae)

Pentatomidae, the most diverse family of Pentatomoidea, is found worldwide. Currently, the phylogenetic relationships among Pentatomidae tribes remain unstable, and subfamily divergence has not been estimated. Here, we sequenced and analyzed the complete mitochondrial genomes of two species of Lelia, and studied the phylogenetic relationships among Pentatominae tribes. We also selected three available fossil as the calibration points in the family, and preliminarily discussed the divergence time of Pentatomidae. Trees of Pentatomidae were reconstructed using the Bayesian inference method. Divergence times of Pentatominae were estimated based on the nucleotide sequences of protein-coding genes with a relaxed clock log-normal model in BEASTv.1.8.2. The results showed that the gene arrangements, nucleotide composition, and codon preferences were highly conserved in Lelia. Further, a phylogenetic analysis recovered Eysarcorini, Strachiini, Phyllocephalini, and Menidini as monophyletic with strong support, however, the monophyly of Antestiini, Nezarini, Carpocorini, Pentatomini and Cappaeini were rejected. Moreover, Pentatominae diverged from Pentatomidae soon after the origin of the Cretaceous Period, at approximately 110.38 Ma. This study enriches the mitochondrial genome database of Pentatomidae and provides a reference for further phylogenetic studies, and provides a more accurate estimate of divergence time.

Describe the morphology and mitochondrial genome of Mecidea indica Dallas, 1851 (Hemiptera, Pentatomidae), with its phylogenetic position

We here describe the external morphology and complete mitochondrial genome characteristics of Mecidea indica Dallas, 1851, and clarify the evolutionary rate and divergence time. The M. indica mitochondrial genome length is 15,670 bp, and it exhibits a typical high A+T-skew (76.31%). The sequence shows strong synteny with the original gene arrangement of Drosophila yakuba Burla, 1954 without rearrangement. The M. indica mitochondrial genome characteristics were analyzed, and phylogenetic trees of Pentatomidae were reconstructed using Bayesian methods based on different datasets of the mitochondrial genome datasets. Phylogenetic analysis shows that M. indica belongs to Pentaotominae and form a sister-group with Anaxilaus musgravei Gross, 1976, and Asopinae is highly supported as monophyletic. Molecular clock analysis estimates a divergence time of Pentatomidae of 122.75 Mya (95% HPD: 98.76-145.43 Mya), within the Mesozoic Cretaceous; the divergence time of M. indica and A. musgravii was no later than 50.50 Mya (95% HPD: 37.20-64.80 Mya). In addition, the divergence time of Asopinae was 62.32 Mya (95% HPD: 47.08-78.23 Mya), which was in the Paleogene of the Cenozoic era. This study is of great significance for reconstructing the phylogeny of Pentatomidae and providing insights into its evolutionary history.

Comparative mitogenomic analysis of three bugs of the genus Hygia Uhler, 1861 (Hemiptera, Coreidae) and their phylogenetic position

Hygia Uhler, 1861 is the largest genus in the bug family Coreidae. Even though many species of this genus are economically important, the complete mitogenomes of Hygia species have not yet been reported. Therefore, in the present study, the complete mitogenomes of three Hygia species, H.lativentris (Motschulsky, 1866), H.bidentata Ren, 1987, and H.opaca (Uhler, 1860), are sequenced and characterized, and submitted in a phylogenetic analysis of the Coreidae. The results show that mitogenomes of the three species are highly conserved, typically with 37 genes plus its control region. The lengths are 16,313 bp, 17,023 bp, and 17,022 bp, respectively. Most protein-coding genes (PCGs) in all species start with the standard codon ATN and terminate with one of three stop codons: TAA, TAG, or T. The tRNAs secondary structures of all species have a typical clover structure, except for the trnS1 (AGC) in H.bidentata, which lacks dihydrouridine (DHU) arm that forms a simple loop. Variation in the length of the control region led to differences in mitochondrial genome sizes. The maximum-likelihood (ML) and Bayesian-inference (BI) phylogenetic analyses strongly supported the monophyly of Hygia and its position within Coreidae, and the relationships are ((H.bidentata + (H.opaca + (H.lativentris + Hygia sp.))). The results provide further understanding for future phylogenetic studies of Coreidae.

Comparative mitogenomics and phylogenetic analyses of the genus Menida (Hemiptera, Heteroptera, Pentatomidae)

In order to explore the genetic diversity and phylogenetic relationship of the genus Menida Motschulsky, 1861 and reveal the molecular evolution of the family Pentatomidae, subfamily Pentatominae, complete mitochondrial genomes of three species of Menida were sequenced, and the phylogenetic relationships of tribes within the subfamily Pentatominae were studied based on these results. The mitochondrial genomes of Menidamusiva (Jakovlev, 1876), M.lata Yang, 1934, and M.metallica Hsiao & Cheng, 1977 were 16,663 bp, 16,463 bp, and 16,418 bp, respectively, encoding 37 genes and including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and a control region. The mitochondrial genome characteristics of Menida were compared and analyzed, and the phylogenetic tree of the Pentatominae was constructed based on the mitochondrial genome datasets using Bayesian inference (BI) and maximum likelihood (MI) methods. The results showed that gene arrangements, nucleotide composition, codon preference, gene overlaps, and RNA secondary structures were highly conserved within the Menida and had more similar characteristics in Pentatominae. The phylogenetic analysis shows a highly consistent topological structure based on BI and ML methods, which supported that the genus Menida belongs to the Pentatominae and is closely related to Hoplistoderini. The examined East Asian species of Menida form a monophyletic group with the internal relationships: (M.musiva + (M.lata + (M.violacea + M.metallica))). In addition, these results support the monophyly of Eysarcorini and Strachiini. Placosternum and Cappaeini are stable sister groups in the evolutionary branch of Pentatominae. The results of this study enrich the mitochondrial genome databases of Pentatominae and have significance for further elucidation of the phylogenetic relationships within the Pentatominae.

The complete mitochondrial genome of Aeschrocoristuberculatus and A.ceylonicus (Hemiptera, Pentatomidae) and its phylogenetic implications

Aeschrocoristuberculatus and A.ceylonicus (Hemiptera, Pentatomidae, Pentatominae) are mainly distributed in southern China, India, Myanmar, and Sri Lanka. Both species are also common agricultural pests. However, only the morphology of the genus Aeschrocoris has previously been studied, and molecular data have been lacking. In this study, the whole mitochondrial genomes of A.tuberculatus and A.ceylonicus are and annotated. The lengths of the complete mitochondrial genomes of the two species are 16,134 bp and 16,142 bp, respectively, and both contain 37 typical genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and a control region. The mitochondrial genome structure, gene order, nucleotide composition, and codon usage of A.tuberculatus and A.ceylonicus are consistent with those of typical Pentatomidae. Most PCGs of both species use ATN as the start codon, except atp8, nad1, and cox1, which use TTG as the start codon. cox1, cox2, and atp6 use a single T, and nad1 use TAG as the stop codon; the remaining PCGs have TAA as the stop codon. The A+T contents of the two species are 73.86% and 74.08%, respectively. All tRNAs have a typical cloverleaf structure, with the exception of trnS1, which lacks a dihydrouridine arm. The phylogenetic tree is reconstructed using the maximum-likelihood method based on the newly obtained mitochondrial genome sequences and 87 existing mitochondrial genomes of Pentatomoidea from the NCBI database and two species of Lygaeoidea as outgroups. The phylogenetic trees strongly support the following relationships: (Urostylididae + ((Acanthosomatidae + ((Cydnidae + (Dinidoridae + Tessaratomidae)) + (Scutelleridae + Plataspidae))) + Pentatomidae). This study enriches the mitochondrial genome database of Pentatomoidea and provides a reference for further phylogenetic studies.

Comparative analysis and phylogeny of mitochondrial genomes of Pentatomidae (Hemiptera: Pentatomoidea)

The Phyllocephalini is a group of herbivorous insects in Pentatomidae, which lack distinctive morphological characteristics and systematic studies. Up to now, there are only two complete mitochondrial genomes of Phyllocephalini have been reported. In this study, we sequenced and analyzed the complete mitochondrial genomes of three Phyllocephalini species, Gonopsis coccinea, Gonopsimorpha nigrosignata, and Chalcopis glandulosus, which were 16,534, 16,531, and 16,534 bp in length, respectively. The mitochondrial genomes contained 37 genes, including 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region. The gene arrangement was consistent with that of the putative ancestral insect, with no rearrangement. The cox1 gene of Pentatomidae showed the lowest evolutionary rate among the protein-coding genes, the mean genetic distance of species, genera, and subfamilies of Pentatomidae increased hierarchically based on cox1 gene. The 16S rRNA of Pentatomidae was more conserved than 12S rRNA in sequence and secondary structure. All tRNAs could be folded into a typical cloverleaf structure except trnS1. The stem region was more conserved than the loop region in the secondary structure of tRNAs within Pentatomidae. Gonopsis coccinea and Gonopsimorpha nigrosignata had one type of tandem repetition unit in the control region, while C. glandulosus had two types. The heterogeneity analysis of Pentatomidae showed that Phyllocephalinae was the most heterogeneous. Phylogenetic trees based on the newly obtain mitochondrial genomes along with other 50 mitochondrial genomes of Pentatomidae using Bayesian Inference and Maximum Likelihood strongly supported the following three relationships: (((Anaxilaus + (Plautia + Glaucias)) + (Nezara + Palomena)) + (Eysarcorini + Carpocorini)), (Hoplistoderini + (Menidini + Asopinae)), and ((Sephelini + Halyini) + (Caystrini + (Cappaeini + (Placosternum + Phyllocephalini)))). The relationships within Phyllocephalini were (Chalcopis + (Dalsira + (Gonopsimorpha + Gonopsis))). Our results provide valuable molecular data for further phylogenetic analyses of Pentatomidae.

Genome Organization and Comparative Evolutionary Mitochondriomics of Brown Planthopper, Nilaparvata lugens Biotype 4 Using Next Generation Sequencing (NGS)

Nilaparvata lugens is the main rice pest in India. Until now, the Indian N. lugens mitochondrial genome has not been sequenced, which is a very important basis for population genetics and phylogenetic evolution studies. An attempt was made to sequence two examples of the whole mitochondrial genome of N. lugens biotype 4 from the Indian population for the first time. The mitogenomes of N. lugens are 16,072 and 16,081 bp long with 77.50% and 77.45% A + T contents, respectively, for both of the samples. The mitochondrial genome of N. lugens contains 37 genes, including 13 protein-coding genes (PCGs) (cox1-3, atp6, atp8, nad1-6, nad4l, and cob), 22 transfer RNA genes, and two ribosomal RNA (rrnS and rrnL) subunits genes, which are typical of metazoan mitogenomes. However, both samples of N. lugens mitogenome in the present study retained one extra copy of the trnC gene. Additionally, we also found 93 bp lengths for the atp8 gene in both of the samples, which were 60–70 bp less than that of the other sequenced mitogenomes of hemipteran insects. The phylogenetic analysis of the 19 delphacids mitogenome dataset yielded two identical topologies when rooted with Ugyops sp. in one clade, and the remaining species formed another clade with P. maidis and M. muiri being sisters to the remaining species. Further, the genus Nilaparvata formed a separate subclade with the other genera (Sogatella, Laodelphax, Changeondelphax, and Unkanodes) of Delphacidae. Additionally, the relationship among the biotypes of N. lugens was recovered as the present study samples (biotype-4) were separated from the three biotypes reported earlier. The present study provides the reference mitogenome for N. lugens biotype 4 that may be utilized for biotype differentiation and molecular-aspect-based future studies of N. lugens.

Characterizing the Complete Mitochondrial Genome of Arma custos and Picromerus lewisi (Hemiptera: Pentatomidae: Asopinae) and Conducting Phylogenetic Analysis

We characterized the mitochondrial genome (mitogenome) and conducted phylogenetic analyses of 48 Hemiptera species by sequencing and analyzing the mitogenome of Arma custos (Fabricius) and Picromerus lewisi (Scott). The complete mitogenomes of the two predators were 16,024 bp and 19,587 bp in length, respectively, and it contained 37 classical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs), and a control region. Most PCGs in these predators use ATN as the start codon. This research revealed that the genes of the two natural enemy species have an A + T content of 75.40% and all tRNAs have a typical cloverleaf structure, with the exception of trnS1, which lacks a dihydrouridine arm. This is the first study to compare the mitochondrial genetic structure of two predatory insects; the mitochondrial genetic structure of individual predatory insects has been sequenced in previous studies. Here, phylogenetic analysis on the basis of amino acid and nucleotide sequences of 13 mitochondrial PCGs using Bayesian inference and maximum likelihood methods were conducted to generate similar tree topologies, which suggested that the two predators with close genetic relationships belong to Asopinae subfamily. Furthermore, the monophyly of the Pentatomoidea superfamily is well accepted despite limited taxon and species sampling. Finally, their complete mitogenome provided data to establish a predator-prey food web, which is the foundation of effective pest management. Our results also enhanced the database of natural enemy insects.

Comparative analysis of twelve mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha) and their phylogenetic implications

Here, the complete mitochondrial genomes (mitogenomes) of 12 Caliscelidae species, Augilina tetraina, Augilina triaina, Symplana brevistrata, Symplana lii, Neosymplana vittatum, Pseudosymplanella nigrifasciata, Symplanella brevicephala, Symplanella unipuncta, Augilodes binghami, Cylindratus longicephalus, Caliscelis shandongensis, and Peltonotellus sp., were determined and comparatively analyzed. The genomes varied from 15,424 to 16,746 bp in size, comprising 37 mitochondrial genes and an A+T-rich region. The typical gene content and arrangement were similar to those of most Fulgoroidea species. The nucleotide compositions of the mitogenomes were biased toward A/T. All protein-coding genes (PCGs) started with a canonical ATN or GTG codon and ended with TAN or an incomplete stop codon, single T. Among 13 PCGs in 16 reported Caliscelidae mitogenomes, cox1 and atp8 showed the lowest and highest nucleotide diversity, respectively. All PCGs evolved under purifying selection, with atp8 considered a comparatively fast-evolving gene. Phylogenetic relationships were reconstructed based on 13 PCGs in 16 Caliscelidae species and five outgroups using maximum likelihood and Bayesian inference analyses. All species of Caliscelidae formed a steadily monophyletic group with high support. Peltonotellini was present at the basal position of the phylogenetic tree. Augilini was the sister group to Caliscelini and Peltonotellini.

Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest

Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.

Halyomorpha halys (Hemiptera: Pentatomidae) Genetic Diversity in North America and Europe

The brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae), is an invasive species in North America and Europe that damages many different host plants. Substantial work has been conducted on the genetic diversity and invasion pathways of H. halys in some of the countries where it has been found, based on mitochondrial sequences. The main objective of the present study was to further explore the genetic diversity of invasive populations of H. halys exploiting both mitochondrial and nuclear markers. We used two molecular markers: the mitochondrial Cytochrome Oxidase I (COI) gene, an ideal standardized molecular marker for distinguishing closely related species, and the ribosomal Internal Transcribed Spacer 1 (ITS1), because only a few sequences of H. halys exist to this point in global databases. We used specimens from eight populations from Greece, Italy, Canada, and the US. Among the 14 haplotypes retrieved based on the mtCOI gene, two of them (H162–H163) were detected for the first time. These two haplotypes were found in specimens from Canada, Italy, and the US. Concerning the ITS1 region, 24 haplotypes were identified, with 15 being unique for a sampled population. In Greece and the US, 14 and 12 haplotypes were found, respectively, with 7 and 6 of them being unique for Greece and the US, respectively. Our analysis of the nuclear genes of H. halys indicates high genetic diversity of the invading populations in North America and Europe.

Complete Mitochondrial Genome of Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) and Phylogenetic Analysis of Pentatomomorpha Species

Dinorhynchus dybowskyi (Hemiptera: Pentatomidae: Asopinae) is used as a biological control agent against various insect pests for its predatory. In the present study, the complete mitochondrial genome (mitogenome) of the species was sequenced using the next-generation sequencing technology. The results showed that the mitogenome is 15,952 bp long, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a control region. Furthermore, the gene order and orientation of this mitogenome are identical to those of most heteropterans. There are 21 intergenic spacers (of length 1-28 bp) and 13 overlapping regions (of length 1-23 bp) throughout the genome. The control region is 1,291 bp long. The start codon of the PCGs is ATN, except cox1 (TTG), and stop codon is TAA, except nad1 (TAG). The 22 tRNAs exhibit a typical cloverleaf secondary structure, except trnS1, which lacks a dihydrouridine (DHU) arm and trnV, where the DHU arm forms a simple loop. The analyses based on nucleotide sequences of the 13 PCGs by Bayesian Inference and maximum likelihood methods. The results support the monophyly of five superfamilies Aradoidea, Pentatomoidea, Pyrrhocoroidea, Lygaeoidea, and Coreoidea. Within Pentatomoidea, the relationship observed is as follows: (Plataspidae + Urostylididae) + (Pentatomidae + (Acanthosomatidae + (Cydnidae + (Scutelleridae + (Dinidoridae + Tessaratomidae))))), and D. dybowskyi was placed in Pentatomidae and close to Eurydema gebleri.

Application of RNA-seq for mitogenome reconstruction, and reconsideration of long-branch artifacts in Hemiptera phylogeny

Hemiptera make up the largest nonholometabolan insect assemblage. Despite previous efforts to elucidate phylogeny within this group, relationships among the major sub-lineages remain uncertain. In particular, mitochondrial genome (mitogenome) data are still sparse for many important hemipteran insect groups. Recent mitogenomic analyses of Hemiptera have usually included no more than 50 species, with conflicting hypotheses presented. Here, we determined the nearly complete nucleotide sequence of the mitogenome for the aphid species of Rhopalosiphum padi using RNA-seq plus gap filling. The 15,205 bp mitogenome included all mitochondrial genes except for trnF. The mitogenome organization and size for R. padi are similar to previously reported aphid species. In addition, the phylogenetic relationships for Hemiptera were examined using a mitogenomic dataset which included sequences from 103 ingroup species and 19 outgroup species. Our results showed that the seven species representing the Aleyrodidae exhibit extremely long branches, and always cluster with long-branched outgroups. This lead to the failure of recovering a monophyletic Hemiptera in most analyses. The data treatment of Degen-coding for protein-coding genes and the site-heterogeneous CAT model show improved suppression of the long-branch effect. Under these conditions, the Sternorrhyncha was often recovered as the most basal clade in Hemiptera.

The Complete Mitochondrial Genome of Mindarus keteleerifoliae (Insecta: Hemiptera: Aphididae) and Comparison with Other Aphididae Insects

The mitogenome of Mindarus keteleerifoliae Zhang (Hemiptera: Aphididae) is a 15,199 bp circular molecule. The gene order and orientation of M. keteleerifoliae is similarly arranged to that of the ancestral insect of other aphid mitogenomes, and, a tRNA isomerism event maybe identified in the mitogenome of M. keteleerifoliae. The tRNA-Trp gene is coded in the J-strand and the same sequence in the N-strand codes for the tRNA-Ser gene. A similar phenomenon was also found in the mitogenome of Eriosoma lanigerum. However, whether tRNA isomers in aphids exist requires further study. Phylogenetic analyses, using all available protein-coding genes, support Mindarinae as the basal position of Aphididae. Two tribes of Aphidinae were recovered with high statistical significance. Characteristics of the M. keteleerifoliae mitogenome revealed distinct mitogenome structures and provided abundant phylogenetic signals, thus advancing our understanding of insect mitogenomic architecture and evolution. But, because only eight complete aphid mitogenomes, including M. keteleerifoliae, were published, future studies with larger taxon sampling sizes are necessary.

Comparative mitogenomic analysis of the superfamily Pentatomoidea (Insecta: Hemiptera: Heteroptera) and phylogenetic implications

BACKGROUND

Insect mitochondrial genomes (mitogenomes) are the most extensively used genetic marker for evolutionary and population genetics studies of insects. The Pentatomoidea superfamily is economically important and the largest superfamily within Pentatomomorpha with over 7,000 species. To better understand the diversity and evolution of pentatomoid species, we sequenced and annotated the mitogenomes of Eurydema gebleri and Rubiconia intermedia, and present the first comparative analysis of the 11 pentatomoid mitogenomes that have been sequenced to date.

RESULTS

We obtained the complete mitogenome of Eurydema gebleri (16,005 bp) and a nearly complete mitogenome of Rubiconia intermedia (14,967 bp). Our results show that gene content, gene arrangement, base composition, codon usage, and mitochondrial transcription termination factor sequences are highly conserved in pentatomoid species, especially for species in the same family. Evolutionary rate analyses of protein-coding genes reveal that the highest and lowest rates are found in atp8 and cox1 and distinctive evolutionary patterns are significantly correlated with the G + C content of genes. We inferred the secondary structures for two rRNA genes for eleven pentatomoid species, and identify some conserved motifs of RNA structures in Pentatomidea. All tRNA genes in pentatomoid mitogenomes have a canonical cloverleaf secondary structure, except for two tRNAs (trnS1 and trnV) which appear to lack the dihydrouridine arm. Regions that are A + T-rich have several distinct characteristics (e.g. size variation and abundant tandem repeats), and have potential as species or population level molecular markers. Phylogenetic analyses based on mitogenomic data strongly support the monophyly of Pentatomoidea, and the estimated phylogenetic relationships are: (Urostylididae + (Plataspidae + (Pentatomidae + (Cydnidae + (Dinidoridae + Tessaratomidae))))).

CONCLUSIONS

This comparative mitogenomic analysis sheds light on the architecture and evolution of mitogenomes in the superfamily Pentatomoidea. Mitogenomes can be effectively used to resolve phylogenetic relationships of pentatomomorphan insects at various taxonomic levels. Sequencing more mitogenomes at various taxonomic levels, particularly from closely related species, will improve the annotation accuracy of mitochondrial genes, as well as greatly enhance our understanding of mitogenomic evolution and phylogenetic relationships in pentatomoids.

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

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

Hemipteran mitochondrial genomes: features, structures and implications for phylogeny

The study of Hemipteran mitochondrial genomes (mitogenomes) began with the Chagas disease vector, Triatoma dimidiata, in 2001. At present, 90 complete Hemipteran mitogenomes have been sequenced and annotated. This review examines the history of Hemipteran mitogenomes research and summarizes the main features of them including genome organization, nucleotide composition, protein-coding genes, tRNAs and rRNAs, and non-coding regions. Special attention is given to the comparative analysis of repeat regions. Gene rearrangements are an additional data type for a few families, and most mitogenomes are arranged in the same order to the proposed ancestral insect. We also discuss and provide insights on the phylogenetic analyses of a variety of taxonomic levels. This review is expected to further expand our understanding of research in this field and serve as a valuable reference resource.

Sequencing of the mitochondrial genome of the avocado lace bug Pseudacysta perseae (Heteroptera, Tingidae) using a genome skimming approach

Lace bugs (Tingidae) are a family of phytophagous heteropterans, some of which are important agricultural and forestry pests. They currently comprise around 2500 species distributed worldwide, for which only one mitochondrial genome has been described so far. We sequenced the complete mitochondrial genome and the nuclear ribosomal gene segment of the avocado lace bug Pseudacysta perseae using a genome skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including the one of the sycamore lace bug Corythucha ciliata, were retrieved to allow for comparisons and phylogenetic analyses. P. perseae mitochondrial genome was determined to be 15,850 bp long, and presented the typical organisation of insect mitogenomes. The phylogenetic analysis placed P. perseae as a sister to C. ciliata but did not confirm the monophyly of Miroidae including Tingidae. Our results contradicted widely accepted phylogenetic hypothesis, which highlights the limits of analyses based on mitochondrial data only. Shotgun sequencing approaches should provide substantial improvements in harmonizing mitochondrial and nuclear databases.

Shotgun assembly of the assassin bug Brontostoma colossus mitochondrial genome (Heteroptera, Reduviidae)

The complete mitochondrial genome of the assassin bug Brontostoma colossus (Distant, 1902) (Heteroptera: Reduviidae) has been sequenced using a genome-skimming approach on an Illumina Hiseq 2000 platform. Fifty-four additional heteropteran mitogenomes, including five assassin bug species, were retrieved to allow for comparisons and phylogenetic analyses. The mitochondrial genome of B. colossus was determined to be 16,625 bp long, and consists of 13 protein-coding genes (PCGs), 23 transfer-RNA genes (tRNAs), two ribosomal-RNA genes (rRNAs), and one control region. The nucleotide composition is biased toward adenine and thymine (A+T=73.4%). Overall, architecture, nucleotide composition and genome asymmetry are similar among all available assassin bug mitogenomes. All PCGs have usual start-codons (Met and Ile). Three T and two TA incomplete termination codons were identified adjacent to tRNAs, which was consistent with the punctuation model for primary transcripts processing followed by 3' polyadenylation of mature mRNA. All tRNAs exhibit the classic clover-leaf secondary structure except for tRNASer(AGN) in which the DHU arm forms a simple loop. Two notable features are present in the B. colossus mitogenome: (i) a 131 bp duplicated unit including the complete tRNAArg gene, resulting in 23 potentially functional tRNAs in total, and (ii) a 857 bp duplicated region comprising 277 bp of the srRNA gene and 580 bp of the control region. A phylogenetic analysis based on 55 true bug mitogenomes confirmed that B. colossus belongs to Reduviidae, but contradicted a widely accepted hypothesis. This highlights the limits of phylogenetic analyses based on mitochondrial data only.

The complete mitochondrial genome of Cervaphis quercus (Insecta: Hemiptera: Aphididae: Greenideinae)

The mitochondrial genome of Cervaphis quercus has been sequenced and annotated. The entire genome of 15,272 bp encodes two ribosomal RNA genes (rrnL and rrnS), 22 transfer RNA (tRNA) genes, 13 protein-coding genes and a control region. The genome has the same gene order as that found in the inferred ancestral insect. Nucleotide composition is highly A+T biased. All protein-coding genes use standard mitochondrial initiation codons. Secondary structure models of the two ribosomal RNA genes of C. quercus are similar to those proposed for other insects. All tRNAs have the classic clover-leaf structure, except for the dihydrouridine (DHU) arm of trnS (AGN), which forms a simple loop. The presence of structural elements in the control region is also discussed, with an emphasis on the possible regulation of replication and/or transcription. Comparison with mitochondrial genomes of other aphid species shows their gene arrangements are conserved; however, the variety of repeat regions in species from a different aphid subfamily, Aphidinae, suggests that they resulted from independent evolutionary events.

The complete mitochondrial genome sequence of Sogatella furcifera (Horváth) and a comparative mitogenomic analysis of three predominant rice planthoppers

The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the most destructive pests of rice crops in many Asian countries. Using long-PCR and shotgun library methods, we sequenced the entire mitochondrial genomes (mt-genomes) of two WBPH individuals. Total lengths of the mt-genome of the two WBPH individuals were 16,612 bp and 16,654 bp with an identical AT content of 76.19%. Among the 13 protein coding genes (PCGs), only nad5 used an atypical initiation codon GTG. Most of the tRNA genes had the typical cloverleaf secondary structure except that the dihydrouridine (DHU) arms in two trnS genes and the TΨC arm of trnG gene did not form a stable stem-loop structure. Similar to the brown planthopper (BPH), Nilaparvata lugens (Stål), and the small brown planthopper (SBPH), Laodelphax striatellus (Fallén), some extraordinary features were observed in the WBPH mt-genome. These include similar gene rearrangement pattern, unusually short length of the atp8 gene and variable numbers of tandem repeat (VNTR) structure in control region. Interestingly, the same tandem repeat unit with stable secondary structure appeared in two different planthoppers, WBPH and SBPH, which belong to two different genera of the Delphacidae. This peculiar feature provides a direct evidence for the close relationship between the two planthoppers and updates our understanding of the evolutionary characteristics of mitochondrial control region. Comparison with two other predominant rice planthoppers (BPH and SBPH) revealed that different PCGs of mitochondria exhibit different evolutionary patterns.

The complete mitochondrial genomes of two rice planthoppers, Nilaparvata lugens and Laodelphax striatellus: conserved genome rearrangement in Delphacidae and discovery of new characteristics of atp8 and tRNA genes

Background

Nilaparvata lugens (the brown planthopper, BPH) and Laodelphax striatellus (the small brown planthopper, SBPH) are two of the most important pests of rice. Up to now, there was only one mitochondrial genome of rice planthopper has been sequenced and very few dependable information of mitochondria could be used for research on population genetics, phylogeographics and phylogenetic evolution of these pests. To get more valuable information from the mitochondria, we sequenced the complete mitochondrial genomes of BPH and SBPH. These two planthoppers were infected with two different functional Wolbachia (intracellular endosymbiont) strains (wLug and wStri). Since both mitochondria and Wolbachia are transmitted by cytoplasmic inheritance and it was difficult to separate them when purified the Wolbachia particles, concomitantly sequencing the genome of Wolbachia using next generation sequencing method, we also got nearly complete mitochondrial genome sequences of these two rice planthoppers. After gap closing, we present high quality and reliable complete mitochondrial genomes of these two planthoppers.

Results

The mitogenomes of N. lugens (BPH) and L. striatellus (SBPH) are 17, 619 bp and 16, 431 bp long with A + T contents of 76.95% and 77.17%, respectively. Both species have typical circular mitochondrial genomes that encode the complete set of 37 genes which are usually found in metazoans. However, the BPH mitogenome also possesses two additional copies of the trnC gene. In both mitochondrial genomes, the lengths of the atp8 gene were conspicuously shorter than that of all other known insect mitochondrial genomes (99 bp for BPH, 102 bp for SBPH). That two rearrangement regions (trnC-trnW and nad6-trnP-trnT) of mitochondrial genomes differing from other known insect were found in these two distantly related planthoppers revealed that the gene order of mitochondria might be conservative in Delphacidae. The large non-coding fragment (the A+T-rich region) putatively corresponding responsible for the control of replication and transcription of mitochondria contained a variable number of tandem repeats (VNTRs) block in different natural individuals of these two planthoppers. Comparison with a previously sequenced individual of SBPH revealed that the mitochondrial genetic variation within a species exists not only in the sequence and secondary structure of genes, but also in the gene order (the different location of trnH gene).

Conclusion

The mitochondrial genome arrangement pattern found in planthoppers was involved in rearrangements of both tRNA genes and protein-coding genes (PCGs). Different species from different genera of Delphacidae possessing the same mitochondrial gene rearrangement suggests that gene rearrangements of mitochondrial genome probably occurred before the differentiation of this family. After comparatively analyzing the gene order of different species of Hemiptera, we propose that except for some specific taxonomical group (e.g. the whiteflies) the gene order might have diversified in family level of this order. The VNTRs detected in the control region might provide additional genetic markers for studying population genetics, individual difference and phylogeographics of planthoppers.

Mitochondrial genomes of two Barklice, Psococerastis albimaculata and Longivalvus hyalospilus (Psocoptera: Psocomorpha): contrasting rates in mitochondrial gene rearrangement between major lineages of Psocodea

The superorder Psocodea has ∼10,000 described species in two orders: Psocoptera (barklice and booklice) and Phthiraptera (parasitic lice). One booklouse, Liposcelis bostrychophila and six species of parasitic lice have been sequenced for complete mitochondrial (mt) genomes; these seven species have the most rearranged mt genomes seen in insects. The mt genome of a barklouse, lepidopsocid sp., has also been sequenced and is much less rearranged than those of the booklouse and the parasitic lice. To further understand mt gene rearrangements in the Psocodea, we sequenced the mt genomes of two barklice, Psococerastis albimaculata and Longivalvus hyalospilus, the first representatives from the suborder Psocomorpha, which is the most species-rich suborder of the Psocodea. We found that these two barklice have the least rearranged mt genomes seen in the Psocodea to date: a protein-coding gene (nad3) and five tRNAs (trnN, trnS1, trnE, trnM and trnC) have translocated. Rearrangements of mt genes in these two barklice can be accounted for by two events of tandem duplication followed by random deletions. Phylogenetic analyses of the mt genome sequences support the view that Psocoptera is paraphyletic whereas Phthiraptera is monophyletic. The booklouse, L. bostrychophila (suborder Troctomorpha) is most closely related to the parasitic lice. The barklice (suborders Trogiomorpha and Psocomorpha) are closely related and form a monophyletic group. We conclude that mt gene rearrangement has been substantially faster in the lineage leading to the booklice and the parasitic lice than in the lineage leading to the barklice. Lifestyle change appears to be associated with the contrasting rates in mt gene rearrangements between the two lineages of the Psocodea.

The complete mitochondrial genome of Dolycoris baccarum (Insecta: Hemiptera: Pentatomidae)

The complete mitochondrial genome (mitogenome) of Dolycoris baccarum (Hemiptera: Pentatomidae) has been sequenced and annotated in this study. This mitogenome is 16,549 bp in length with an A+T content of 73.4%, and contains the typical 37 genes that are arranged in the same order as that of the putative ancestor of hexapods. All protein-coding genes (PCGs) start with ATN codons except for cox1 that uses TTG as the initial codon. Eleven PCGs stop with termination codon TAA, and cox1 and cox2 have single T as the incomplete stop codon. All the transfer RNA genes have the typical clover leaf secondary structure, except for trnS1 (AGN) that lacks the dihydrouridine arm as known in many other metazoa. The control region is located between rrnS and trnI, and is composed of 479 bp of non-repeat region and 1401 bp of repeat region. This is the third completely sequenced mitogenome from the family Pentatomidae of Hemiptera.

The complete mitochondrial genome and novel gene arrangement of the unique-headed bug Stenopirates sp. (Hemiptera: Enicocephalidae)

Many of true bugs are important insect pests to cultivated crops and some are important vectors of human diseases, but few cladistic analyses have addressed relationships among the seven infraorders of Heteroptera. The Enicocephalomorpha and Nepomorpha are consider the basal groups of Heteroptera, but the basal-most lineage remains unresolved. Here we report the mitochondrial genome of the unique-headed bug Stenopirates sp., the first mitochondrial genome sequenced from Enicocephalomorpha. The Stenopirates sp. mitochondrial genome is a typical circular DNA molecule of 15, 384 bp in length, and contains 37 genes and a large non-coding fragment. The gene order differs substantially from other known insect mitochondrial genomes, with rearrangements of both tRNA genes and protein-coding genes. The overall AT content (82.5%) of Stenopirates sp. is the highest among all the known heteropteran mitochondrial genomes. The strand bias is consistent with other true bugs with negative GC-skew and positive AT-skew for the J-strand. The heteropteran mitochondrial atp8 exhibits the highest evolutionary rate, whereas cox1 appears to have the lowest rate. Furthermore, a negative correlation was observed between the variation of nucleotide substitutions and the GC content of each protein-coding gene. A microsatellite was identified in the putative control region. Finally, phylogenetic reconstruction suggests that Enicocephalomorpha is the sister group to all the remaining Heteroptera.

The complete mitochondrial genome of the damsel bug Alloeorhynchus bakeri (Hemiptera: Nabidae)

The complete sequence of the mitochondrial DNA (mtDNA) of the damsel bug, Alloeorhynchus bakeri, has been completed and annotated in this study. It represents the first sequenced mitochondrial genome of heteropteran family Nabidae. The circular genome is 15, 851 bp in length with an A+T content of 73.5%, contains the typical 37 genes that are arranged in the same order as that of the putative ancestor of hexapods. Nucleotide composition and codon usage are similar to other known heteropteran mitochondrial genomes. All protein-coding genes (PCGs) use standard initiation codons (methionine and isoleucine), except COI, which started with TTG. Canonical TAA and TAG termination codons are found in eight protein-coding genes, the remaining five (COI, COII, COIII, ND5, ND1) have incomplete termination codons (T or TA). PCGs of two strands present opposite CG skew which is also reflected by the nucleotide composition and codon usage. All tRNAs have the typical clover-leaf structure, except the dihydrouridine (DHU) arm of tRNA(Ser (AGN))which forms a simple loop as known in many other metazoa. Secondary structure models of the ribosomal RNA genes of A. bakeri are presented, similar to those proposed for other insect orders. There are six domains and 45 helices and three domains and 27 helices in the secondary structures of rrnL and rrnS, respectively. The major non-coding region (also called control region) between the small ribosomal subunit and the tRNA(Ile )gene includes two special regions. The first region includes four 133 bp tandem repeat units plus a partial copy of the repeat (28 bp of the beginning), and the second region at the end of control region contains 4 potential stem-loop structures. Finally, PCGs sequences were used to perform a phylogenetic study. Both maximum likelihood and Bayesian inference analyses highly support Nabidae as the sister group to Anthocoridae and Miridae.

The architecture and complete sequence of mitochondrial genome of an assassin bug Agriosphodrus dohrni (Hemiptera: Reduviidae)

The 16, 470 bp nucleotide sequence of the mitochondrial genome (mitogenome) of an assassin bug from the reduviid subfamily Harpactorinae, Agriosphodrus dohrni, has been revealed. The entire genome encodes for two ribosomal RNA genes (rrnL and rrnS), 22 transfer RNA (tRNA) genes, 13 protein-coding genes, and a control region. The nucleotide composition is biased toward adenine and thymine (A+T = 72.2%). Comparative analysis with two other reduviid species Triatoma dimidiata and Valentia hoffmanni, exhibited highly conserved genome architectures including genome contents, gene order, nucleotide composition, codon usage, amino acid composition, as well as genome asymmetry. All protein-coding genes use standard mitochondrial initiation codons (methionine and isoleucine), except that nad1 starts with GTG. All tRNAs have the classic clover-leaf structure, except that the dihydrouridine (DHU) arm of tRNA(Ser(AGN)) forms a simple loop. Secondary structure comparisons of the two mitochondrial ribosomal subunits among sequenced assassin bugs show that the sequence and structure of rrnL is more conservative than that of rrnS. The presence of structural elements in the control region is also discussed, with emphasis on their implications in the regulation of replication and/or transcription of the reduviid mitogenome. The phylogenetic analyses indicated that within Reduviidae, Harpactorinae is a sister group to the Salyavatinae + Triatominae clade.

Systematics and evolution of Heteroptera: 25 years of progress

Heteroptera, or true bugs, are part of the most successful radiation of nonholometabolous insects. Twenty-five years after the first review on the influence of cladistics on systematic research in Heteroptera, we summarize progress, problems, and future directions in the field. The few hypotheses on infraordinal relationships conflict on crucial points. Understanding relationships within Gerromorpha, Nepomorpha, Leptopodomorpha, Cimicomorpha, and Pentatomomorpha is improving, but progress within Enicocephalomorpha and Dipsocoromorpha is lagging behind. Nonetheless, the classifications of several superfamily-level taxa within the Pentatomomorpha, such as Aradoidea, Coreoidea, and Pyrrhocoroidea, are still unaffected by cladistic studies. Progress in comparative morphology is slow and drastically impedes our understanding of the evolution of major clades. Molecular systematics has dramatically contributed to accelerating the generation and testing of hypotheses. Given the fascinating natural history of true bugs and their status as model organisms for evolutionary studies, integration of cladistic analyses in a broader biogeographic and evolutionary context deserves increased attention.