The complete mitochondrial genome of Bactrocera biguttula (Bezzi) (Diptera: Tephritidae) and phylogenetic relationships with other Dacini

Phylogenomic analysis and molecular identification of true fruit flies

The family Tephritidae in the order Diptera, known as true fruit flies, are agriculturally important insect pests. However, the phylogenetic relationships of true fruit flies, remain controversial. Moreover, rapid identification of important invasive true fruit flies is essential for plant quarantine but is still challenging. To this end, we sequenced the genome of 16 true fruit fly species at coverage of 47-228×. Together with the previously reported genomes of nine species, we reconstructed phylogenetic trees of the Tephritidae using benchmarking universal single-copy ortholog (BUSCO), ultraconserved element (UCE) and anchored hybrid enrichment (AHE) gene sets, respectively. The resulting trees of 50% taxon-occupancy dataset for each marker type were generally congruent at 88% nodes for both concatenation and coalescent analyses. At the subfamily level, both Dacinae and Trypetinae are monophyletic. At the species level, Bactrocera dorsalis is more closely related to Bactrocera latifrons than Bactrocera tryoni. This is inconsistent with previous conclusions based on mitochondrial genes but consistent with recent studies based on nuclear data. By analyzing these genome data, we screened ten pairs of species-specific primers for molecular identification of ten invasive fruit flies, which PCR validated. In summary, our work provides draft genome data of 16 true fruit fly species, addressing the long-standing taxonomic controversies and providing species-specific primers for molecular identification of invasive fruit flies.

First report of the complete mitochondrial genome of Carpomya pardalina (Bigot) (Diptera: Tephritidae) and phylogenetic relationships with other Tephritidae

Carpomya pardalina is known for its potential invasiveness, which poses a significant and alarming threat to Cucurbitaceae crops. It is considered a highly perilous pest species that requires immediate attention for quarantine and prevention. Due to the challenges in distinguishing pests of the Tephritidae family based on morphological characteristics, it is imperative to elucidate the mitochondrial genomic information of C. pardalina. In this study, the mitochondrial genome sequence of C. pardalina was determined and analyzed using next-generation sequencing. The results revealed that the mitogenome sequence had a total length of 16,257 bp, representing a typical circular molecule. It consisted of 13 PCGs, two rRNA genes, 22 tRNA genes and a non-coding region. The structure and organization of the mitochondrial genome of C. pardalina were found to be typical and similar to the published homologous sequences of other fruit flies in the Tephritidae family. Phylogenetic analysis confirmed that C. pardalina belongs to the Carpomya genus, which is consistent with traditional morphological taxonomy. Additionally, Carpomya and Rhagoletis were identified as sister groups. This study presents the first report of the complete mitochondrial genome of C. pardalina, which can serve as a valuable resource for future investigations in species diagnosis, evolutionary biology, prevention and control measures.

The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea

BACKGROUND

In this study, the complete mitogenome of Hemigrapsus sinensis was the first identified and analyzed.

OBJECTIVE

The complete mitochondrial genome of Hemigrapsus sinensis (Brachyura, Grapsoidea, Varunidae) and its phylogenetic position within Grapsoidea.

METHODS

The sample of Hemigrapsus sinensis was collected and DNA was extracted. After sequencing, NOVOPlasty was used for sequence assembly. Annotate sequences with MITOS WebServer, tRNAscan-SE2.0, and NCBI database. MEGA was used for sequence analysis and Phylosuite was used for phylogenetic tree construction. DnaSP was used to calculate Ka/Ks.

RESULTS

This mitochondrial genome shows that it was 15,900 bp and encoded 13 PCGs, 22 tRNA genes, two rRNA genes, and one control region. The genome composition tends to A + T (74.34%) and presents a negative GC-skew (- 0.22) and AT-skew (- 0.03). The PCGs initiation codon was the typical ATN and termination codon was the typical TAN, incomplete T or missing. The ML and BI trees showed that H. sinensis was most closely related to Hemigrapsus and clustered together with the Varunidae. And our phylogenetic trees provide proof that Ocypodoidea and Grapsoidea may be of common origin. Meanwhile, in the phylogenetic tree, parallel mixing of Chiromantes and Orisarma raised doubts over the traditional classification system. Besides, Incomplete Lineage sorting (ILS) was observed in Varunidae. In the subsequent analysis of evolution rate, we found that all of the PCGs (NAD4 was not calculated) had undergone negative selections, indicating the conservation of mitochondrial genes of H. sinensis during the evolution.

CONCLUSION

Therefore, researching the complete mitogenome of H. sinensis would be contributing to molecular taxonomy, phylogenetic relationship, and breeding optimization within the Grapsoidea superfamily.

Argopistes sexvittatus and Argopistes capensis (Chrysomelidae: Alticini): Mitogenomics and Phylogeny of Two Flea Beetles Affecting Olive Trees

The genus Argopistes (Chrysomelidae: Alticini) is the only group of flea beetles specialized in plant hosts in the family Oleaceae. In southern Africa, Argopistes are often found feeding on African Wild Olive (Olea europaea subsp. cuspidata) and European cultivated olive (O. e. subsp. europaea), and heavy infestations can be devastating to mature trees and compromise the development of young trees. Despite their negative agricultural impact, African Argopistes are an understudied group for which no genetic data were available. We assessed the species diversity of olive flea beetles in the Western Cape province of South Africa, the largest olive-producing region in sub-Saharan Africa, by collecting adult specimens on wild and cultivated olive trees between 2015 and 2017. Argopistes sexvittatus Bryant, 1922 (n = 289) dominated at all sampling sites, and Argopistes capensis Bryant, 1944 (n = 2) was found only once. Argopistes oleae Bryant, 1922, a third species previously reported in the region, was not found. The complete mitogenomes of one A. capensis and two A. sexvittatus (striped and black morphotypes) individuals were sequenced for phylogenetic reconstruction in the context of other 64 species. The two olive flea beetle species form a monophyletic clade with other Argopistes, supporting the hypothesis that the exclusive feeding habit on Oleaceae is an evolutionary adaptation in this genus.

Mitogenomics of the Olive Seed Weevil, Anchonocranus oleae Marshall and Implications for Its Phylogenetic Position in Curculionidae

Simple Summary

Anchonocranus oleae is a southern African weevil that feeds on the seeds of the African Wild Olive, a close relative of the European cultivated olive tree. The species is known to occur in the Western Cape of South Africa, the main region of olive production in Southern Africa. We generated reference DNA barcodes and the complete mitogenome of A. oleae as part of our ongoing genetic cataloguing of insects associated with wild and cultivated olives in South Africa. The phylogenetic position of A. oleae in the family Curculionidae was inferred to be in the Curculioninae, Conoderinae, Cossoninae, Molytinae, and Scolytinae (CCCMS) clade but could not be precisely determined due to the paucity of genetic data for adequate taxonomic context, highlighting the need for further coverage of related tribes and genera. Nevertheless, the data generated in this study contribute to the enrichment of baseline information on olive-associated insects, in general, and on the genus Anchonocranus, in particular.

Abstract

Anchonocranus oleae Marshall (Coleoptera: Curculionidae) is a seed-feeding weevil native to southern Africa; its larvae are known to develop in the fruits of the African Wild Olive and, more rarely, cultivated olives. The species has been mainly found in the Western Cape province of South Africa, but it has remained in relative obscurity because it does not seem to represent a current threat to commercial olive production. As part of an ongoing effort to produce baseline genetic data for olive-associated entomofauna in South Africa, we generated reference DNA barcodes for A. oleae collected from wild and cultivated olives and sequenced its mitogenome for assessment of the phylogenetic position of the species in the family Curculionidae. The mitochondrial phylogeny estimate indicated that A. oleae shares a common ancestor with Elaidobius (tribe Derelomini), but a definite and close relationship to this tribe and the precise tribal placement of A. oleae in the subfamily Curculioninae could not be inferred due to the lack of representative mitogenomes of other relevant curculionine tribes and genera. This study will assist future work on the DNA-based species identification, genetic diversity, and phylogenetic position of the genus Anchonocranus and related taxa.

Comparative mitochondrial genomes of the Rhus gall aphid Kaburagia rhusicola subspecies with variable gall shapes

Rhus gall aphids (Hemiptera: Aphididae: Eriosomatinae) stimulate the formation of galls on their primary host plants (sumacs: Rhus spp., Anacardiaceae). The shapes of galls are often used as an extended phenotype to identify the aphid species and subspecies. We collected four Rhus galls with conspicuously different shapes formed by Kaburagia rhusicola aphids, whose sequences of the complete mitochondrial genomes (mitogenomes) were obtained by high-throughput sequencing. Each mitogenome was assembled into a circular molecule containing 13 protein-coding genes, two rRNAs, 22 tRNAs and one control region. All the protein-coding genes had a typical ATN initiation codon and TAA termination codon except for cox1 and nad4, which had a single T as stop codon. All the tRNAs could be folded as a typical clover-leaf secondary structure, except for trnS1 lacking a dihydrouridine (DHU) arm. The relative synonymous codon usage and ratio of nonsynonymous to synonymous substitution rates showed that the four K. rhusicola samples were highly similar to the subspecies K. r. ovogallis. The phylogenetic analyses grouped these samples with K. r. ovogallis in a clade sister to K. r. rhusicola. All these molecular analyses demonstrated that our current samples represented one subspecies of Kaburagia rhusicola, i.e., K. r. ovogallis, and the gall shape was variable even at the subspecies level in Kaburagia gall aphids.

The Complete Mitochondrial Genome of Stichopus naso (Aspidochirotida: Stichopodidae: Stichopus) and Its Phylogenetic Position

The mitochondrial genome is widely used to study the molecular evolution of and perform phylogenetic analyses on animals. In this study, the complete mitochondrial genome (mitogenome) of Stichopus naso was sequenced. The mitogenome was 16,239 bp in length and contained 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The genome composition showed positive AT-skew (0.023) and negative GC-skew (−0.158). The order of the mitochondrial genes was consistent with those from the Stichopus and Isostichopus species, whereas it was different from those of other species of Aspidochirotida. The phylogenetic analysis, based on the nucleotide sequences of 13 PCGs through the methods of Bayesian inference (BI) and maximum likelihood (ML), indicated that S. naso has close relationships with S. horrens and S. monotuberculatus, and belongs to a member of Stichopodidae. Our study provides a reference mitogenome for further molecular evolution studies and phylogenetic research on sea cucumbers.

Comparative mitogenomics of Drosophilidae and the evolution of the Zygothrica genus group (Diptera, Drosophilidae)

The Zygothrica genus group of Drosophilidae encompasses more than 437 species and five genera. Although knowledge regarding its diversity has increased, uncertainties about its monophyly and position within Drosophilidae remain. Genomic approaches have been widely used to address different phylogenetic questions and analyses involving the mitogenome have revealed a cost-efficient tool to these studies. Thus, this work aims to characterize mitogenomes of three species of the Zygothrica genus group (from the Hirtodrosophila, Paraliodrosophila and Zygothrica genera), while comparing them with orthologous sequences from other 23 Drosophilidae species and addressing their phylogenetic position. General content concerning gene order and overlap, nucleotide composition, start and stop codon, codon usage and tRNA structures were compared, and phylogenetic trees were constructed under different datasets. The complete mitogenomes characterized for H. subflavohalterata affinis H002 and P. antennta present the PanCrustacea gene order with 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein coding genes and an A+T rich region with two T-stretched elements. Some peculiarities such as the almost complete overlap of genes tRNAH/ND4, tRNAF/ND5 and tRNAS2/ND1 are reported for different Drosophilidae species. Non-canonical secondary structures were encountered for tRNAS1 and tRNAY, revealing patterns that apply at different phylogenetic scales. According to the best depiction of the mitogenomes evolutionary history, the three Neotropical species of the Zygothrica genus group encompass a monophyletic lineage sister to Zaprionus, composing with this genus a clade that is sister to the Drosophila subgenus.

Species Diversity and Phylogenetic Relationships of Olive Lace Bugs (Hemiptera: Tingidae) Found in South Africa

Simple Summary

Olive lace bugs feed on wild and cultivated Olea europaea, causing a negative impact on plant vitality and development. These insects are known to affect olive orchards in South Africa, the country where most of the olive and olive products on the continent are produced. However, the diversity of species of these pests is not clear. Morphological analysis and DNA barcoding showed the presence of Cysteochila lineata, Plerochila australis, Neoplerochila paliatseasi and Neoplerochila sp. Further analyses of genetic divergence and phylogenetic clustering in 30 species in 18 genera of Tingidae using new and publicly available DNA barcodes showed that the majority of sequences deposited on BOLD Systems were correctly assigned to species. The complete mitochondrial genomes of the four species found in South Africa were sequenced to assess their phylogenetic position within Tingidae. The four olive lace bugs formed one cluster of species, and the genus Cysteochila was not monophyletic as C. lineata grouped with the other three olive lace bugs but C. chiniana was placed in a different cluster. This result suggests that lace bug species that feed on olive trees may have a common ancestor and calls for further research on potential adaptations to O. europaea.

Abstract

Olive lace bugs (Hemiptera: Tingidae) are small sap-sucking insects that feed on wild and cultivated Olea europaea. The diversity of olive lace bug species in South Africa, the most important olive producer on the continent, has been incompletely surveyed. Adult specimens were collected in the Western Cape province for morphological and DNA-based species identification, and sequencing of complete mitogenomes. Cysteochila lineata, Plerochila australis, Neoplerochila paliatseasi and Neoplerochila sp. were found at 12 sites. Intra- and interspecific genetic divergences and phylogenetic clustering in 30 species in 18 genera of Tingidae using new and publicly available DNA barcodes showed high levels of congruity between taxonomic and genetic data. The phylogenetic position of the four species found in South Africa was inferred using new and available mitogenomes of Tingidae. Notably, olive lace bugs formed a cluster of closely related species. However, Cysteochila was non-monophyletic as C. lineata was recovered as a sister species to P. australis whereas Cysteochila chiniana, the other representative of the genus, was grouped with Trachypeplus jacobsoni and Tingis cardui in a different cluster. This result suggests that feeding on O. europaea may have a common origin in Tingidae and warrants future research on potential evolutionary adaptations of olive lace bugs to this plant host.

New Mitochondrial Gene Rearrangement in Psyttalia concolor, P. humilis and P. lounsburyi (Hymenoptera: Braconidae), Three Parasitoid Species of Economic Interest

The family Braconidae consists mostly of specialized parasitoids, some of which hold potential in biocontrol of agricultural pests. Psyttalia concolor, Psyttalia humilis and Psyttalia lounsburyi are parasitoids associated with Bactrocera oleae, a major pest of cultivated olives. The native range of Psyttalia concolor is the Mediterranean, and P. humilis and P. lounsburyi are native to sub-Saharan Africa. This study reports the mitochondrial genomes of the three species, thus laying the foundation for mitogenomic analyses in the genus Psyttalia. Comparative mitogenomics within Braconidae showed a novel gene arrangement in Psyttalia in involving translocation and inversion of transfer RNA genes. The placement of Psyttalia in the subfamily Opiinae was well-supported, and the divergence between Psyttalia and its closest relative (Diachasmimorpha longicaudata) was at ~55 MYA [95% highest posterior density (HPD): 34-83 MYA]. Psyttalia lounsburyi occupied the most basal position among the three Psyttalia, having diverged from the other two species ~11 MYA (95% HPD: 6-17 MYA). Psyttalia concolor and P. humilis were recovered as sister species diverged at ~2 MYA (95% HPD: 1.1-3.6 MYA). This phylogeny combining new sequences and a set of 31 other cyclostomes and non-cyclostomes highlights the importance of a comprehensive taxonomic coverage of Braconidae mitogenomes to overcome the lack of robustness in the placement of several subfamilies.

Five mitochondrial genomes of black fungus gnats (Sciaridae) and their phylogenetic implications

Sciaridae is a family of great species diversity, distributed worldwide, that includes important agricultural pests of cultivated mushrooms and plants produced in greenhouses. Here we sequenced five nearly complete mitochondrial genomes representing three subfamilies of Sciaridae. The lengths of these mitogenomes range from 13,849 bp to 16,923 bp with 13 protein-coding genes (PCGs), 20-22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (CR). Compared with other dipteran species, rearrangements in Sciaridae are more common. Inversion or transition is observed frequently of trnL2, and in the tRNA clusters trnI-trnQ-trnM, trnW-trnC-trnY, and trnA-trnR-trnN-trnS1-trnE-trnF. Phylogenetic relationships within the family were reconstructed based on these newly sequenced species, combined with the published mitogenomes of related families, and recovered the topology within Sciaroidea as Cecidomyiidae + (Sciaridae + Keroplatidae). Relationships recovered within Sciaridae were Sciarinae + ('Pseudolycoriella group' + Megalosphyinae).

Τhe Complete Mitochondrial Genome of Bactrocera carambolae (Diptera: Tephritidae): Genome Description and Phylogenetic Implications

Bactrocera carambolae is one of the approximately 100 sibling species of the Bactrocera dorsalis complex and considered to be very closely related to B. dorsalis. Due to their high morphological similarity and overlapping distribution, as well as to their economic impact and quarantine status, the development of reliable markers for species delimitation between the two taxa is of great importance. Here we present the complete mitochondrial genome of B. carambolae sourced from its native range in Malaysia and its invaded territory in Suriname. The mitogenome of B. carambolae presents the typical organization of an insect mitochondrion. Comparisons of the analyzed B. carambolae sequences to all available complete mitochondrial sequences of B. dorsalis revealed several species-specific polymorphic sites. Phylogenetic analysis based on Bactrocera mitogenomes supports that B. carambolae is a differentiated taxon though closely related to B. dorsalis. The present complete mitochondrial sequences of B. carambolae could be used, in the frame of Integrative Taxonomy, for species discrimination and resolution of the phylogenetic relationships within this taxonomically challenging complex, which would facilitate the application of species-specific population suppression strategies, such as the sterile insect technique.

Complete mitochondrial genome of two Thitarodes species (Lepidoptera, Hepialidae), the host moths of Ophiocordyceps sinensis and phylogenetic implications

Thitarodes (Lepidoptera, Hepialidae) is the only genus that hosts to the Ophiocordyceps sinensis, a traditional Chinese medicine considered as a powerful medicinal supplement. In this study, the complete mitochondrial genomes (mitogenomes) of two species, T. damxungensis and T. pui, have been sequenced, which are 15,928 bp and 15,362 bp in size respectively, and both contain 13 protein-coding genes (PCGs), 2 rRNAs, 22 tRNAs and an AT-rich region. Like other hepialoids, the gene arrangement of the mitogenomes of T. damxungensis and T. pui is identical to the ancestral arrangement but differs from those of other lepidopteran species on account of the different arrangements of trnM, trnI, and trnQ. The size of AT-rich region is 545 bp in T. damxungensis and 1030 bp in T. pui. Tandem repetition in the AT-rich region is responsible for the length difference of the A + T-rich region in both species. In Hepialidae, the phylogenetic study based on the dataset of the sequences that combined the protein-coding genes and RNA genes suggested that the species T. yunnanensis should still belong to the genus Thitarodes rather than Ahamns, which is different from the results based on the traditional phylogeny.