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

Identification and characterization of a laterally transferred alternative oxidase (AOX) in a terrestrial insect, the dipteran Pseudolycoriella hygida

Alternative oxidase (AOX) (EC 1.10.3.11) is a terminal oxidase in the mitochondrial inner membrane that branches the canonical electron transport system (ETS). AOX is ubiquitous in plants, frequently found in fungi and protists and presents a more sporadic distribution in metazoans. More recently, AOX has gained attention due to its potential application in gene therapy for treatment of mitochondrial diseases. Here we characterized the AOX in the basal Dipteran, Pseudolycoriella hygida using a combination of genomic analyses, molecular, functional and in vivo survival assays. AOX is a single copy gene that encodes three developmental stage specific protein isoforms. AOX localizes to the mitochondria in adult thoracic muscles, which present cyanide-resistant respiration that is sensitive to the AOX inhibitor salicylhydroxamic acid (SHAM). Both the cyanide-resistant respiration and AOX levels gradually increase during aging, but are not influenced by thermal stress. Thoracic mitochondria respire using substrates derived from several metabolic routes, such as pyruvate, proline, acylcarnitine, NADH and glycerol-3P, and present values of oxidative phosphorylation capacity ((P-L)/E = 0.70) and coupling (P/L = 4.35; L/E = 0.21). Adult flies exhibit a high survival resistance for SHAM-sensitive complex III inhibition. Together, our results demonstrate the presence of a functional AOX in a terrestrial arthropod and provide insights regarding AOX function in animals and evolution of respiratory systems in metazoans. Psl. hygida emerges as a natural and valuable model for comprehensive AOX research at the whole-organism level which complements models expressing the heterologous enzyme.

Complete mitochondrial genome of Plecialongiforceps Duda, 1933 (Diptera, Bibionidae) and its implications for a phylogeny of the family Bibionidae

Over the past decade, the prevalence of mass outbreaks involving non-native insects has sparked concerns about their potential negative impact on human inhabited areas and local environments. Plecialongiforceps Duda, 1933 (Diptera, Bibionidae) was recently recognized as an invasive pest in South Korea, causing public nuisance through mass outbreaks in the Seoul Metropolitan Area during early summer. In this study, we present the first complete mitochondrial genome of Plecialongiforceps, generated from the PacBio HiFi long-read sequencing data. Notably, the length of the circular genome is found to be larger than any annotated reference sequences of mitochondrial genomes for the infraorder Bibionomorpha, which is attributable to an unusually long A+T rich control region. We conducted a phylogenetic analysis of Bibionomorpha, focusing specifically on the family Bibionidae, using nearly all available mitochondrial genome data to elucidate relationships among genera within Bibionidae. Our phylogeny of Bibionomorpha recovered a strong monophyly of the family Bibionidae and its three subfamilies: Bibioninae (Bibio + Dilophus), Hesperininae (Hesperinus + Penthetria), and Pleciinae (Plecia), corroborating the recently proposed taxonomic classification system of Bibionidae. Furthermore, we discuss evolutionary trends within Bibionidae based on our well-supported higher relationships of the superfamily Bibionoidea.

Morphology and DNA barcodes of four species of Bradysia hilaris group from China (Diptera, Sciaridae)

Four morphologically allied species of the Bradysia hilaris group were studied from China. In a DNA metabarcoding based dipteran diversity study in Zhejiang, eastern China, a hyper-abundant sciarid species was discovered. It was further recognized in this study to be new to science, Bradysia tianmuensis Du & Huang sp. nov., as well as a morphologically similar species, Bradysia curvula Du & Huang sp. nov. Both new species were found to be fairly similar morphologically to the holotype of Bradysia noduspina Yang, Zhang & Yang, 1993 from Guizhou in western China. However, the paratype of B. noduspina appeared to be different from the holotype and determined to be new to science, Bradysia chikunae Du & Huang sp. nov. A phylogenetic tree of all the available 31 COI sequences of the Bradysia hilaris group was provided. Molecular work conducted in the current study also supports Bradysia tianmuensis Du & Huang sp. nov. and Bradysia curvula Du & Huang sp. nov. as new to science thus the four species were described or redescribed accompanied by detailed imagery of habitus and other characters useful for determination.

Comparative Analysis of Complete Mitochondrial Genomes of Five Chromodorididae Species (Nudibranchia:Doridina)

Mitochondrial genome is an important molecular marker for exploring the phylogenetic relationships of species and revealing molecular evolution. In the present study, 5 mitogenomes of Chromodorididae (Chromodoris lochi, Chromodoris colemani, Chromodoris elisabethina, Chromodoris annae and Hypselodoris whitei) were systemically investigated. The lengths of the mitogenomes sequences were 14248 bp, 14257 bp, 14252 bp, 14254 bp and 14856 bp, respectively. Most protein-coding genes (PCGs) were initiated with the common ATG codon and terminated with the TAA and TAG. We calculated Ka/Ks values for all 13 PCGs of Chromodorididae species, all ratios were less than 1, indicating selection by purification. Phylogenetic relationships were constructed by Bayesian inference (BI) and maximum likelihood (ML) methods based on all complete genomes of 50 species, primarily from the family Chromodorididae (Doridina) and 2 outgroups. This phylogenetic tree provided further additional references for the classification of the suborder Doridina. Gene rearrangement suggested a more conserved pattern of gene sequences in the superfamily Chromodoridoidea. These results and newly sequenced will contribute to a better understanding of Chromodorididae and provide reference for further phylogenetic studies.

Two New Mitogenomes of Bibionidae and Their Comparison within the Infraorder Bibionomorpha (Diptera)

Despite the worldwide distribution and rich diversity of the infraorder Bibionomorpha in Diptera, the characteristics of mitochondrial genomes (mitogenomes) are still little-known, and the phylogenetics and evolution of the infraorder remains controversial. In the present study, we report complete and annotated mitogenome sequences of Penthetria simplioipes and Plecia hardyi representing Bibionidae. This is the first report of the complete mitogenomes for the superfamily Bibionoidea. There are 37 genes in each of the complete mitogenomes of all 20 studied species from eight families of four superfamilies within infraorder Bibionomorpha. The Ka/Ks analysis suggests that all 13 PCGs have undergone purifying selection. The gene rearrangement events exist in some families (Keroplatidae, Sciaridae, and Cecidomyiidae) but not in Mycetophilidae in Sciaroidea and also in Scatopsoidea, Anisopodoidea, and Bibionoidea, which suggests that these rearrangement events are derived in the late period in the evolution of the Bibionomorpha. The phylogenetic analysis suggests the phylogenetic relationships of Scatopsoidea + (Anisopodoidea + (Bibionoidea + Sciaroidea)) in Bibionomorpha. The divergence time analysis suggests that Bibionomorpha originated in the Triassic, Scatopsoidea and Anisopodoidea in the late Triassic, Bibionoidea in the Jurassic, and Sciaroidea in the Jurassic to the Cretaceous. The work lays a base for the study of mitogenomes in Bibionomorpha but further work and broader taxon sampling are necessary for a better understanding of the phylogenetics and evolution of the infraorder.

Biocatalytic potential of Pseudolycoriella CAZymes (Sciaroidea, Diptera) in degrading plant and fungal cell wall polysaccharides

Soil biota has a crucial impact on soil ecology, global climate changes, and effective crop management and studying the diverse ecological roles of dipteran larvae deepens the understanding of soil food webs. A multi-omics study of Pseudolycoriella hygida comb. nov. (Diptera: Sciaroidea: Sciaridae) aimed to characterize carbohydrate-active enzymes (CAZymes) for litter degradation in this species. Manual curation of 17,881 predicted proteins in the Psl. hygida genome identified 137 secreted CAZymes, of which 33 are present in the saliva proteome, and broadly confirmed by saliva CAZyme catalytic profiling against plant cell wall polysaccharides and pNP-glycosyl substrates. Comparisons with two other sciarid species and the outgroup Lucilia cuprina (Diptera: Calliphoridae) identified 42 CAZyme families defining a sciarid CAZyme profile. The litter-degrading potential of sciarids corroborates their significant role as decomposers, yields insights to the evolution of insect feeding habits, and highlights the importance of insects as a source of biotechnologically relevant enzymes.

The Genus Spinopygina gen. nov. (Diptera, Sciaridae) from Western North America: Preliminary Molecular Phylogeny and Description of Seven New Species

The genus Spinopygina gen. nov. (type species Camptochaeta uniceps Hippa & Vilkamaa, 1994) from western North America is described. The genus includes the following eight species: Spinopygina acerfalx sp. nov.; S. aurifera sp. nov.; S. camura sp. nov.; S. edura sp. nov.; S. peltata sp. nov.; S. plena sp. nov.; S. quadracantha sp. nov.; and S. uniceps (Hippa & Vilkamaa, 1994) comb. nov., transferred from Corynoptera Winnertz. The new species are described and Spinopygina uniceps is re-diagnosed. The species are keyed and illustrated. In the maximum-likelihood phylogenetic hypothesis based on four gene fragments (28S, 18S, 16S and COI), Spinopygina gen. nov. appears as the sister group of Claustropyga Hippa, Vilkamaa & Mohrig, 2003. In the same analysis, a remarkable, undescribed species is placed within Camptochaeta Hippa & Vilkamaa clade.

The complete mitochondrial genome of Simulium jisigouense (Diptera: Simuliidae) and phylogenetic analysis of Simuliidae

The family Simuliidae belongs to Diptera whose systematic position is still strongly debated. A few mitochondrial genomes (mitogenomes) of Simuliidae and none of the subgenus Montisimulium in the genus Simulium have previously been available. Therefore, the mitogenome of Simulium jisigouense Chen, Zhang and Liu, 2008 was sequenced to better understand the diversity of mitogenomes within this family. The complete mitogenome of S. jisigouense was 16,384 bp long. It contained 37 genes including 22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs, and an A + T-rich region, which was the same as the arrangement of mitogenomes of ancestral insects. Almost all PCGs used the typical ATN as start codons, except COI used TTG. Almost all tRNAs could be folded into cloverleaf structures except the dihydrouridine (DHU) arm of tRNASer(AGN), which formed a loop. The phylogenetic analysis revealed that Simuliidae was monophyletic and was the sister group to Thaumaleidae. Subgenus Simulium was recovered as paraphyletic and needs more comprehensive sampling in future studies. Divergence time estimation showed that Simuliidae diverged from Thaumaleidae at 239.24 Ma and the subgenera of Simulium diverged from each other from 162.46 to 75.08 Ma.

Characterization of the mitochondrial genomes of Bradysia hygida, Phytosciara flavipes and Trichosia splendens (Diptera: Sciaridae) and novel insights on the control region of sciarid mitogenomes

Sciarids, also called "fungus gnats" are small, almost entirely dark-coloured insects. Sciarid larvae feed on different substrates and can infest agricultural crops and mushroom nurseries, causing economic losses. Of the 2174 Diptera mitogenome sequences currently available in GenBank, only eight are from the Sciaridae family, none of which are complete circular molecules. Here we describe the mitogenome sequences of three sciarid species: Phytosciara flavipes, Trichosia splendens and Bradysia hygida and provide novel insights on the control region of sciarid mitogenomes. The assembled mitogenomes range from 16,062 bp in P. flavipes to 17,095 bp in B. hygida. All 13 protein coding genes, 22 tRNAs and 2 rRNAs characteristic of insect mitogenomes were identified, but the sequence of the control region could not be determined. Experimental results suggest that the B. hygida control region is about 21 kb long resulting in a 37 kb long mitogenome which constitutes the largest insect mitochondrial genome described so far. Phylogenetic analysis using all Bibionomorpha mitogenome sequences available in GenBank strongly supports the Sciaridae monophyly and led to the identification of species and subfamily specific gene rearrangements. Our study extends the knowledge of this large and diverse insect family that includes agricultural pest species.

Mitogenomes provide new insights of evolutionary history of Boreheptagyiini and Diamesini (Diptera: Chironomidae: Diamesinae)

Mitogenomes have been widely used for phylogenetic reconstruction of various Dipteran groups, but specifically for chironomid, they have not been carried out to resolve the relationships. Diamesinae (Diptera: Chironomidae) are important bioindicators for freshwater ecosystem monitoring, but its evolutionary history remains uncertain for lack of information. Here, coupled with one previously published and 30 new mitogenomes of Diamesinae, we carried out comparative mitogenomic analysis and phylogenetic analysis. Mitogenomes of Diamesinae were conserved in structure, and all genes arranged in the same order as the ancestral insect mitogenome. All protein-coding genes in Diamesinae were under stronger purifying selection than those of other nonbiting midge species, which may exhibit signs of adaptation to life at cold living conditions. Phylogenetic analyses strongly supported the monophyly of Diamesinae, with Boreheptagyiini deeply nested within Diamesini. In addition, phylogenetic relationship of selected six genera was resolved, except Sympotthastia remained unstable. Our study revealed that the mitogenomes of Diamesinae are highly conserved, and they are practically useful for phylogenetic inference.

First report of the complete mitogenome of Tanypus punctipennis Meigen, 1818 (Diptera, Chironomidae) from Hebei Province, China

Tanypus punctipennis Meigen, 1818 is an important bioindicator for freshwater ecosystems monitoring. Although COI barcode analyses have been performed on T. punctipennis, the mitogenome of this taxon has not been assembled and analyzed. Here, the complete mitogenome of T. punctipennis was sequenced and analyzed to confirm the systematic and phylogenetic history of this species. The mitogenome is 16,215 bp long with high A + T content, and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a noncoding control region. The phylogenomic analysis supports monophyletic Tanypodinae and close relationship between T. punctipennis and Clinotanypus. Our results indicate that mitogenomes showed strong signals in phylogenetic reconstructions at the genus level of Tanypodinae.

Metabarcoding reveals massive species diversity of Diptera in a subtropical ecosystem

Diptera is often considered to be the richest insect group due to its great species diversity and broad ecological versatility. However, data on dipteran diversity from subtropical ecosystems have hitherto been scarce, due to the lack of studies conducted at an appropriate large scale. We investigated the diversity and composition of Diptera communities on Tianmu Mountain, Zhejiang, China, using DNA metabarcoding technology, and evaluated their dynamic responses to the effects of slope aspect, season, and altitudinal zone. A total of 5,092 operational taxonomic units (OTUs) were discovered and tentatively assigned to 72 dipteran families, including 2 family records new for China and 30 family records new for the locality. Cecidomyiidae, Sciaridae, and Phoridae were the predominant families, representing 53.6% of total OTUs, while 52 families include >95% unidentified and presumed undescribed species. We found that the community structure of Diptera was significantly affected by aspect, seasonality (month) and elevation, with richer diversity harbored in north-facing than south-facing slopes, and seasonality a more profound driver of community structure and diversity than elevation. Overall, massive species diversity of Diptera communities was discovered in this subtropical ecosystem of east China. The huge diversity of potentially undescribed species only revealed by metabarcoding now requires more detailed taxonomic study, as a step toward an evolutionary integration that accumulates information on species' geographic ranges, ecological traits, functional roles, and species interactions, and thus places the local communities in the context of the growing knowledge base of global biodiversity and its response to environmental change.

First report of the complete mitogenome of Microchironomus tabarui Sasa, 1987 (Diptera, Chironomidae) from Hebei Province, China

Microchironomus tabarui Sasa, 1987 is an important bioindicator for freshwater ecosystem monitoring. Although COI barcode analyes have been performed on M. tabarui, the mitogenome of this taxon has not been assembled and analyzed. Here the complete mitogenome of M. tabarui was sequenced and analyzed to confirm the systematic and phylogenetic history of this species. The mitogenome is 15,667 bp long with high A + T content and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a noncoding control region. The phylogenomic analysis support monophyletic Chironominae and close relationship between M. tabarui and Chironomus. Our results indicate that mitogenomes showed strong signals in phylogenetic reconstructions at the genus level of Chironominae.

First complete mitogenomes of Diamesinae, Orthocladiinae, Prodiamesinae, Tanypodinae (Diptera: Chironomidae) and their implication in phylogenetics

BACKGROUND

The mitochondrial genome (mitogenome) has been extensively used for phylogenetic and evolutionary analysis in Diptera, but the study of mitogenome is still scarce in the family Chironomidae.

METHODS

Here, the first complete mitochondrial genomes of four Chironomid species representing Diamesinae, Orthocladiinae, Prodiamesinae and Tanypodinae are presented. Coupled with published mitogenomes of two, a comparative mitochondrial genomic analysis between six subfamilies of Chironomidae was carried out.

RESULTS

Mitogenomes of Chironomidae are conserved in structure, each contains 37 typical genes and a control region, and all genes arrange the same gene order as the ancestral insect mitogenome. Nucleotide composition is highly biased, the control region displayed the highest A + T content. All protein coding genes are under purifying selection, and the ATP8 evolves at the fastest rate. In addition, the phylogenetic analysis covering six subfamilies within Chironomidae was conducted. The monophyly of Chironomidae is strongly supported. However, the topology of six subfamilies based on mitogenomes in this study is inconsistent with previous morphological and molecular studies. This may be due to the high mutation rate of the mitochondrial genetic markers within Chironomidae. Our results indicate that mitogenomes showed poor signals in phylogenetic reconstructions at the subfamily level of Chironomidae.

Mitogenomes provide insights into the phylogeny of Mycetophilidae (Diptera: Sciaroidea)

The family Mycetophilidae (Diptera: Sciaroidea) consists of more than 4,500 described species distributed worldwide. Among them, dozens of species have been reported to be economically important to cultivated mushrooms and crops. Relationships among subfamilies in Mycetophilidae have been controversial by using morphological characters or gene markers. In this study, five mycetophilid mitogenomes representing four subfamilies were sequenced and analyzed with 15 published sciaroid mitogenomes as ingroup, while another two species representing two closely related families were chosen as outgroup. All of the sequenced mitogenomes contain 37 genes arranged in the ancestral order, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region (CR). Among mycetophilid mitogenomes, Leu, Ile, Phe, and Met are the most frequently encoded amino acids (AA), with TTA (Leu), ATT (Ile), TTT (Phe) and ATA (Met) being the most frequent codons. Meanwhile, the phylogenetic results reconstructed based on PCGs, PCGs + rRNAs and AA sequences respectively show that the clade of Sciaroidea was well separated from outgroup, further confirming its monophyly. The phylogenetic relationships within Mycetophilidae were recovered as (Manotinae + Sciophilinae) + (Mycomyinae + Mycetophilinae). Mapped to the phylogram, the gene rearrangements occur frequently in the crown group, implying extremely rapid evolutionary rates in Sciaridae and Cecidomyiidae, which might be the reason why the two families have such high species diversity.

Complete mitochondrial genome of Pnyxia scabiei (Diptera: Sciaridae)

The potato scab-gnat, Pnyxia scabiei, was recorded as a pest attacking potato tubers and greenhouse cucumber plants. The mitochondrial genome of a total length of 15,437 bp was sequenced, including 13 protein-coding genes, 22 tRNA genes, and two rRNA genes with A + T content of 77.2%. Six gene overlaps were found from 1 to 34 bp. Phylogenetic analysis showed that P. scabiei was closely related to Trichosia lengersdorfi + Sciara ruficauda. The study provided further data for species diversification in Sciaridae.