Insights into the phylogeny of Hemiptera from increased mitogenomic taxon sampling

Ultraconserved elements from transcriptome and genome data provide insight into the phylogenomics of Sternorrhyncha (Insecta: Hemiptera)

Sternorrhyncha, one of the four major suborders of Hemiptera, is a phytophagous taxon inclusive of nearly 18 000 described species. The phylogenetic relationships within the taxon and the earliest-branching lineage of its infraorders remain incompletely understood. This study attempted to illuminate the phylogenetic relationships within Sternorrhyncha through the use of maximum likelihood, Bayesian inference and maximum parsimony analyses, employing ultraconserved element (UCE) data from 39 genomic and 62 transcriptomic datasets and thereby representing most families within the taxon. The probe set Hemiptera 2.7Kv1 was used to recover a total of 2731 UCE loci: from 547 to 1699 (with an average of 1084) across all genomic datasets and from 108 to 849 (with an average of 329) across all transcriptomic datasets. All three types of phylogenetic analyses employed in this study produced robust statistical support for Sternorrhyncha being a monophyletic group. The different methods of phylogenetic analysis produced inconsistent descriptions of topological structure at the infraorder level: while maximum likelihood and Bayesian inference analyses produced strong statistical evidence (100%) indicating the clade Psylloidea + Aleyrodoidea to be a sister of the clade Aphidoidea (Aphidomorpha) + Coccoidea (Coccomorpha), the maximum parsimony analysis failed to recover a similar result. Our results also provide detail on the phylogenetic relationships within each infraorder. This study presents the first use of UCE data to investigate the phylogeny of Sternorrhyncha. It also shows the viability of amalgamating genomic and transcriptomic data in studies of phylogenetic relationships, potentially highlighting a resource-efficient approach for future inquiries into diverse taxa through the integration of varied data sources.

Two new species of Erythroneurini (Hemiptera, Cicadellidae, Typhlocybinae) from southern China based on morphology and complete mitogenomes

Erythroneurine leafhoppers (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) are utilized to resolve the relationship between the four erythroneurine leafhopper (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini): Arboridia (Arboridia) rongchangensis sp. nov., Thaia (Thaia) jiulongensis sp. nov., Mitjaevia bifurcata Luo, Song & Song, 2021 and Mitjaevia diana Luo, Song & Song, 2021, the two new species are described and illustrated. The mitochondrial gene sequences of these four species were determined to update the mitochondrial genome database of Erythroneurini. The mitochondrial genomes of four species shared high parallelism in nucleotide composition, base composition and gene order, comprising 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and an AT control region, which was consistent with majority of species in Cicadellidae; all genes revealed common trait of a positive AT skew and negative GC skew. The mitogenomes of four species were ultra-conservative in structure, and which isanalogous to that of others in size and A + T content. Phylogenetic trees based on the mitogenome data of these species and another 24 species were built employing the maximum likelihood and Bayesian inference methods. The results indicated that the four species belong to the tribe Erythroneurini, M. diana is the sister-group relationship of M. protuberanta + M. bifurcata. The two species Arboridia (Arboridia) rongchangensis sp. nov. and Thaia (Thaia) jiulongensis sp. nov. also have a relatively close genetic relationship with the genus Mitjaevia.

Mitogenome of the stink bug Aelia fieberi (Hemiptera: Pentatomidae) and a comparative genomic analysis between phytophagous and predatory members of Pentatomidae

Aelia fieberi Scott, 1874 is a pest of crops. The mitogenome of A. fieberi (OL631608) was decoded by next-generation sequencing. The mitogenome, with 41.89% A, 31.70% T, 15.44% C and 10.97% G, is 15,471 bp in size. The phylogenetic tree showed that Asopinae and Phyllocephalinae were monophyletic; however, Pentatominae and Podopinae were not monophyletic, suggesting that the phylogenetic relationships of Pentatomoidae are complex and need revaluation and revision. Phytophagous bugs had a ~20-nucleotide longer in nad2 than predatory bugs. There were differences in amino acid sequence at six sites between phytophagous bugs and predatory bugs. The codon usage analysis indicated that frequently used codons used either A or T at the third position of the codon. The analysis of amino acid usage showed that leucine, isoleucine, serine, methionine, and phenylalanine were the most abundant in 53 species of Pentatomoidae. Thirteen protein-coding genes were evolving under purifying selection, cox1, and atp8 had the strongest and weakest purifying selection stress, respectively. Phytophagous bugs and predatory bugs had different evolutionary rates for eight genes. The mitogenomic information of A. fieberi could fill the knowledge gap for this important crop pest. The differences between phytophagous bugs and predatory bugs deepen our understanding of the effect of feeding habit on mitogenome.

First complete mitochondrial genome of the tribe Coccini (Hemiptera, Coccomorpha, Coccidae) and its phylogenetic implications

Soft scale insects (Hemiptera, Coccidae) are important pests of various agricultural and horticultural crops and ornamental plants. They have negative impacts on agriculture and forestry. The tribe Coccini represents one of the most ancient evolutionary lineages of soft scale insects. However, no complete Coccini mitochondrial genome (mitogenome) is available in public databases. Here, we described the complete mitogenome of Coccushesperidum L., 1758. The 15,566 bp mitogenome of C.hesperidum had a high A+T content (83.4%) and contained a typical set of 37 genes, with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Only seven tRNAs had the typical clover-leaf secondary structure and the remaining tRNAs lacked the DHU arm, TψC arm or both. Moreover, a comparative analysis of all reported scale insect mitogenomes from GenBank database was performed. The mitogenomes of scale insects showed high similarities in base composition and A+T content. Additionally, our phylogenetic analysis confirmed the monophyly of Coccomorpha and revealed that the archaeococcoids were the most basal lineage within Coccomorpha, while Ericeruspela and Didesmococcuskoreanus, belonging to Coccidae, were often mixed with Aclerdidae, making Coccidae a paraphyletic group. These findings expand the mitogenome database of scale insects and provide new insights on mitogenome evolution for future studies across different insect groups.

The First Complete Mitochondrial Genome of the Genus Pachycondyla (Formicidae, Ponerinae) and Insights into the Phylogeny of Ants

Ants are the standout group among eusocial insects in terms of their exceptional species richness and ecological dominance. The phylogenetic relationships among the group remain elusive. Mitochondrial genome sequences, as a kind of molecular marker, have been widely utilized in the phylogenetic analysis of insects. However, the number of ant mitogenomes published is still very limited. In this study, we utilized next-generation sequencing to determine the complete mitogenome of Pachycondyla annamita (Formicidae, Ponerinae). This is the first mitogenome from the genus Pachycondyla. Two gene rearrangements were identified in the mitogenome, the transposition of trnQ and trnM and the transposition of trnV and rrnS. The secondary structures of tRNAs were predicted. The tRNA genes trnR and trnS1 lacked the dihydrouridine (DHU) arm, and the trnE lacked the TΨC (T) arm. Phylogenetic analyses of the mitochondrial protein-coding genes under maximum likelihood (ML) and Bayesian inference (BI) criteria resulted in conflicting hypotheses. BI analysis using amino acid data with the site-heterogeneous mixture model produced a tree topology congruent with previous studies. The Formicidae was subdivided into two main clades, namely the "poneroid" clade and the "formicoid" clade. A sister group relationship between Myrmicinae and Formicinae was recovered within the "formicoid" clade.

Mitochondrial genomes of soft scales (Hemiptera: Coccidae): features, structures and significance

BACKGROUND

Soft scales (Hemiptera: Coccidae), including important agricultural and forestry pests, are difficult to identify directly by morphological characters. Mitochondrial genomes (mitogenomes) have been widely used in species identification and phylogenetic research. However, only three complete mitogenomes, and very few mitochondrial genes of scale insects (Hemiptera: Coccoidea) can be searched in GenBank. Mitogenome comparisons between scale insects or between scale insects and other hemipteran species have not yet been reported.

RESULTS

In this study, detailed annotation of three new mitogenomes and comparative analysis of scale insects were completed, as well as comparative analysis of the gene composition, gene arrangement, codon usage and evolutionary forces between scale insects and 488 other hemipteran species for the first time. We found that high A + T content, gene rearrangement and truncated tRNAs are common phenomena in soft scales. The average A + T content and codon usage bias of scale insects are higher and stronger than those of other hemipteran insects, respectively. The atp8 gene of Hemiptera and nine other protein-coding genes of scale insects are under positive selection with higher evolutionary rates.

CONCLUSIONS

The study revealed the particularity of the scale insect mitogenomes, which will provide a good reference for future research on insect phylogenetic relationships, insect pest control, biogeography and identification.

Revisiting the Phylogenetic Relationship and Evolution of Gargarini with Mitochondrial Genome (Hemiptera: Membracidae: Centrotinae)

In this study, we newly sequenced and analyzed the complete mitochondrial genomes of five genera and six species in Gargarini: Antialcidas floripennae, Centrotoscelus davidi, Kotogargara minuta, Machaerotypus stigmosus, Tricentrus fulgidus, and Tricentrus gammamaculatus. The mitochondrial genomes contain 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. The lengths of the mitochondrial genomes are 15,253 bp to 15,812 bp, and the AT contents of the obtained mitogenomes indicate a strong AT bias, ranging from 75.8% to 78.5%. The start codons of all PCGs show that most start with a typical ATN (ATA/T/G/C) codon and less start with T/GTG; the stop codon TAA is frequently used, and TAG and a single T are less used. In Gargarini mitogenomes, all tRNA genes can be folded into the canonical cloverleaf secondary structure, except for trnaS1, which lacks a stable dihydrouridine (DHU) stem and is replaced by a simple loop. At the same time, the phylogenetic analysis of the tribe Gargarini based on sequence data of 13 PCGs from 18 treehopper species and four outgroups revealed that the 10 Gargarini species form a steady group with strong support and form a sister group with Leptocentrini, Hypsauchenini, Centrotini, and Leptobelini. Diversification within Gargarini is distinguished by a Later Cretaceous divergence that led to the rapid diversification of the species. Moreover, the ancestral state reconstructions analysis showed the absence of the suprahumeral horn, which was confirmed as the ancestor characteristic of the treehopper, which has evolved from simple to complex. Our results shed new light specifically on the molecular and phylogenetic evolution of the pronotum in Gargarini.

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.

Enhanced Resolution of Evolution and Phylogeny of the Moths Inferred from Nineteen Mitochondrial Genomes

The vast majority (approximately 90%) of Lepidoptera species belong to moths whose phylogeny has been widely discussed and highly controversial. For the further understanding of phylogenetic relationships of moths, nineteen nearly complete mitochondrial genomes (mitogenomes) of moths involved in six major lineages were sequenced and characterized. These mitogenomes ranged from 15,177 bp (Cyclidia fractifasciata) to 15,749 bp (Ophthalmitis albosignaria) in length, comprising of the core 37 mitochondrial genes (13 protein-coding genes (PCGs) + 22 tRNAs + two rRNAs) and an incomplete control region. The order and orientation of genes showed the same pattern and the gene order of trnM-trnI-trnQ showed a typical rearrangement of Lepidoptera compared with the ancestral order of trnI-trnQ-trnM. Among these 13 PCGs, ATP8 exhibited the fastest evolutionary rate, and Drepanidae showed the highest average evolutionary rate among six families involved in 66 species. The phylogenetic analyses based on the dataset of 13 PCGs suggested the relationship of (Notodontidae + (Noctuidae + Erebidae)) + (Geometridae + (Sphingidae + Drepanidae)), which suggested a slightly different pattern from previous studies. Most groups were well defined in the subfamily level except Erebidae, which was not fully consistent across bayesian and maximum likelihood methods. Several formerly unassigned tribes of Geometridae were suggested based on mitogenome sequences despite a not very strong support in partial nodes. The study of mitogenomes of these moths can provide fundamental information of mitogenome architecture, and the phylogenetic position of moths, and contributes to further phylogeographical studies and the biological control of pests.

Comparison of mitogenomes of three Petalocephala species (Hemiptera: Cicadellidae: Ledrinae) and their phylogenetic analysis

Ledrinae is a unique group of leafhoppers with a distinct appearance. Petalocephala is the largest Ledrinae genus that is difficult to identify except by dissecting the male genitals. To date, research on Ledrinae is relatively less compared with other leafhoppers. Therefore, to better understand this group, we sequenced and analyzed three complete Petalocephala mitochondrial genomes. We comparatively analyzed these general Petalocephala genomic features (including size, AT content, AT/GC skew, 13 protein-coding gene nucleotide compositions, etc.), and predicted 22 transfer RNA secondary structures. We obtained highly consistent phylogenetic results within Cicadellidae based on mitogenomic data using the maximum likelihood and Bayesian methods. Our results showed that all subfamilies were monophyletic and had a high node support rate, and there was a sister group relationship between Ledrinae and all other leafhopper groups. Furthermore, treehoppers were found to originate from leafhoppers and showed sister group relationships with Megophthalminae. Within Ledrinae, all phylogenetic trees supporting phylogenetic relationships were as follows: ([P. dicondylica + P. gongshanensis] + [Tituria pyramidata + [Ledra auditura + P. gongshanensis]]) Based on the complete mitogenome phylogenetic analysis and the comparison of morphological characteristics, we propose that Petalocephala is not monophyletic.

Mitogenomic phylogeny of Typhlocybinae (Hemiptera: Cicadellidae) reveals homoplasy in tribal diagnostic morphological traits

The subfamily Typhlocybinae is a ubiquitous, highly diverse group of mostly tiny, delicate leafhoppers. The tribal classification has long been controversial and phylogenetic methods have only recently begun to test the phylogenetic status and relationships of tribes. To shed light on the evolution of Typhlocybinae, we performed phylogenetic analyses based on 28 newly sequenced and 19 previously sequenced mitochondrial genomes representing all currently recognized tribes. The results support the monophyly of the subfamily and its sister-group relationship to Mileewinae. The tribe Zyginellini is polyphyletic with some included genera derived independently within Typhlocybini. Ancestral character state reconstruction suggests that some morphological characters traditionally considered important for diagnosing tribes (presence/absence of ocelli, development of hind wing submarginal vein) are homoplastic. Divergence time estimates indicate that the subfamily arose during the Middle Cretaceous and that the extant tribes arose during the Late Cretaceous. Phylogenetic results support establishment of a new genus, Subtilissimia Yan & Yang gen. nov., with two new species, Subtilissimia fulva Yan & Yang sp. nov. and Subtilissimia pellicula Yan & Yang sp. nov.; but indicate that two previously recognized species of Farynala distinguished only by the direction of curvature of the processes of the aedeagus are synonyms, that is, Farynala dextra Yan & Yang, 2017 equals Farynala sinistra Yan & Yang, 2017 syn. nov. A key to tribes of Typhlocybinae is provided.

A New Sternorrhynchan Genus and Species from the Triassic Period of China That Is Likely Related to Protopsyllidioid (Insecta, Hemiptera)

Simple Summary

The new sternorrhynchan Triassopsyllidiida pectinata gen. et sp. nov. is described from the latest Middle Triassic Tongchuan biota of China. The phylogenetic relationships of the Protopsyllidioidea are discussed.

Abstract

Triassopsyllidiida pectinata gen. et sp. nov. is described from the latest Middle Triassic Tongchuan biota of China and tentatively attributed to the superfamily Protopsyllidioidea. Its forewing venation is unique among this superfamily in the anteriorly pectinate vein ScP + RA and the presence of a veinlet between R and M + CuA. Its exact position in this group remains uncertain, mainly because of the weak diagnostic value of the wing venation characters in these insects. The phylogenetic relationships of the Protopsyllidioidea are discussed.

Comparative Analysis of Mitochondrial Genomes among Twelve Sibling Species of the Genus Atkinsoniella Distant, 1908 (Hemiptera: Cicadellidae: Cicadellinae) and Phylogenetic Analysis

Simple Summary

Atkinsoniella is a large genus of 98 species across the world and 88 species recorded in China within the globally distributed subfamily Cicadellinae, which is phytophagous, and some of which have been reported as important agricultural pests. Some Atkinsoniella species are very similar in morphological characteristics, making accurate identification at species level confusing. To provide further evidence toward understanding the relationships within the genus Atkinsoniella and subfamily Cicadellinae, mitogenomes of 12 Atkinsoniella sibling species were obtained and annotated. Their characteristics were comparatively analyzed. In addition, the comprehensive phylogenetic relationship within the subfamily Cicadellinae was determined based on three mitochondrial datasets using both the maximum-likelihood (ML) and Bayesian inference (BI) methods. The results suggested that the genus Atkinsoniella was recovered as a monophyletic group. The branches of the 12 newly sequenced species were clearly separated, with most nodes receiving strong support in all analyses, indicating that mitogenomics is an effective method for identifying closely related species and understanding their phylogenetic and evolutionary relationships.

Abstract

The herbivorous leafhopper genus Atkinsoniella Distant, 1908 (Hemiptera: Cicadellidae: Cicadellinae), a large genus of subfamily Cicadellinae, consists of 98 valid species worldwide and 88 species recorded in China. Some species of the genus are very similar in morphological characteristics, so they are difficult to identify accurately. In this study, 12 mitochondrial genomes of Atkinsoniella species with similar morphological characteristics were first obtained through high-throughput sequencing, which featured a typical circular molecule of 15,034–15,988 bp in length. The arrangement and orientation of 37 genes were identical to those of typical Cicadellidae mitogenomes. The phylogenetic relationship within the subfamily Cicadellinae was reconstructed using maximum-likelihood (ML) and Bayesian inference (BI) methods based on three concatenated datasets. The topological structures of the six obtained phylogenetic trees were highly consistent. The results suggested that Atkinsoniella was recovered as a monophyletic group and emerged as a sister group with the monophyletic clade of Bothrogonia, Paracrocampsa (part), and Draeculacephala (part). The branches of the 12 newly sequenced species were clearly separated, with most nodes receiving strong support in all analyses. In addition, the key to the 12 Atkinsoniella species was provided to identify species according to morphological characteristics. This study further promotes research on the classification, genetics, evolution, and phylogeny of the genus Atkinsoniella and subfamily Cicadellinae.

Prey life-history influences the evolution of egg mass and indirectly reproductive investment in a group of free-living insect predators

The balance between risk and benefit of exploiting resources drives life-history evolution in organisms. Predators are naturally recognized as major drivers of the life-history evolution of their prey. Although prey may also influence the life-history evolution of their predators in the context of an evolutionary arms race, there is far more evidence of the role of predators than of prey.The goal of this study was to investigate the role of prey in life-history evolution of predators using ladybird beetle predators of aphids and coccids. These particular ladybirds and their prey were chosen because literature shows that the pace of life of aphids is faster than that of coccids and this difference is reflected in the life histories of the ladybirds that specialize on feeding on aphids or coccids.Thirty-four species of ladybird predators of aphids and eight of coccids belonging to five different tribes were collected and reared in the laboratory. The females were weighed as well as their eggs, and their reproductive investment estimated as the number of ovarioles. Phylogenetic relatedness was controlled for in the statistical analyses.Controlling for female mass revealed that ladybird predators of aphids lay bigger eggs than ladybird predators of coccids. This difference is not influenced by phylogenetic relatedness but only by the type of prey eaten. We suggest that ladybird predators of coccids lay smaller eggs because neonate larvae do not have to search, catch, and subdue prey. Both types of ladybirds have a similar reproductive investment relative to their body mass when phylogeny is controlled for.Recognizing the influence of prey on the life-history evolution of predators is important for understanding food web dynamics. From an applied perspective, this fine evolutionary tuning of prey-predator relationships should be used to guide and increase the efficiency of biological control programs.

Characterization of the morphology and complete mitochondrial genomes of Eupteryx minusula and Eupteryx gracilirama (Hemiptera: Cicadellidae: Typhlocybinae) from Karst area, Southwest China

Background

The hemipteran insect family Cicadellidae (leafhoppers) includes >2,600 valid genera and >22,000 valid species worldwide, including >2,000 species in China. Typhlocybinae, second largest subfamilies of Cicadellidae, is widely distributed in the six major zoogeographic regions of the world, including >4,000 species worldwide and >1,000 species in China. Previously, morphological analysis are often effective to the way of taxonomy, but it did not combine with molecular biology. Therefore, morphology and mitochondrial genomes (mitogenomes) of two leafhopper species, Eupteryx (Eupteryx) minusculaLindberg, 1929 and Eupteryx (Stacla) graciliramaHou, Zhang & Huang, 2016 were studied and analyzed. This study analyzed the morphological and molecular characteristics of the two leafhoppers, and showed whether the results of the two identifications were consistent.

Methods

Based on the method of comparison, mitogenomes and morphology were analyzed to prove the relationship between the two leafhoppers.

Results

Although two focal species are classified in two different subgenera of the same genus, they still share many morphological features, such as the moderately produced crown fore margin; the milky yellow apical part of scutellum; the pronotum, basal triangles of scutellum, and forewing are dark with several colorless patches on the surface; the light yellow face, without any spots or stripes, and so on. The circular mitogenomes are 16,944 bp long in E. minuscula (GenBank: MN910279) and 17,173 bp long in E. gracilirama (GenBank: MT594485). All of the protein-coding genes are starting with ATN, except for some in mitogenome, which has a single T or TAN as a stop codon. All tRNAs have the typical cloverleaf-shaped structure except for trnS1 (AGN) (E. minuscula) which has a reduced DHU arm. Moreover, these two mitogenomes have trnR with an unpaired base in the acceptor stem. The phylogenetic relationships between E. minuscula and E. gracilirama in respect to related lineages were reconstructed using Maximum likelihood and Maximum parsimony analyses.

Discussion

The result showed that the tribe Typhlocybini is a sister to the tribes Erythroneurini and Empoascini, and five genera, Bolanusoides, Typhlocyba, Eupteryx, Zyginella and Limassolla are forming a single clade. E. minuscula and E. gracilirama are clustered together, supporting the monophyly of the genus Eupteryx. The above conclusions are consistent with the traditional classification of the subfamily.

Nine Mitochondrial Genomes of the Pyraloidea and Their Phylogenetic Implications (Lepidoptera)

Simple Summary

The Pyraloidea is a large superfamily of Lepidoptera in species composition. To date, the higher-level phylogenetic relationships in this group remain unresolved, and many taxa, with taxonomic positions historically established by morphological characters, need to be confirmed through sequencing of DNA, including mitochondrial genome sequences (mitogenomes). Here, we newly generated nine complete mitogenomes for Pyraloidea that shared identical gene content, and arrangements that are typical of Lepidoptera. The current phylogenetic results confirmed previous multilocus studies, indicating the effectiveness of mitogenomes for inference of Pyraloidea higher-level relationships. Unexpectedly, Orybina Snellen was robustly placed as basal to the remaining Pyralidae taxa, rather than nested in the Pyralinae of Pyralidae as morphologically defined and placed. Our results bring a greater understanding to Pyraloidea phylogeny, and highlight the necessity of sequencing more pyraloid taxa to reevaluate their phylogenetic positions.

Abstract

The Pyraloidea is one of the species-rich superfamilies of Lepidoptera and contains numerous economically important pest species that cause great loss in crop production. Here, we sequenced and annotated nine complete mitogenomes for Pyraloidea, and further performed various phylogenetic analyses, to improve our understanding of mitogenomic evolution and phylogeny of this superfamily. The nine mitogenomes were circular, double-stranded molecules, with the lengths ranging from 15,214 bp to 15,422 bp, which are comparable to other reported pyraloid mitogenomes in size. Gene content and arrangement were highly conserved and are typical of Lepidoptera. Based on the hitherto most extensive mitogenomic sampling, our various resulting trees showed generally congruent topologies among pyraloid subfamilies, which are almost in accordance with previous multilocus studies, indicating the suitability of mitogenomes in inferring high-level relationships of Pyraloidea. However, nodes linking subfamilies in the “non-PS clade” were not completely resolved in terms of unstable topologies or low supports, and future investigations are needed with increased taxon sampling and molecular data. Unexpectedly, Orybina Snellen, represented in a molecular phylogenetic investigation for the first time, was robustly placed as basal to the remaining Pyralidae taxa across our analyses, rather than nested in Pyralinae of Pyralidae as morphologically defined. This novel finding highlights the need to reevaluate Orybina monophyly and its phylogenetic position by incorporating additional molecular and morphological evidence.

Characterization of the complete mitochondrial genome of Myrmuslateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmuslateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (-0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M.lateralis and Chorosomamacilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

The mitochondrial genomes of Tortricidae: nucleotide composition, gene variation and phylogenetic performance

BACKGROUND

Mitochondrial genomes (mitogenomes) have greatly improved our understanding of the backbone phylogeny of Lepidoptera, but few studies on comparative mitogenomics below the family level have been conducted. Here, we generated 13 mitogenomes of eight tortricid species, reannotated 27 previously reported mitogenomes, and systematically performed a comparative analysis of nucleotide composition, gene variation and phylogenetic performance.

RESULTS

The lengths of completely sequenced mitogenomes ranged from 15,440 bp to 15,778 bp, and the gene content and organization were conserved in Tortricidae and typical for Lepidoptera. Analyses of AT-skew and GC-skew, the effective number of codons and the codon bias index all show a base bias in Tortricidae, with little heterogeneity among the major tortricid groups. Variations in the divergence rates among 13 protein-coding genes of the same tortricid subgroup and of the same PCG among tortricid subgroups were detected. The secondary structures of 22 transfer RNA genes and two ribosomal RNA genes were predicted and comparatively illustrated, showing evolutionary heterogeneity among different RNAs or different regions of the same RNA. The phylogenetic uncertainty of Enarmoniini in Tortricidae was confirmed. The synonymy of Bactrini and Olethreutini was confirmed for the first time, with the representative Bactrini consistently nesting in the Olethreutini clade. Nad6 exhibits the highest phylogenetic informativeness from the root to the tip of the resulting tree, and the combination of the third coding positions of 13 protein-coding genes shows extremely high phylogenetic informativeness.

CONCLUSIONS

This study presents 13 mitogenomes of eight tortricid species and represents the first detailed comparative mitogenomics study of Tortricidae. The results further our understanding of the evolutionary architectures of tortricid mitogenomes and provide a basis for future studies of population genetics and phylogenetic investigations in this group.

Structural features of the mitogenome of the leafhopper genus Cladolidia (Hemiptera: Cicadellidae: Coelidiinae) and phylogenetic implications in Cicadellidae

The first two complete mitogenomes of the leafhopper genus Cladolidia (C. biungulata and C. robusta) were sequenced and annotated to further explore the phylogeny of Cladolidia. Both the newly sequenced mitogenomes have a typical circular structure, with lengths of 15,247 and 15,376 bp and A + T contents of 78.2% and 78%, respectively. We identified a highly conserved genome organization in the two Cladolidia spp. through comparative analysis that included the following assessments: genome content, gene order, nucleotide composition, codon usage, amino acid composition, and tRNA secondary structure. Moreover, we detected the base heterogeneity of Cicadellidae mitogenomic data and constructed phylogenetic trees using the nucleotide alignments of 12 subfamilies of 58 leafhopper species. We noted a weak heterogeneity in the base composition among the Cicadellidae mitogenomes. Phylogenetic analyses showed that the monophyly of each subfamily was generally well supported in the family Cicadellidae; the main topology was as follows: (Deltocephalinae + (Treehoppers + ((Megophthalminae + (Macropsinae + (Hylicinae + (Coelidiinae +Iassinae)) + (Idiocerinae + (Cicadellinae + (Typhlocybinae + (Mileewinae + (Evacanthinae +Ledrinae)))))))))). Within Coelidiinae, phylogenetic analyses revealed that C. biungulata and C. robusta belong to Coelidiinae and the monophyly of Cladolidia is well supported. In addition, on the basis of complete mitogenome phylogenetic analysis and the comparison of morphological characteristics, we further confirm the genus Olidiana as a paraphyletic group, suggesting that the genus may need taxonomic revisions.

Mitogenomics of Cladocera (Branchiopoda): Marked gene order rearrangements and independent predation roots

Cladocera (Crustacea: Branchiopoda) is a key group of invertebrates. Despite a long history of phylogenetic research, relationships within this group remain disputed. We here provide new insights based on 15 new mitochondrial genomes obtained from high-throughput sequencing (HTS) and 40 mitogenomes extracted from published HTS datasets. Together with 25 mitogenomes from GenBank, we generated a matrix of 80 mitogenomes, 44 of them belonging to Cladocera. We also obtained a matrix with 168 nuclear orthologous genes to further assess the phylogenetic result from mitogenomes based on published data and one new HTS data ofLeptodora. Maximum likelihood and Bayesian phylogenetic analyses recovered all Branchiopoda orders as monophyletic and supported a sister-group relationship between Anomopoda and Onychopoda, making the taxon Gymnomera paraphyletic and supporting an independent origin of predatory Haplopoda and Onychopoda. The nuclear phylogeny and topological tests also support Gymnomera as paraphyletic, and the nuclear phylogeny strongly supports a sister-group relationship between Ctenopoda and Haplopoda. We provide a fossil-calibrated time tree, congruent with a Carboniferous origin for Cladocera and a subsequent diversification of the crown group of Anomopoda, Onychopoda, and Ctenopoda, at least in the Triassic. Despite their long evolutionary history, non-Cladoceran Branchiopoda exhibited high mitogenome structural stability. On the other hand, 21 out of 24 gene rearrangements occurred within the relatively younger Cladocera. We found the differential base compositional skewness patterns between Daphnia s.s. and Ctenodaphnia, which might be related to the divergence between these taxa. We also provide evidence to support the recent finding that Spinicaudata possesses mitogenomes with inversed compositional skewness without gene rearrangement. Such a pattern has only been reported in Spinicaudata.

External structures of the metathoracic scent gland efferent system in the true bug superfamily Pyrrhocoroidea (Hemiptera: Heteroptera: Pentatomomorpha)

Pyrrhocoroidea represents an important group of true bugs (Insecta: Hemiptera: Heteroptera) which includes fire bugs, cotton stainers and other taxa widely used in experimental studies or known as pests. However, the morphology and phylogeny of Pyrrhocoroidea have been only poorly studied so far. Here, structures of the external scent efferent system of the metathoracic scent glands are examined in 64 out of 71 currently valid genera of Pyrrhocoroidea and scanning electron micrographs are provided for most taxa. Several characters are revealed which define each of the three higher taxa within Pyrrhocoroidea: Larginae (small auriculate peritreme lacking manubrium and median furrow; metathoracic spiracle never surrounded by evaporatorium), Physopeltinae (large, widely open ostiole; large peritremal disc with manubrium [new term], lacking median furrow; mace-like mycoid filter processes of equal shape and size on both anterior and posterior margins of metathoracic spiracle), and Pyrrhocoridae (elongate auriculate peritreme with deep median furrow). Within Pyrrhocoridae, three main types (A, B and C) of the external scent efferent system are distinguished, differring in the amount of reductions. The findings are interpreted in the context of phylogenetic hypotheses available for Pyrrhocoroidea and their close relatives, Coreoidea and Lygaeoidea. An updated identification key to the families and subfamilies of Pyrrhocoroidea applicable for both sexes is provided.

Characterization of Three Complete Mitogenomes of Flatidae (Hemiptera: Fulgoroidea) and Compositional Heterogeneity Analysis in the Planthoppers' Mitochondrial Phylogenomics

Although sequences of mitogenomes have been widely used for investigating phylogenetic relationship, population genetics, and biogeography in many members of Fulgoroidea, only one complete mitogenome of a member of Flatidae has been sequenced. Here, the complete mitogenomes of Cerynia lineola, Cromna sinensis, and Zecheuna tonkinensis are sequenced. The gene arrangements of the three new mitogenomes are consistent with ancestral insect mitogenomes. The strategy of using mitogenomes in phylogenetics remains in dispute due to the heterogeneity in base composition and the possible variation in evolutionary rates. In this study, we found compositional heterogeneity and variable evolutionary rates among planthopper mitogenomes. Phylogenetic analysis based on site-homogeneous models showed that the families (Delphacidae and Derbidae) with high values of Ka/Ks and A + T content tended to fall together at a basal position on the trees. Using a site-heterogeneous mixture CAT + GTR model implemented in PhyloBayes yielded almost the same topology. Our results recovered the monophyly of Fulgoroidea. In this study, we apply the heterogeneous mixture model to the planthoppers’ phylogenetic analysis for the first time. Our study is based on a large sample and provides a methodological reference for future phylogenetic studies of Fulgoroidea.

Mitogenomics of five Olidiana leafhoppers (Hemiptera: Cicadellidae: Coelidiinae) and their phylogenetic implications

Similar morphological characteristics and limited molecular data of Olidiana resulted in their unknown phylogenetic statuses and equivocal relationships. To further understand the genus Olidiana, we sequenced and annotated five Olidiana complete mitochondrial genomes (mitogenomes). Our results show that Olidiana mitogenomes range from 15,205 bp to 15,993 bp in length and include 37 typical genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and a control region. Their nucleotide composition, codon usage, features of control region, and tRNA secondary structures are similar to other members of Cicadellidae. We constructed the phylogenetic tree of Cicadellidae using the maximum likelihood (ML) and Bayesian inference (BI) methods based on all valid mitogenome sequences. The most topological structure of the obtained phylogenetic tree is consistent. Our results support the monophyletic relationships among 10 subfamilies within Cicadellidae and confirm Iassinae and Coelidiinae to be sister groups with high approval ratings. Interestingly, Olidiana was inferred as a paraphyletic group with strong support via both ML and BI analyses. These complete mitogenomes of five Olidiana species could be useful in further studies for species diagnosis, evolution, and phylogeny research within Cicadellidae.

Higher-level phylogenetic relationships of rove beetles (Coleoptera, Staphylinidae) inferred from mitochondrial genome sequences

Rove beetles (Staphylinidae) and allied families constitute a huge radiation of Coleoptera, but basal relationships in this group remain controversial. In this study, we newly sequenced eight mitogenomes of representatives of Staphylinidae by using next-generation sequencing method. Together with 99 existing mitogenomes of Staphyliniformia, (sub)family relationships were investigated with ML and Bayesian searches under various substitution models and data recoding schemes. The results consistently supported Scydmaenidae and Silphidae to be subordinate groups of Staphylinidae. Within the monophyletic Staphylinidae (including Scydmaenidae and Silphidae), the hypothesis of four major subfamily groups cannot be confirmed. Bayesian inferences under the site-heterogeneous mixture model generally supported the basal position of major clades corresponding to the Omaliine group. At the subfamily level, the monophyly of Pselaphinae, Oxytelinae, Scaphidiinae, Steninae and Staphylininae was supported. However, the subfamilies Omaliinae, Tachyporinae, Aleocharinae and Paederinae were each non-monophyletic.

The Complete Mitochondrial Genome of Four Hylicinae (Hemiptera: Cicadellidae): Structural Features and Phylogenetic Implications

To reveal mtgenome characterizations and reconstruct phylogenetic relationships of Hylicinae, the complete mtgenomes of four hylicine species, including Nacolus tuberculatus, Hylica paradoxa, Balala fujiana, and Kalasha nativa, were sequenced and comparatively analyzed for the first time. We also carried out the richest (11) subfamily sampling of Cicadellidae to date, and reconstructed phylogenetic relationships of Membracoidea among 61 species based on three datasets using maximum likelihood and Bayesian inference analyses. All new sequenced mtgenomes are molecules ranging from 14,918 to 16,221 bp in length and are double stranded, circular in shape. The gene composition and arrangement of these mtgenomes are consistent with members of Membracoidea. Among 13 protein-coding genes, most show typical ATN start codons and TAR (TAA/TAG) or an incomplete stop codon T-, and several genes start by TTG/GTG. Results of the analysis for sliding window, nucleotide diversity, and nonsynonymous substitution/synonymous substitution indicate cox1 is a comparatively slower-evolving gene while atp8 is the fastest gene. In line with previous researches, phylogenetic results indicate that treehopper families are paraphyletic with respect to family Cicadellidae and also support the monophyly of all involved subfamilies including Hylicinae. Relationships among the four hylicine genera were recovered as (Hylica + (Nacolus + (Balala + Kalasha))).

Characterization of Two Complete Mitochondrial Genomes of Ledrinae (Hemiptera: Cicadellidae) and Phylogenetic Analysis

Mitochondrial genomes are widely used for investigations into phylogeny, phylogeography, and population genetics. More than 70 mitogenomes have been sequenced for the diverse hemipteran superfamily Membracoidea, but only one partial and two complete mtgenomes mitochondrial genomes have been sequenced for the included subfamily Ledrinae. Here, the complete mitochondrial genomes (mitogenomes) of two additional Ledrinae species are newly sequenced and comparatively analyzed. Results show both mitogenomes are circular, double-stranded molecules, with lengths of 14,927 bp (Tituria sagittata) and 14,918 bp (Petalocephala chlorophana). The gene order of these two newly sequenced Ledrinae is highly conserved and typical of members of Membracoidea. Similar tandem repeats in the control region were discovered in Ledrinae. Among 13 protein-coding genes (PCGs) of reported Ledrinae mitogenomes, analyses of the sliding window, nucleotide diversity, and nonsynonymous substitution (Ka)/synonymous substitution (Ks) indicate atp8 is a comparatively fast-evolving gene, while cox1 is the slowest. Phylogenetic relationships were also reconstructed for the superfamily Membracoidea based on expanded sampling and gene data from GenBank. This study shows that all subfamilies (sensu lato) are recovered as monophyletic. In agreement with previous studies, these results indicate that leafhoppers (Cicadellidae) are paraphyletic with respect to the two recognized families of treehoppers (Aetalionidae and Membracidae). Relationships within Ledrinae were recovered as (Ledra + (Petalocephala + Tituria)).

The Phylogenetic Implications of the Mitochondrial Genomes of Macropsis notata and Oncopsis nigrofasciata

Macropsinae are forest pests that feed on woody plants. They can damage the growth of trees and crops, and some species can also spread plant pathogens. Due to their widespread effects, these leafhoppers are of great economic significance, which is why there is a need to study their genomes. To fill the gap in the mitochondrial genomic data of the subfamily Macropsinae, we sequenced the complete mitochondrial genomes of Macropsis notata and Oncopsis nigrofasciata (which were 16,323 and 15,927 bp long, respectively). These two species are representative species of the leafhoppers group (Cicadellidae); the mitochondrial genomes of these species range from a length of 15,131 bp (Trocnadella arisana) to 16,811 bp (Parocerus laurifoliae). Both mitogenomes contained 37 typical insect mitochondrial genes and a control region; there were no long non-coding sequences. The genes within the mitogenome were very compact. The mitogenomes from both species contained two kinds of parallel repeat units in the control region. The whole mitogenomes of Macropsinae showed a heavy AT nucleotide bias (M. notata 76.8% and O. nigrofasciata 79.0%), a positive AT Skew (0.15 and 0.12), and a negative GC Skew (-0.14 and -0.08). Upon comparative ML and BI analysis, some clade relationships were consistent among the six trees. Most subfamilies were reconstructed into monophyletic groups with strong support in all analyses, with the exception of Evacanthinae and Cicadellinae. Unlike the results of previous research, it was shown that although all Deltocephalinae species are grouped into one clade, they were not the sister group to all other leafhoppers. Further, Cicadellinae and Evacanthinae were occasionally reconstructed as a polyphyletic and a paraphyletic group, respectively, possibly due to the limited numbers of samples and sequences. This mitogenome information for M. notata and O. nigrofasciata could facilitate future studies on the mitogenomic diversity and evolution of the related Membracoidea, and eventually help to control their effects on plants for the betterment of society at large.

The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes

A number of species in Bipolaris are important plant pathogens. Due to a limited number of synapomorphic characters, it is difficult to perform species identification and to estimate phylogeny of Bipolaris based solely on morphology. In this study, we sequenced the complete mitochondrial genome of Bipolaris sorokiniana, and presented the detailed annotation of the genome. The B. sorokiniana mitochondrial genome is 137,775 bp long, and contains two ribosomal RNA genes, 12 core protein-coding genes, 38 tRNA genes. In addition, two ribosomal protein genes (rps3 gene and rps5 gene) and the fungal mitochondrial RNase P gene (rnpB) are identified. The large genome size is mostly determined by the presence of numerous intronic and intergenic regions. A total of 28 introns are inserted in eight core protein-coding genes. Together with the published mitochondrial genome sequences, we conducted a preliminary phylogenetic inference of Dothideomycetes under various datasets and substitution models. The monophyly of Capnodiales, Botryosphaeriales and Pleosporales are consistently supported in all analyses. The Venturiaceae forms an independent lineage, with a distant phylogenetic relationship to Pleosporales. At the family level, the Mycosphaerellaceae, Botryosphaeriaceae. Phaeosphaeriaceae, and Pleosporaceae are recognized in the majority of trees.

Phylomitogenomic analyses on collembolan higher taxa with enhanced taxon sampling and discussion on method selection

Collembola are a basal group of Hexapoda renowned for both unique morphological characters and significant ecological roles. However, a robust and plausible phylogenetic relationship between its deeply divergent lineages has yet to be achieved. We carried out a mitophylogenomic study based on a so far the most comprehensive mitochondrial genome dataset. Our data matrix contained mitogenomes of 31 species from almost all major families of all four orders, with 16 mitogenomes newly sequenced and annotated. We compared the linear arrangements of genes along mitochondria across species. Then we conducted 13 analyses each under a different combination of character coding, partitioning scheme and heterotachy models, and assessed their performance in phylogenetic inference. Several hypothetical tree topologies were also tested. Mitogenomic structure comparison revealed that most species share the same gene order of putative ancestral pancrustacean pattern, while seven species from Onychiuridae, Poduridae and Symphypleona bear different levels of gene rearrangements, indicating phylogenetic signals. Tomoceroidea was robustly recovered for the first time in the presence of all its families and subfamilies. Monophyly of Onychiuroidea was supported using unpartitioned models alleviating LBA. Paronellidae was revealed polyphyletic with two subfamilies inserted independently into Entomobryidae. Although Entomobryomorpha has not been well supported, more than half of the analyses obtained convincing topologies by placing Tomoceroidea within or near remaining Entomobryomorpha. The relationship between elongate-shaped and spherical-shaped collembolans still remained ambiguous, but Neelipleona tend to occupy the basal position in most trees. This study showed that mitochondrial genomes could provide important information for reconstructing the relationships among Collembola when suitable analytical approaches are implemented. Of all the data refining and model selecting schemes used in this study, the combination of nucleotide sequences, partitioning model and exclusion of third codon positions performed better in generating more reliable tree topology and higher node supports than others.

Comparative mitogenomes of six species in the subfamily Iassinae (Hemiptera: Cicadellidae) and phylogenetic analysis

For elucidating phylogenetic relationships among members of the family Cicadellidae, mitogenomes of six members of the subfamily Iassinae, including Batracomorphus lateprocessus, Iassus dorsalis, Krisna concava, Krisna rufimarginata, Gessius rufidorsus, and Trocnadella arisana, were sequenced. The mitogenomes are 14,724-15,356-bp long. Moreover, typical 37 genes in mitogenomes were identified; arrangement of these genes in the studied species was consistent with that in the inferred ancestral insects, except for tRNA genes, with a simple switch between the positions of trnI and trnQ in Trocnadella arisana. Most protein-coding genes in the Iassinae mitogenomes showed typical ATN start codons (ATA/ATT/ATC/ATG) and TAR (TAA/TAG) or an incomplete stop codon T--; ATP8 of all sequenced species showed the start codon TTG. The secondary structures of 16S rRNA and 12S rRNA were predicted. 16S rRNA comprised 6 domains with 43 helices, and 12S rRNA comprised 3 domains with 25 helices. All subfamilies, except Cicadellinae and Evacanthinae, were recovered as monophyletic. As reported previously, treehoppers originated from paraphyletic Cicadellidae. Iassinae and Coelidiinae, Megophthalminae and treehoppers, and Cicadellinae and Evacanthinae were sister groups with high nodal support.

Mitochondrial genome of Bolanusoides shaanxiensis (Cicadellidae: Typhlocybinae: Typhlocybini), with its phylogenetic analysis

The mitochondrial genome of one leafhopper species Bolanusoides shaanxiensis was sequenced and annotated. The mitogenome is 15,724 bp in length, containing 37 typical genes and a control region. The A + T content of the whole mitogenome is 78.9%. Most of PCGs started with ATN and stopped with TAA, except for ATP8 started with TTG, COX2, COX3 and ND5 used incomplete T as stop codon. The phylogeny tree is monophyletic among 31 related species. The relationships of B. shaanxiensis and Typhlocyba sp. were closer than others. This study further enriched mitogenome database of the tribe Typhlocybini.