Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversity analysis using mito-metagenomics

Structures and genetic information of control region in mitogenomes of Odonata

Mitogenome data of Odonata is accumulating and widely used in phylogenetic analysis. However, noncoding regions, especially control region, were usually omitted from the phylogenetic reconstruction. In an effort to uncover the phylogenetic insights offered by the control region, we have amassed 65 Odonata mitogenomes and conducted an examination of their control regions. Our analysis discovered that species belonging to Anisoptera and Anisozygoptera exhibited a stem-loop structure, which was formed by a conserved polyC-polyG stretch located near the rrns gene (encoding 12S rRNA). Conversely, the polyC-polyG region was not a conserved fragment in Zygoptera. The length and number of repetitions within the control region were identified as the primary determinants of its overall length. Further, sibling species within Odonata, particularly those in the genus Euphaea, displayed similar patterns of repetition in their control region. Collectively, our research delineates the structural variations within the control region of Odonata and suggests the potential utility of this region in elucidating phylogenetic relationships among closely related species.

Drawing mitochondrial genomes with circularMT

SUMMARY

Mitochondrial DNA sequences are used extensively in phylogeographic and phylogenetic studies for a wide range of organisms. With the advent of low-cost, high throughput 'next generation' DNA sequencing, and user-friendly bioinformatics pipelines for generating and annotating whole mitochondrial genome assemblies, the analysis of whole mitochondrial genomes has become an important component of phylogenomic studies for taxa with high species diversity but limited coverage for other genomic resources. An important step in characterizing de novo mitochondrial genome assemblies is to evaluate and describe structural rearrangements relative to reference taxa. Accessible tools are needed to help visualize gene and noncoding feature complement, their order and strand orientation. However, there are few dedicated applications that generate high quality genome diagrams. Here we present circularMT and circularMT-console that allow users to create highly customizable, publication quality images, of linear and circular mitochondrial genome maps, either individually, or integrated into an analysis pipeline.

AVAILABILITY AND IMPLEMENTATION

Both applications are implemented in C#, with binaries, source code and user guides available on GitHub (https://github.com/msjimc/circularMT). An archive of the published version is available on Zenodo (https://zenodo.org/records/10912319).

SUPPLEMENTARY INFORMATION

This paper has no supplementary data.

Complete mitochondrial genome of the Minois paupera Alphéraky, 1888 (nymphalidae: satyrinae) and its phylogenetic analysis

The present study firstly reported a complete mitochondrial genome of Minois paupera (Alphéraky, 1888), a Satyrinae species endemic to China. This mitogenome is circular, 15,213 bp in length, and consists of 37 typical mitochondrial genes, including 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. The phylogenetic position was inferred using 31 previously published complete mitogenomes, and the results reveal that M. paupera is the most closely related to Minois dryas. The complete mitogenome of M. paupera provides useful genetic information for further research on the phylogeography and phylogeny of the genus Minois.

The complete mitochondrial genome of Sigara lateralis (Leach, 1817) (Nepomorpha: Corixidae)

The Sigara lateralis (Leach, 1817) is a small aquatic insect belonging to the family Corixidae. The study aims to reveal the genomic data of the mitochondrial genome of S. lateralis. The length of its circular mitochondrial genome is 15,725 bp long with an A + T bias (75.96%). The mitogenome comprises 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two rRNA genes. The phylogenetic analyses showed that the S. lateralis is the closest to S. septemlineata. These findings will help the conservation of Corixidae from the perspective of genetic evolution.

Complete Mitochondrial Genomes and Phylogenetic Analysis of Genus Henricia (Asteroidea: Spinulosida: Echinasteridae)

The genus Henricia is known to have intraspecific morphological variations, making species identification difficult. Therefore, molecular phylogeny analysis based on genetic characteristics is valuable for species identification. We present complete mitochondrial genomic sequences of Henricia longispina aleutica, H. reniossa, and H. sanguinolenta for the first time in this study. This study will make a significant contribution to our understanding of Henricia species and its relationships within the class Asteroidea. Lengths of mitochondrial genomes of the three species are 16,217, 16,223, and 16,194 bp, respectively, with a circular form. These genomes contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a D-loop. The gene order and direction aligned with other asteroid species. Phylogenetic relationship analysis showed that our Henricia species were in a monophyletic clade with other Henricia species and in a large clade with species (Echinaster brasiliensis) from the same family. These findings provide valuable insight into understanding the phylogenetic relationships of species in the genus Henricia.

A New Species of Scymnus (Coleoptera, Coccinellidae) from Pakistan with Mitochondrial Genome and Its Phylogenetic Implications

In this study, a new species of the subgenus Pullus belonging to the Scymnus genus from Pakistan, Scymnus (Pullus) cardi sp. nov., was described and illustrated, with information on its distribution, host plants, and prey. Additionally, the completed mitochondrial genome (mitogenome) of the new species using high-throughput sequencing technology was obtained. The genome contains the typical 37 genes (13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs) and a non-coding control region, and is arranged in the same order as that of the putative ancestor of beetles. The AT content of the mitogenome is approximately 85.1%, with AT skew and GC skew of 0.05 and -0.43, respectively. The calculated values of relative synonymous codon usage (RSCU) determine that the codon UUA (L) has the highest frequency. Furthermore, we explored the phylogenetic relationship among 59 representatives of the Coccinellidae using Bayesian inference and maximum likelihood methods, the results of which strongly support the monophyly of Coccinellinae. The phylogenetic results positioned Scymnus (Pullus) cardi in a well-supported clade with Scymnus (Pullus) loewii and Scymnus (Pullus) rubricaudus within the genus Scymnus and the tribe Scymnini. The mitochondrial sequence of S. (P.) cardi will contribute to the mitochondrial genome database and provide helpful information for the identification and phylogeny of Coccinellidae.

Comparative Mitogenome of Phylogenetic Relationships and Divergence Time Analysis within Potamanthidae (Insecta: Ephemeroptera)

Potamanthidae belongs to the superfamily Ephemeroidea but has no complete mt genome released in the NCBI (except for two unchecked and one partial mt genome). Since the sister clade to Potamanthidae has always been controversial, we sequenced seven mt genomes of Potamanthidae (two species from Rhoenanthus and five species from Potamanthus) in order to rebuild the phylogenetic relationships of Potamanthidae in this study. The divergence time of Potamanthidae was also investigated by utilizing five fossil calibration points because of the indeterminate origin time. In addition, because Rhoenanthus coreanus and Potamanthus luteus are always in low-temperature environments, we aimed to explore whether these two species were under positive selection at the mt genome level. Amongst the 13 PCGs, CGA was used as the start codon in COX1, whereas other genes conformed to initiating with an ATN start codon. From this analysis, UUA (L), AUU (I), and UUU (F) had the highest usage. Furthermore, the DHU arm was absent in the secondary structure of S1 in all species. By combining the 13 PCGs and 2 rRNAs, we reconstructed the phylogenetic relationship of Potamanthidae within Ephemeroptera. The monophyly of Potamanthidae and the monophyly of Rhoenanthus and Potamanthus were supported in the results. The phylogenetic relationship of Potamanthidae + (Ephemeridae + Polymitarcyidae) was also recovered with a high prior probability. The divergence times of Potamanthidae were traced to be 90.44 Mya (95% HPD, 62.80-121.74 Mya), and the divergence times of Rhoenanthus and Potamanthus originated at approximately 64.77 Mya (95% HPD, 43.82-88.68 Mya), thus belonging to the late Pliocene Epoch or early Miocene Epoch. In addition, the data indicated that R. coreanus was under negative selection and that ATP8 and ND2 in Potamanthidae had a high evolutionary rate.

Characterization of the complete mitochondrial genome of an endemic species in China, Aulocera merlina (Lepidoptera: Nymphalidae: Satyrinae) and phylogenetic analysis within Satyrinae

The mitochondrial genome (mitogenome) has been extensively used as molecular markers in determining the insect phylogenetic relationships. In order to resolve the relationships among tribes and subtribes of Satyrinae at the mitochondrial genomic level, we obtained the complete mitogenome of Aulocera merlina (Oberthür, 1890) (Lepidoptera: Nymphalidae: Satyrinae) with a size of 15,259 bp. The mitogenome consisted of 37 typical genes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. The gene organization and arrangement were similar to those of all other known Satyrinae mitogenomes. All PCGs were initiated with the canonical codon pattern ATN, except for the cox1 gene, which used an atypical CGA codon. Nine PCGs used the complete stop codon TAA, while the remaining PCGs (cox1, cox2, nad4, and nad5) were terminated with a single T nucleotide. The canonical cloverleaf secondary structures were found in all tRNAs, except for trnS1 which lacked a dihydrouridine arm. The 448 bp A + T-rich region was located between rrnS and trnM, and it included the motif ATAGA followed by a 19-bp poly-T stretch and a microsatellite-like (TA)6 element preceded by the ATTTA motif. The phylogenetic tree, inferred using Bayesian inference and maximum likelihood methods, generated similar tree topologies, revealing well-supported monophyletic groups at the tribe level and recovering the relationship ((Satyrini + Melanitini) + ((Amathusiini + Elymniini) + Zetherini)). The close relationship between Satyrina and Melanargiina within the Satyrini was widely accepted. Additionally, Lethina, Parargina, and Mycalesina were closely related and collectively formed a sister group to Coenonymphina. Moreover, A. merlina was closely related to Oeneis buddha within the Satyrina. These findings will provide valuable information for future studies aiming to elucidate the phylogenetic relationships of Satyrinae.

Complete Mitochondrial Genome of the Eggplant Fruit and Shoot Borer, Leucinodes orbonalis Guenée (Lepidoptera: Crambidae), and Comparison with Other Pyraloid Moths

The eggplant fruit and shoot borer (EFSB) (Leucinodes orbonalis Guenée) is a devastating lepidopteran pest of eggplant (Solanum melongena L.) in the Philippines. Management of an insect pest like the EFSB requires an understanding of its biology, evolution, and adaptations. Genomic resources provide a starting point for understanding EFSB biology, as the resources can be used for phylogenetics and population structure studies. To date, genomic resources are scarce for EFSB; thus, this study generated its complete mitochondrial genome (mitogenome). The circular mitogenome is 15,244 bp-long. It contains 37 genes, namely 13 protein-coding, 22 tRNA, and 2 rRNA genes, and has conserved noncoding regions, motifs, and gene syntenies characteristic of lepidopteran mitogenomes. Some protein-coding genes start and end with non-canonical codons. The tRNA genes exhibit a conserved cloverleaf structure, with the exception in trnS1. Partitioned phylogenetic analysis using 72 pyraloids generated highly supported maximum likelihood and Bayesian inference trees revealing expected basal splits between Crambidae and Pyralidae, and Spilomelinae and Pyraustinae. Spilomelinae was recovered to be paraphyletic, with the EFSB robustly placed before the split of Spilomelinae and Pyraustinae. Overall, the EFSB mitogenome resource will be useful for delineations within Spilomelinae and population structure analysis.

Characteristics and phylogenetic analysis of the complete mitochondrial genome of Erasmia pulchella Hope, 1840 (lepidoptera: zygaenidae)

Erasmia pulchella has brightly colored wings and releases toxic cyanide as a defense against predation. At present, the molecular phylogenetic status of this species is still unclear. Here, we presented the first complete mitochondrial genome of the genus Erasmia, which was assembled from data generated using a genome skimming method. The assembled mitogenome was 15,197 bp in length and consists of 37 genes, including 13 protein-coding genes, two rRNAs, 22 tRNAs, and a control region. Phylogenetic analysis based on both maximum likelihood (ML) and Bayesian inference (BI) revealed that E. pulchella was most closely related to Amesia sanguiflua.

The Complete Mitochondrial Genome of Chilo infuscatellus (Lepidoptera: Pyralidae), and Related Phylogenetic Analysis

The Chilo infuscatellus (Lepidoptera: Pyralidae) is a significant pest of sugarcane in China. The genome-level characteristics of this pest are important genetic resources for identification, phylogenetic analysis, and even management. In the present study, the complete mitogenome of C. infuscatellus was sequenced and characterized. The assembled mitochondrial genome is 15,252 bp in length and includes 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and an A + T-rich region. Except for the CGA codon for the cox1 gene, the PCGs are initiated with ATN codons (ATG, ATT, and ATA). These PCGs are terminated with TAA or an incomplete termination codon of a single T. Except for the loss of the "DHU" arm for trnS1, the tRNA genes were folded into the typical cloverleaf structure. The A + T-rich region has a high AT content of 96.19% and contains the motifs "ATAGA" and "ATTTA", as well as a 19 bp poly-T stretch and microsatellite regions. The C. infuscatellus mitogenome exhibits a conserved gene order among lepidopteran insects, with a rearrangement of the trnM gene compared to the ancestral insect gene order. Phylogenetic analysis based on the 13 PCGs using Bayesian inference (BI) and maximum likelihood (ML) methods confirmed the monophyly of Pyralidae and Crambidae within Pyraloidea. The relationships between subfamilies in Pyralidae can be described as (Galleriinae + (Phycitinae + (Pyralinae + Epipaschiinae))). The "PS clade" and "non-PS clade" were formed within the family Crambidae. These findings provide valuable genetic resources for the identification, phylogenetic analysis, and management of sugarcane borers, contributing significantly to our understanding of the phylogeny of Pyraloidea insects and their evolution.

The complete mitochondrial genome of Chlorogomphus shanicus Wilson, 2002 (Anisoptera: Chlorogomphidae), an endemic species in South China

In this study, the complete mitochondrial genome of Chlorogomphus shanicus Wilson, 2002 was reported, and the maximum-likelihood (ML) phylogenetic tree was constructed using 13 protein-coding genes (PCGs). The total length of the mitogenome of C. shanicus was 15,497 bp. Twelve PCGs started with ATN codons, except cox1 began with TTG codon. Most transfer RNA genes (tRNAs) were predicted to fold in a typical cloverleaf structure, except the trnS1 (gct), which lacked a dihydrouridine arm that had been simplified to a loop. The phylogenetic tree showed that Anisoptera was split into two clades, and revealed that C. shanicus was closely related to Cordulegaster boltonii (Donovan, 1807) which is endemic to Europe.

Complete mitochondrial genome of Parasa sinica: New insights into the phylogeny of Limacodidae

In this study, the whole mitochondrial genome (mitogenome) of Parasa sinica was sequenced. It contains 15,306 base pairs (bp), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and one non-coding regulatory area (CR), all of which are shared by other lepidopterans. It follows the same gene order as ordinary lepidopterans. Further, out of these 37 genes, 23 are present on the heavy strand whereas the remaining 14 are located on the light strand. The A + T composition of the mitogenome is relatively high. Although P. sinica has a negative AT-skew and GC-skew, the GC-skew value is significantly lower than the AT-skew value. All PCGs, with the exception of CO1, carry the same start codon (ATN). All tRNAs exhibit the usual cloverleaf secondary structure. We identified the conserved motif "ATAGA + poly-T″ found in other lepidopteran insects at the beginning of the CR. We collected the concatenated PCGs sequences in the mitochondrial genome of 15 species of Zygaenoidea, with the sequences of Geometridae as outgroups, including P. sinica, and constructed phylogenetic trees using Bayesian inference (BI) and maximum likelihood (ML) methods. The monolineage of each superfamily is usually well supported. Based on phylogenetic analysis, P. sinica is a member of family Limacodidae, strongly supporting the monophyly of the Zygaenoidea groups.

Use of carrion fly iDNA metabarcoding to monitor invasive and native mammals

Severely fragmented habitats increase the risk of extirpation of native mammal populations through isolation, increased edge effects, and predation. Therefore, monitoring the movement of mammal populations through anthropogenically altered landscapes can inform conservation. We used metabarcoding of invertebrate-derived DNA (iDNA) from carrion flies (Calliphoridae and Sarcophagidae) to track mammal populations in the wheat belt of southwestern Australia, where widespread clearing for agriculture has removed most of the native perennial vegetation and replaced it with an agricultural system. We investigated whether the localization of the iDNA signal reflected the predicted distribution of 4 native species-echidna (Tachyglossus aculeatus), numbat (Myrmecobius fasciatus), woylie (Bettongia penicillata), and chuditch (Dasyurus geoffroii)-and 2 non-native, invasive mammal species-fox (Vulpes vulpes) and feral cat (Felis catus). We collected bulk iDNA samples (n = 150 samples from 3428 carrion flies) at 3 time points from 3 conservation reserves and 35 road edges between them. We detected 14 of the 40 mammal species known from the region, including our target species. Most detections of target taxa were in conservation reserves. There were a few detections from road edges. We detected foxes and feral cats throughout the study area, including all conservation reserves. There was a significant difference between the diversity (F3, 98  = 5.91, p < 0.001) and composition (F3, 43  = 1.72, p < 0.01) of taxa detections on road edges and conservation reserves. Conservation reserves hosted more native biodiversity than road edges. Our results suggest that the signals from iDNA reflect the known distribution of target mammals in this region. The development of iDNA methods shows promise for future noninvasive monitoring of mammals. With further development, iDNA metabarcoding could inform decision-making related to conservation of endangered taxa, invasive species management, and impacts of habitat fragmentation.

Metagenomics reveals the structure of Mastrevirus-host interaction network within an agro-ecosystem

As highly pervasive parasites that sometimes cause disease, viruses are likely major components of all natural ecosystems. An important step towards both understanding the precise ecological roles of viruses and determining how natural communities of viral species are assembled and evolve is obtaining full descriptions of viral diversity and distributions at ecosystem scales. Here, we focused on obtaining such 'community-scale' data for viruses in a single genus. We chose the genus Mastrevirus (family Geminiviridae), members of which have predominantly been found infecting uncultivated grasses (family Poaceae) throughout the tropical and sub-tropical regions of the world. We sampled over 3 years, 2,884 individual Poaceae plants belonging to thirty different species within a 2-ha plot which included cultivated and uncultivated areas on the island of Reunion. Mastreviruses were found in ∼8 per cent of the samples, of which 96 per cent did not have any discernible disease symptoms. The multitude of host-virus associations that we uncovered reveals both the plant species that most commonly host mastreviruses and the mastrevirus species (such as maize streak virus and maize streak Reunion virus) that have especially large host ranges. Our findings are consistent with the hypothesis that perennial plant species capable of hosting years-long mixed mastrevirus infections likely play a disproportionately important role in the generation of inter-species and inter-strain mastrevirus recombinants.

Complete mitochondrial genomes of two moths in the tribe Trichaeini (Lepidoptera: Crambidae) and their phylogenetic implications

The complete mitochondrial genomes of two Prophantis species in the tribe Trichaeini (Lepidoptera: Crambidae) were sequenced using high-throughput sequencing technology. They were assembled and annotated: The complete mitogenomes of P. octoguttalis and P. adusta were 15,197 and 15,714 bp, respectively, and contain 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and an A + T-rich region. Their arrangement was consistent with the first sequenced mitogenome of Bombyx mori (Bombycidae) in Lepidoptera, which had the trnM-trnI-trnQ rearrangement. The nucleotide composition was obviously AT-biased, and all PCGs, except for the cox1 gene (CGA), used ATN as the start codon. Except for trnS1, which lacked the DHU stem, all tRNA genes could fold into the clover-leaf structure. The features of these two mitogenomes were highly consistent with those of other species of Spilomelinae in previous studies. Phylogenetic trees of Crambidae were reconstructed based on mitogenomic data using maximum likelihood and Bayesian inference analysis methods. Results showed that Trichaeini in this study robustly constitute a monophyletic group in Spilomelinae, with the relationships (Trichaeini + Nomophilini) + ((Spilomelini + (Hymeniini + Agroterini)) + Margaroniini). However, the affinities of the six subfamilies Acentropinae, Crambinae, Glaphyriinae, Odontiinae, Schoenobiinae, and Scopariinae within the "non-PS Clade" in Crambidae remained doubtful with unstable topologies or low supports.

Small population of the largest water strider after the late Pleistocene and the implications for its conservation

Climate oscillation and its synergistic impacts on habitat fragmentation have been identified as threatening the survival of some extant species. However, the mechanisms by which semi-aquatic insects impacted by such events remain poorly understood. Herein, we studied the largest water strider in the world, Gigantometra gigas, to explore the effect of these two factors on its evolutionary history. The sequences of mitogenomic and nrDNA cluster were utilized to reconstruct phylogenetic relationship among G. gigas populations and its demographic history. Mitochondrial genes were separately reconstructed topologies of that populations and detected remarkable differences. We found that G. gigas populations conform to the isolation-by-distance model, and decline occurred at about 120 ka, which was probably influenced by the climate change during the late Pleistocene and eventually maintained a small effective population size (Ne) around 85,717. The populations in Guangdong Province of China are worthy of note in that they exhibit low genetic diversity, a small Ne around 18,899 individuals, and occupy an area with little suitable future habitat for G. gigas. This work recommends that conservation efforts are implemented to ensure the long-term survival of small G. gigas populations, and notes that further evaluation of their extinction risk under the impacts of human activities is required.

Mitochondrial genome of Poecilimon cretensis (Orthoptera: Tettigoniidae: Phaneropterinae): Strong phylogenetic signals in gene overlapping regions

We report the complete mitochondrial genome of the Cretan bush cricket Poecilimon cretensis. The mitogenome consists of 13 protein-coding regions, 22 tRNAs, two rRNAs, and one control region. The length of mitogenome in P. cretensis varies between15477 and 15631 bp, mainly due to variability in control region. The start and stop codons of protein coding genes exhibit the general pattern in Phaneropterinae. Phylogenetic tree constructed with the mitogenome obtained during this study and 12 mitogenomes of Phaneropterinae downloaded from GenBank, placed P. cretensis in Barbitistini as sister group to Poecilimon luschani. Data indicate that the gene overlapping pattern exhibit strong phylogenetic signals.  

Climatic oscillation promoted diversification of spinous assassin bugs during Pleistocene glaciation

Insect speciation is among the most fascinating topics in evolutionary biology; however, its underlying mechanisms remain unclear. Allopatric speciation represents one of the major types of speciation and is believed to have frequently occurred during glaciation periods, when climatic oscillation may have caused suitable habitats to be fragmented repeatedly, creating geographical isolation among populations. However, supporting evidence for allopatric speciation of insects in East Asia during the Pleistocene glaciation remains lacking. We aim to investigate the effect of climatic oscillation during the Pleistocene glaciation on the diversification pattern and evolutionary history of hemipteran insects and to test the hypothesis of Pleistocene species stability using spinous assassin bugs Sclomina (Hemiptera: Reduviidae), a small genus widely distributed in southern China but was later found to have cryptic species diversity. Here, using the whole mitochondrial genome (mitogenome) and nuclear ribosomal RNA genes, we investigated both interspecific and intraspecific diversification patterns of spinous assassin bugs. Approximate Bayesian computation, ecological niche modeling, and demographic history analyses were also applied to understand the diversification process and driven factors. Our data suggest that the five species of Sclomina are highly diverged, despite three of them currently being cryptic. Speciation occurred during the Pleistocene when suitable distribution areas were possibly fragmented. Six phylogeographic groups in the type species S. erinacea were identified, among which two groups underwent expansion during the early Last Glacial Period and after Last Glacier Maximum. Our analyses suggest that this genus may have experienced climate-driven habitat fragmentation and postglacial expansion in the Pleistocene, promoting allopatric speciation and intraspecific diversification. Our results reveal underestimated species diversity in a small insect group and illustrate a remarkable example of allopatric speciation of insects in East Asia promoted by Pleistocene climatic oscillations. These findings provide important insights into the speciation processes and aid the conservation of insect species diversity.

DNA High-Throughput Sequencing for Arthropod Gut Content Analysis to Evaluate Effectiveness and Safety of Biological Control Agents

The search for effective biological control agents without harmful non-target effects has been constrained by the use of impractical (field direct observation) or imprecise (cage experiments) methods. While advances in the DNA sequencing methods, more specifically the development of high-throughput sequencing (HTS), have been quickly incorporated in biodiversity surveys, they have been slow to be adopted to determine arthropod prey range, predation rate and food web structure, and critical information to evaluate the effectiveness and safety of a biological control agent candidate. The lack of knowledge on how HTS methods could be applied by ecological entomologists constitutes part of the problem, although the lack of expertise and the high cost of the analysis also are important limiting factors. In this review, we describe how the latest HTS methods of metabarcoding and Lazaro, a method to identify prey by mapping unassembled shotgun reads, can serve biological control research, showing both their power and limitations. We explain how they work to determine prey range and also how their data can be used to estimate predation rates and subsequently be translated into food webs of natural enemy and prey populations helping to elucidate their role in the community. We present a brief history of prey detection through molecular gut content analysis and also the attempts to develop a more precise formula to estimate predation rates, a problem that still remains. We focused on arthropods in agricultural ecosystems, but most of what is covered here can be applied to natural systems and non-arthropod biological control candidates as well.

The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes

Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to allow such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.

Complete mitochondrial genome data and phylogenetic analysis of the Great Marquis, Bassarona dunya (Doubleday, 1848) (Lepidoptera: Nymphalidae: Limenitidinae) from Malaysia

The Great Marquis or Bassarona dunya is a butterfly species commonly found in the tropical regions of Asia, America, and Africa. This butterfly is a member of the subfamily Limenitidinae and the classification within this subfamily has been unstable. Here, we report the first complete mitochondrial genome (mitogenome) of B. dunya sampled from Malaysia. The mitogenome is 15,242 bp long, comprising a set of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and an A + T rich region. All PCGs were initiated by the typical ATN codon, except for COX1 which started with a CGA start codon. Nine PCGs were terminated with a TAA or TAG stop codon, while COX1, COX2, NAD4, and NAD5 ended with an incomplete T. The 12S and 16S rRNAs were 716 bp and 1269 bp in length, respectively. Phylogenetic analysis supported the placement of B. dunya within Limenitidinae with a high support value.

The Complete Mitogenomes of Three Grasshopper Species with Special Notes on the Phylogenetic Positions of Some Related Genera

Clarifying phylogenetic position and reconstructing robust phylogeny of groups using various evidences are an eternal theme for taxonomy and systematics. In this study, the complete mitogenomes of Longzhouacris mirabilis, Ranacris albicornis, and Conophyma zhaosuensis were sequenced using next-generation sequencing (NGS), and the characteristics of the mitogenomes are presented briefly. The mitogenomes of the three species are all circular molecules with total lengths of 16,164 bp, 15,720 bp, and 16,190 bp, respectively. The gene structures and orders, as well as the characteristics of the mitogenomes, are similar to those of other published mitogenomes in Caelifera. The phylogeny of the main subfamilies of Acrididae with prosternal process was reconstructed using a selected dataset of mitogenome sequences under maximum likelihood (ML) and Bayesian inference (BI) frameworks. The results showed that the genus Emeiacris consistently fell into the subfamily Melanoplinae rather than Oxyinae, and the genus Choroedocus had the closest relationship with Shirackiacris of the subfamily Eyprepocnemidinae in both phylogenetic trees deduced from mitogenome protein coding genes (PCGs). This finding is entirely consistent with the morphological characters, which indicate that Emeiacris belongs to Melanoplinae and Choroedocus belongs to Eyprepocnemidinae. In addition, the genera Conophymacris and Xiangelilacris, as well as Ranacris and Menglacris, are two pairs of the closest relatives, but their phylogenetic positions need further study to clarify.

Complete mitochondrial genome of Macromia manchurica Asahina, 1964 (Odonata: Macromiidae)

We describe the first time sequencing and assembly of the complete mitochondrial genome of Macromia manchurica Asahina, 1964 (Odonata; Macromiidae; Macromia). The mitochondrial genome of M. manchurica was found to be 15,560 bp. It contains thirteen protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and AT-rich region. The overall base composition of A. japonicus is A-38.6%, C-17.0%, G-12.5%, and T-31.9%. A phylogenetic analysis of 14 species within the order Odonata and order Ephemeroptera suggested that Macromia amphigena is most closely related to M. manchurica.

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.

The Genetic Diversity and the Divergence Time in Extant Primitive Mayfly, Siphluriscus chinensis Ulmer, 1920 Using the Mitochondrial Genome

In this study, the mitochondrial (mt) genomes of Siphluriscus chinensis (Ephemeroptera: Siphluriscidae) were evaluated in specimens collected from two sites in China: Niutou Mountain, Zhejiang Province (S. chinensis NTS) and Leigong Mountain, Guizhou Province (S. chinensis LGS) and were successfully sequenced. The lengths of the mt genomes of S. chinensis NTS and S. chinensis LGS were 15,904 bp (ON729390) and 15,212 bp (ON729391), respectively. However, an in-depth comparison of the two mt genomes showed significant differences between the specimens collected from the two sites. A detailed analysis of the genetic distance between S. chinensis NTS and S. chinensis LGS was undertaken to further achieve an accurate delimitation of S. chinensis. The genetic distance between S. chinensis NTS and the other three species within Siphluriscidae was a high value, above 12.2%. The two mt genomes were used to reconstruct phylogenetic relationships and estimate divergence time. The results demonstrated robust differences between S. chinensis NTS and S. chinensis LGS, which revealed that a kind of cryptic species existed. Maximum likelihood (ML) and Bayesian inference (BI) analyses produced well-supported phylogenetic trees that showed evolutionary relationships between Siphluriscidae (((S. chinensis HQ875717 + S. chinensis MF352165) + S. chinensis LGS) + S. chinensis NTS). The most recent common ancestor (MRCA) of four species within Siphluriscidae began to diversify during the Neogene [11.80 million years ago (Mya); 95% highest posterior densities (HPD) = 6.17–19.28 Mya], and S. chinensis NTS was first to diverge from the branches of S. chinensis LGS. In short, based on mitochondrial genomes, our results showed that the specimens collected from Leigong Mountain, Guizhou Province (S. chinensis LGS) belonged to S. chinensis, and the specimens collected from Niutou Mountain, Zhejiang Province (S. chinensis NTS) were a cryptic species of S. chinensis.

Characterization of complete mitochondrial genome of the common tiger, Danaus genutia (Lepidoptera: Nymphalidae: Danainae) and phylogenetic implications within the subfamily Danainae

Nymphalidae is the most diverse butterfly family worldwide, with more than 6000 species, whereas the mitogenomic data of nymphalid species, especially the subfamily Danainae, is still lacking for more comprehensive systematic studies. To this contribution, the complete mitogenome of Danaus genutia (Lepidoptera: Nymphalidae: Danainae) was determined via sequencing and annotating. The mitogenome in total consists of 15,255 base pairs (bp), containing 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a 440-bp noncoding A+T-rich region. Furthermore, phylogeny of the subfamily Danainae was reconstructed applying maximum likelihood and Bayesian inference on the basis of the mitogenomic data sets. Combined with our analysis and previous studies, the genus-level phylogenetic relationships within the subfamily Danainae are ((Tirumala + Danaus) + ((Idea + Euploea) + (Ideopsis + Parantica))). This study offers molecular information and provides a new perspective for phylogenetic research within the subfamily Danainae.

The first complete mitochondrial genome of Dufouriellini (Hemiptera: Anthocoridae) and implications for its phylogenetic position

The mitochondrial genome (mitogenome) is extensively used to better understand the phylogenetic relationships within the family level, but there are still limited representations at the tribe level of Anthocoridae. Here we describe the first complete mitogenome of Dufouriellini. The mitogenome of Cardiastethus sp. is 15,209 bp in size, containing 13 typical protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. All genes are arranged in the same gene order as the most other known cimicomorphan mitogenomes. The phylogenetic relationships based on mitogenomes using Bayesian inference and maximum likelihood methods show that Dufouriellini is sister to Anthocorini, and then both of them together form sister group with Oriini. The monophyly of each superfamily of Cimicomorpha is generally well supported. Reduvioidea is basal within Cimicomorpha. The topology of the remaining superfamily is as follows: (Miroidea + (Cimicoidea + (Velocipedoidea + Nabioidea))). This study will help to enhance our understanding of mitochondrial genomic evolution and phylogenetic relationships in the tribe level of Anthocoridae and also superfamily level of Cimicomorpha.

Metabarcoding of Fish Larvae in the Merbok River Reveals Species Diversity and Distribution Along its Mangrove Environment

The Merbok River (north-west of Peninsular Malaysia) is a mangrove estuary that provides habitat for over 100 species of fish, which are economically and ecologically important. Threats such as habitat loss and overfishing are becoming a great concern for fisheries conservation and management. The identification of larval fish in this estuarine system is important to complement information on the adults. This is because the data could inform the spawning behaviour, reproductive biology, selection of nursery grounds and migration route of fish. Such information is invaluable for fisheries and aquatic environmental monitoring, and thus for their conservation and management. However, identifying fish larvae is a challenging task based only on morphology and even traditional DNA barcoding. To address this, DNA metabarcoding was utilised to detect the diversity of fish in the Merbok River. To complete the study, the fish larvae were collected at six sampling sites of the river. The extracted larval DNA was amplified for the Cytochrome Oxidase subunit 1 (COI) and 12S ribosomal RNA (12S rRNA) genes based on the metabarcoding approach using shotgun sequencing on the next-generation sequencing (NGS) Illumina MiSeq platform. Eighty-nine species from 65 genera and 41 families were detected, with Oryzias javanicus, Oryzias dancena, Lutjanus argentimaculatus and Lutjanus malabaricus among the most common species. The lower diversity observed from previous morphological studies is suggested to be mainly due to seasonal variation over the sampling period between the two methods and limited 12S rRNA sequences in current databases. The metabarcode data and a validation Sanger sequencing step using 15 species-specific primer pairs detected three species in common: Oryzias javanicus, Decapterus maruadsi and Pennahia macrocephalus. Several discrepancies observed between the two molecular approaches could be attributed to contaminants during sampling and DNA extraction, which could mask the presence of target species, especially when DNA from the contaminants is more abundant than the target organisms. In conclusion, this rapid and cost-effective identification method using DNA metabarcoding allowed the detection of numerous fish species from bulk larval samples in the Merbok River. This method can be applied to other sites and other organisms of interest.

The first complete mitochondrial genome of Hexagenia rigida Mc Dunnough, 1924 (Ephemeroptera: Ephemeridae) and its phylogeny

The phylogenetic relationship of Ephemeridae (Insect: Ephemeroptera) remains hotly debated using mitochondrial (mt) genomes. All previously reported mt genomes of Ephemeridae belong to the genus Ephemera. This study provides the first complete mt genome sequence from the genus Hexagenia with an analysis of the mitogenome of Hexagenia rigida Mc Dunnough, 1924 (Ephemeroptera: Ephemeridae) and providing new information to discuss the phylogenetic relationships within Ephemeroptera. The complete mt genome of H. rigida was a circular molecule of 16,159 bp in length, containing 37 genes (2 rRNA genes, 13 protein-coding genes, 22 tRNA genes), which showed the typical mt gene arrangement of insects. The AT content of the whole genome was 70.0% and the length of the control region was 1091 bp. All protein-coding genes used ATN as the start codon, and most PCGs used TAA/TAG as the stop codons excluding COI, COII, ND5 and Cyt b that used T as the stop codon. BI and ML phylogenetic trees constructed from 27 species of 13 families showed that Ephemeridae is a sister clade to the clade Polymitarcyidae.

Phylogeny of Coreoidea based on mitochondrial genomes show the paraphyly of Coreidae and Alydidae

Coreoidea (Insecta: Hemiptera: Heteroptera) is a widely distributed and agriculturally important bugs. However, the phylogeny of Coreoidea lacked consensus on higher-level relationships and several studies by comparative morphological characters and molecular data suggested the non-monophyly of two families: Coreidae and Alydidae. The mitochondrial genome (mitogenome) has long been thought to be a significant marker to understand phylogenetic relationships, but the mitogenome in Alydidae is scarce to date. In the present study, we gathered the mitogenomes of 28 species from four families of Coreoidea excluding Hyocephalidae (Alydidae, Coreidae, Rhopalidae, and Stenocephalidae), including four newly sequenced mitogenomes of Alydidae, and conducted mitogenomic organization and phylogenetic studies. We used maximum likelihood and Bayesian inference methods to infer the higher-level phylogeny from the perspective of mitogenomes, primarily to investigate the phylogenetic relationship betweeen Coreidae and Alydidae. We add evidence that neither Alydidae nor Coreidae are monophyletic based on mitogenomes. Newly sequenced mitogenomes of Alydidae have traditional gene structure and gene rearrangement was not found. Alydinae was always recovered as closely related to Pseudophloeinae of the coreid subfamily with high support. The placement of the coreid subfamily Hydarinae and alydid subfamily Micrelytrinae are unstable depending on approach used. In terms of the length and nucleotide composition of the protein coding genes in mitogenomes, Pseudophloeinae and Hydarinae of coreid were more similar to Alydidae. The unsettled classification issues of Coreidae and Alydidae by mitogenomes were demonstrated in this work, indicating that further study is needed.

Cryptic Species Exist in Vietnamella sinensis Hsu, 1936 (Insecta: Ephemeroptera) from Studies of Complete Mitochondrial Genomes

Ephemeroptera (Insecta: Pterygota) are widely distributed all over the world with more than 3500 species. During the last decade, the phylogenetic relationships within Ephemeroptera have been a hot topic of research, especially regarding the phylogenetic relationships among Vietnamellidae. In this study, three mitochondrial genomes from three populations of Vienamella sinensis collected from Tonglu (V. sinensis TL), Chun’an (V. sinensis CN), and Qingyuan (V. sinensis QY) in Zhejiang Province, China were compared to discuss the potential existence of cryptic species. We also established their phylogenetic relationship by combining the mt genomes of 69 Ephemeroptera downloaded from NCBI. The mt genomes of V. sinensis TL, V. sinensis CN, and V. sinensis QY showed the same gene arrangement with lengths of 15,674 bp, 15,674 bp, and 15,610 bp, respectively. Comprehensive analyses of these three mt genomes revealed significant differences in mt genome organization, genetic distance, and divergence time. Our results showed that the specimens collected from Chun’an and Tonglu in Zhejiang Province, China belonged to V. sinensis, and the specimens collected from Qingyuan, Zhejiang Province, China were a cryptic species of V. sinensis. In maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees, the monophyly of the family Vietnamellidae was supported and Vietnamellidae has a close relationship with Ephemerellidae.

Universal Mitochondrial Multi-Locus Sequence Analysis (mtMLSA) to Characterise Populations of Unanticipated Plant Pest Biosecurity Detections

Simple Summary

Agricultural and environmental sustainability requires effective biosecurity responses that prevent the establishment or spread of exotic insect pests. Understanding where new detections may have come from or if recurrent detections are connected contributes to this. Suitable population genetic markers use relatively rapidly evolving gene regions which render the PCR method species-specific at best. Because resource limitations mean these are pre-emptively developed for the highest risk species, populations of other exotic pests are unable to be characterised at the time. Here we have developed a generic method that is useful across species within the same taxonomic Order, including where there is little or no prior knowledge of their gene sequences. Markers are formed by concomitant sequencing of four gene regions. Sequence concatenation was shown to retrieve higher resolution signatures than standard DNA barcoding. The method is encouragingly universal, as illustrated across species in ten fly and 11 moth superfamilies. Although as-yet untested in a biosecurity situation, this relatively low-tech, off-the-shelf method makes a proactive contribution to the toolbox of quarantine agencies at the time of detection without the need for impromptu species-specific research and development.

Abstract

Biosecurity responses to post-border exotic pest detections are more effective with knowledge of where the species may have originated from or if recurrent detections are connected. Population genetic markers for this are typically species-specific and not available in advance for any but the highest risk species, leaving other less anticipated species difficult to assess at the time. Here, new degenerate PCR primer sets are designed for within the Lepidoptera and Diptera for the 3′ COI, ND3, ND6, and 3′ plus 5′ 16S gene regions. These are shown to be universal at the ordinal level amongst species of 14 and 15 families across 10 and 11 dipteran and lepidopteran superfamilies, respectively. Sequencing the ND3 amplicons as an example of all the loci confirmed detection of population-level variation. This supported finding multiple population haplotypes from the publicly available sequences. Concatenation of the sequences also confirmed that higher population resolution is achieved than for the individual genes. Although as-yet untested in a biosecurity situation, this method is a relatively simple, off-the-shelf means to characterise populations. This makes a proactive contribution to the toolbox of quarantine agencies at the time of detection without the need for unprepared species-specific research and development.

Metabarcoding versus mapping unassembled shotgun reads for identification of prey consumed by arthropod epigeal predators

BACKGROUND

A central challenge of DNA gut content analysis is to identify prey in a highly degraded DNA community. In this study, we evaluated prey detection using metabarcoding and a method of mapping unassembled shotgun reads (Lazaro).

RESULTS

In a mock prey community, metabarcoding did not detect any prey, probably owing to primer choice and/or preferential predator DNA amplification, while Lazaro detected prey with accuracy 43-71%. Gut content analysis of field-collected arthropod epigeal predators (3 ants, 1 dermapteran, and 1 carabid) from agricultural habitats in Brazil (27 samples, 46-273 individuals per sample) revealed that 64% of the prey species detections by either method were not confirmed by melting curve analysis and 87% of the true prey were detected in common. We hypothesized that Lazaro would detect fewer true- and false-positive and more false-negative prey with greater taxonomic resolution than metabarcoding but found that the methods were similar in sensitivity, specificity, false discovery rate, false omission rate, and accuracy. There was a positive correlation between the relative prey DNA concentration in the samples and the number of prey reads detected by Lazaro, while this was inconsistent for metabarcoding.

CONCLUSIONS

Metabarcoding and Lazaro had similar, but partially complementary, detection of prey in arthropod predator guts. However, while Lazaro was almost 2× more expensive, the number of reads was related to the amount of prey DNA, suggesting that Lazaro may provide quantitative prey information while metabarcoding did not.

Development and evaluation of a meat mitochondrial metagenomic (3MG) method for composition determination of meat from fifteen mammalian and avian species

BACKGROUND

Bioassessment and biomonitoring of meat products are aimed at identifying and quantifying adulterants and contaminants, such as meat from unexpected sources and microbes. Several methods for determining the biological composition of mixed samples have been used, including metabarcoding, metagenomics and mitochondrial metagenomics. In this study, we aimed to develop a method based on next-generation DNA sequencing to estimate samples that might contain meat from 15 mammalian and avian species that are commonly related to meat bioassessment and biomonitoring.

RESULTS

In this project, we found the meat composition from 15 species could not be identified with the metabarcoding approach because of the lack of universal primers or insufficient discrimination power. Consequently, we developed and evaluated a meat mitochondrial metagenomics (3MG) method. The 3MG method has four steps: (1) extraction of sequencing reads from mitochondrial genomes (mitogenomes); (2) assembly of mitogenomes; (3) mapping of mitochondrial reads to the assembled mitogenomes; and (4) biomass estimation based on the number of uniquely mapped reads. The method was implemented in a python script called 3MG. The analysis of simulated datasets showed that the method can determine contaminant composition at a proportion of 2% and the relative error was < 5%. To evaluate the performance of 3MG, we constructed and analysed mixed samples derived from 15 animal species in equal mass. Then, we constructed and analysed mixed samples derived from two animal species (pork and chicken) in different ratios. DNAs were extracted and used in constructing 21 libraries for next-generation sequencing. The analysis of the 15 species mix with the method showed the successful identification of 12 of the 15 (80%) animal species tested. The analysis of the mixed samples of the two species revealed correlation coefficients of 0.98 for pork and 0.98 for chicken between the number of uniquely mapped reads and the mass proportion.

CONCLUSION

To the best of our knowledge, this study is the first to demonstrate the potential of the non-targeted 3MG method as a tool for accurately estimating biomass in meat mix samples. The method has potential broad applications in meat product safety.

Mitogenomes of Nine Asian Skipper Genera and Their Phylogenetic Position (Lepidoptera: Hesperiidae: Pyrginae)

In this study, complete mitochondrial genomes of nine species representing three tribes in the subfamily Pyrginae sensu lato were newly sequenced. The mitogenomes are closed double-stranded circular molecules, with the length ranging from 15,232 bp to 15,559 bp, which all encode 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. The orientation and gene order of these nine mitogenomes are identical to the inferred ancestral arrangement of insects. All PCGs exhibit the typical start codon ATN except for cox1 (using CGA) and cox2 (using TTG) in Mooreana trichoneura. Most of the PCGs terminate with a TAA stop codon, while cox1, cox2, nad4, and nad5 end with the incomplete codon single T. For the different datasets, we found that the one comprising all 37 genes of the mitogenome produced the highest nodal support, indicating that the inclusion of RNAs improves the phylogenetic signal. This study re-confirmed the status of Capila, Pseudocoladenia, and Sarangesa; namely, Capila belongs to the tribe Tagiadini, and Pseudocoladenia and Sarangesa to the tribe Celaenorrhini. Diagnostic characters distinguishing the two tribes, the length of the forewing cell and labial palpi, are no longer significant. Two populations of Pseudocoladenia dan fabia from China and Myanmar and P. dan dhyana from Thailand are confirmed as conspecific.

Comparative and phylogenomic analyses of mitochondrial genomes in Coccinellidae (Coleoptera: Coccinelloidea)

The Coccinellidae are one of the most familiar beetle families, the ladybirds. Despite the great ecological and economic significance, the phylogenetic relationships of Coccinellidae remain poorly understood. One of the reasons is that the sequenced mitogenomes available for this family are very limited. We sequenced complete or nearly complete mitogenomes from seven species of the tribe Coccinellini with next-generation sequencing. All species have the same gene content and gene order as the putatively ancestral insect mitogenome. A large intergenic spacer region (> 890 bp) was found located between trnI and trnQ. The potential for using secondary structures of the large and small ribosomal subunits for phylogenetic reconstruction was predicted. The phylogenetic relationships were explored through comparative analyses across more than 30 coccinellid species. We performed phylogenetic analyses with both concatenation methods (Maximum Likelihood and Bayesian Inference) and multispecies coalescent method (ASTRAL). Phylogenetic results strongly supported the monophyly of Coccinellidae. Within Coccinellidae, the Epilachnini and the Coccinellini including Halyziini were monophyletic, while the Scymnini and Coccidulini were non-monophyletic.

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.

Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures

Molecular identification of mixed-species pollen samples has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via amplicon sequencing, but whole-genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per sample and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each sample using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k-mer identification method with reference libraries constructed from full-genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 amplicon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but diverged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS-based pollen identification is the lack of representation of plant diversity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed-species pollen samples.

The Primary Complete Mitochondrial Genome of the Lappet Moth Brahmophthalma hearseyi (Lepidoptera: Brahmaeidae) and Related Phylogenetic Analysis

Simple Summary

In this paper, the complete mitochondrial genome (mitogenome) of B. hearseyi was sequenced using long-PCR and primer-walking methods. The results indicated that the mitogenome is a typical circular molecule that is composed of 15,442 bp. Phylogenetic analysis showed that B. hearseyi is clustered into Brahmaeidae, and the phylogenetic relationships are (Brahmaeidae + Lasiocampidae) + (Bombycidae + (Sphingidae + Saturniidae)). This study provides the first mitogenomic resources for the Brahmaeidae.

Abstract

Background: Brahmophthalma hearseyi (Lepidoptera: Brahmaeidae) is widely distributed across China. Its larvae damage the leaves of many plants such as those belonging to the Oleaceae family, causing significant economic losses and seriously affecting the survival and reproduction of Cervus nippon; however, genetic data for this species are scarce. Methods: The complete mitochondrial genome (mitogenome) of B. hearseyi was sequenced using long-PCR and primer-walking methods. Phylogenetic analysis that was based on 13 PCGs and two rRNAs was carried out using the neighbor-joining and Bayesian interference methods. Results: The mitogenome is a typical circular molecule that is made up of 15,442 bp, which includes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and an A + T-rich region (456 bp). All of the PCGs, except for COX1 and COX2, start with ATN codons. COX2 and ND5 use the incomplete termination codon T, and 11 other PCGs use the typical stop codon TAA. All tRNA genes, except for trnS1 and trnS2, display a typical cloverleaf structure; trnS1 lacks the “DHU” arm, whereas trnS2 exhibits two mismatched base pairs in the anticodon stem. Phylogenetic analysis showed that B. hearseyi is clustered into Brahmaeidae, and the phylogenetic relationships are (Brahmaeidae + Lasiocampidae) + (Bombycidae + (Sphingidae + Saturniidae)). Conclusions: This study provides the first mitogenomic resources for the Brahmaeidae.

Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution

The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.

MODB: a comprehensive mitochondrial genome database for Mollusca

Mollusca is the largest marine phylum, comprising about 23% of all named marine organisms, Mollusca systematics are still in flux, and an increase in human activities has affected Molluscan reproduction and development, strongly impacting diversity and classification. Therefore, it is necessary to explore the mitochondrial genome of Mollusca. The Mollusca mitochondrial database (MODB) was established for the Life and Health Big Data Center of Yantai University. This database is dedicated to collecting, sorting and sharing basic information regarding mollusks, especially their mitochondrial genome information. We also integrated a series of analysis and visualization tools, such as BLAST, MUSCLE, GENEWISE and LASTZ. In particular, a phylogenetic tree was implemented in this database to visualize the evolutionary relationships between species. The original version contains 616 species whose mitochondrial genomes have been sequenced. The database provides comprehensive information and analysis platform for researchers interested in understanding the biological characteristics of mollusks.

Database URL: http://modb.ytu.edu.cn/

Three Complete Mitochondrial Genomes of Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis (Insecta: Phasmatodea) and Their Phylogeny

Insects of the order Phasmatodea are mainly distributed in the tropics and subtropics and are best known for their remarkable camouflage as plants. In this study, we sequenced three complete mitochondrial genomes from three different families: Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis. The lengths of the three mitochondrial genomes were 15,896 bp, 16,869 bp, and 17,005 bp, respectively, and the gene composition and structure of the three stick insects were identical to those of the most recent common ancestor of insects. The phylogenetic relationships among stick insects have been chaotic for a long time. In order to discuss the intra- and inter-ordinal relationship of Phasmatodea, we used the 13 protein-coding genes (PCGs) of 85 species for maximum likelihood (ML) and Bayesian inference (BI) analyses. Results showed that the internal topological structure of Phasmatodea had a few differences in both ML and BI trees and long-branch attraction (LBA) appeared between Embioptera and Zoraptera, which led to a non-monophyletic Phasmatodea. Consequently, after removal of the Embioptera and Zoraptera species, we re-performed ML and BI analyses with the remaining 81 species, which showed identical topology except for the position of Tectarchus ovobessus (Phasmatodea). We recovered the monophyly of Phasmatodea and the sister-group relationship between Phasmatodea and Mantophasmatodea. Our analyses also recovered the monophyly of Heteropterygidae and the paraphyly of Diapheromeridae, Phasmatidae, Lonchodidae, Lonchodinae, and Clitumninae. In this study, Peruphasma schultei (Pseudophasmatidae), Phraortes sp. YW-2014 (Lonchodidae), and species of Diapheromeridae clustered into the clade of Phasmatidae. Within Heteropterygidae, O. guangxiensis was the sister clade to O. mouhotii belonging to Dataminae, and the relationship of (Heteropteryginae + (Dataminae + Obriminae)) was recovered.

Comparative Mitogenomic Analysis of Five Awl Skippers (Lepidoptera: Hesperiidae: Coeliadinae) and Their Phylogenetic Implications

Simple Summary

The subfamily Coeliadinae (Lepidoptera: Hesperiidae) is a unique group of over 70 species in the butterfly family, and its mitochondrial genome data still needs to be supplemented. This study sequenced and analyzed five additional complete mitochondrial genomes of the Coeliadinae species (Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis) and compared them in detail with those of the other known skipper mitogenomes. All five of these mitogenomes have the typical lepidopteran mitogenome characteristics of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding region. Our results indicate that their structure, nucleotide composition, codon usage, secondary structure of tRNAs, and so on, are highly conserved. Expanded sampling and gene data from the GenBank, phylogenetic analyses using maximum likelihood, and Bayesian inference methods indicate that Coeliadinae is monophyletic. These results contribute toward refining the phylogeny.

Abstract

To determine the significance of mitochondrial genome characteristics in revealing phylogenetic relationships and to shed light on the molecular evolution of the Coeliadinae species, the complete mitochondrial genomes (mitogenomes) of five Coeliadinae species were newly sequenced and analyzed, including Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis. The results show that all five mitogenomes are double-strand circular DNA molecules, with lengths of 15,340 bp, 15,295 bp, 15,304 bp, 15,295 bp, and 15,289 bp, respectively, and contain the typical 37 genes and a control region. Most protein-coding genes (PCGs) begin with ATN, with 3 types of stop codons including TAA, TAG, and an incomplete codon T-; most of the genes terminate with TAA. All of the transfer RNA genes (tRNAs) present the typical cloverleaf secondary structure except for the trnS1. Several conserved structural elements are found in the AT-rich region. Phylogenetic analyses based on three datasets (PCGs, PRT, and 12PRT) and using maximum likelihood (ML) and Bayesian inference (BI) methods show strong support for the monophyly of Coeliadinae, and the relationships of the five species are (B. exclamationis + ((B. harisa + (B. oedipodea + B. miracula)) + H. schoenherr)).

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.

Insight into the Phylogenetic Relationships among Three Subfamilies within Heptageniidae (Insecta: Ephemeroptera) along with Low-Temperature Selection Pressure Analyses Using Mitogenomes

We determined 15 complete and two nearly complete mitogenomes of Heptageniidae belonging to three subfamilies (Heptageniinae, Rhithrogeninae, and Ecdyonurinae) and six genera (Afronurus, Epeorus, Leucrocuta, Maccaffertium, Stenacron, and Stenonema). Species of Rhithrogeninae and Ecdyonurinae had the same gene rearrangement of CR-I-M-Q-M-ND2, whereas a novel gene rearrangement of CR-I-M-Q-NCR-ND2 was found in Heptageniinae. Non-coding regions (NCRs) of 25-47 bp located between trnA and trnR were observed in all mayflies of Heptageniidae, which may be a synapomorphy for Heptageniidae. Both the BI and ML phylogenetic analyses supported the monophyly of Heptageniidae and its subfamilies (Heptageniinae, Rhithrogeninae, and Ecdyonurinae). The phylogenetic results combined with gene rearrangements and NCR locations confirmed the relationship of the subfamilies as (Heptageniinae + (Rhithrogeninae + Ecdyonurinae)). To assess the effects of low-temperature stress on Heptageniidae species from Ottawa, Canada, we found 27 positive selection sites in eight protein-coding genes (PCGs) using the branch-site model. The selection pressure analyses suggested that mitochondrial PCGs underwent positive selection to meet the energy requirements under low-temperature stress.

The complete mitochondrial genome of Choroterpes (Euthralus) yixingensis (Ephemeroptera: Leptophlebiidae) and its mitochondrial protein-coding gene expression under imidacloprid stress

As one of the most common benthic invertebrates in freshwater, mayflies are very sensitive to changes in water quality and have high requirements for the water environment to allow their nymphs to successfully live and grow. Neonicotinoids, such as imidacloprid, can enter fresh water and pollute the aquatic environment. The present study had two goals: (1) investigate imidacloprid effects on mayfly larvae Choroterpes (Euthralus) yixingensis, and (2) contribute to the phylogenetic status of Ephemeroptera that has always been controversial. Nymphs were collected from Jinhua, China and exposed to different concentrations imidacloprid (5, 10, 20, and 40 μg/L) in the laboratory. Survival of C. yixingensis nymphs decreased as a function of time and imidacloprid concentration with only ~ 55% survival after 72 h exposure to 40 μg/L imidacloprid. After culture under 40 μg/L imidacloprid for 24 h, the steady state transcript levels of mitochondrial COX3, ND4 and ND4L genes were reduced to just 0.07 ± 0.11, 0.30 ± 0.16, and 0.28 ± 0.13 as compared with respective control values (P < 0.01). Steady state transcript levels of ND4 and ND4L were also significantly reduced in a dose-dependent manner (P < 0.05), suggesting that the steady state transcript pattern of these genes in mayfly nymphs can change in response to different levels of environmental contamination. Hence, the mitochondrial protein-coding genes of mayflies could potentially be developed as biomarkers for water ecotoxicity monitoring in the future. In addition, we used the mitochondrial genome sequence of C. yixingensis for an assessment of the phylogenetic tree of Ephemeroptera. The monophyly of Leptophlebiidae was supported and showed that Leptophlebiidae was a sister group to the clade (Baetidae + Caenidae).