The Complete Mitochondrial Genome of Delia antiqua and Its Implications in Dipteran Phylogenetics

Pollinator shift ensures reproductive success in a camouflaged alpine plant

BACKGROUND AND AIMS

There are intrinsic conflicts between signalling to mutualists and concealing (camouflaging) from antagonists. Like animals, plants also use camouflage as a defence against herbivores. However, this can potentially reduce their attractiveness to pollinators.

METHODS

Using Fritillaria delavayi, an alpine camouflaged plant with inter-population floral colour divergence, we tested the influence of floral trait differences on reproduction. We conducted pollination experiments, measured floral morphological characteristics, estimated floral colours perceived by pollinators, analysed floral scent and investigated reproductive success in five populations.

KEY RESULTS

We found that the reproduction of F. delavayi depends on pollinators. Under natural conditions, a flower-camouflaged population had 100 % fruit set and similar seed set to three out of four yellow-flowered populations. Bumblebees are important pollinators in the visually conspicuous yellow-flowered populations, whereas flies are the only pollinator in the flower-camouflaged population, visiting flowers more frequently than bumblebees. The camouflaged flowers cannot be discriminated from the rock background as perceived by pollinators, but may be located by flies through olfactory cues.

CONCLUSIONS

Collectively, our results demonstrate that the flower-camouflaged population has different reproductive traits from the visually conspicuous yellow-flowered populations. A pollinator shift from bumblebees to flies, combined with high visitation frequency, compensates for the attractiveness disadvantage in camouflaged plants.

Phylogenetic insights based on the first complete mitochondrial genome of Isomyia nebulosa (Diptera: Calliphoridae)

To investigate the phylogenetic position of Isomyia Walker, 1860, a genus that suffered from frequent revisions of the taxonomic status following the subfamily Rhiniinae (Diptera, Calliphoridae), we sequenced, assembled, annotated, and analyzed the first complete mitochondrial genome (mitogenome) of Isomyia nebulosa (Townsend, 1917) in this study. This mitogenome is 16,438 bp in length, with a standard set of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and an A + T riched non-coding region without genetic rearrangement as most dipteran mitogenomes, but long intergenic nucleotides (IGNs) between trnQ and trnM are found. The phylogeny yielded by both Bayesian inference and maximum-likelihood analysis for all mitochondrial PCGs and rRNAs of 23 mitogenomes supports the monophyly of the family Calliphoridae and the subfamilies Calliphorinae, Chrysomyinae, and Luciliinae. In addition, I. nebulosa diverged anterior to the above-mentioned three calliphorid subfamilies with high genetic distances.

Comparative Mitochondrial Genomes between the Genera Amiota and Phortica (Diptera: Drosophilidae) with Evolutionary Insights into D-Loop Sequence Variability

To address the limited number of mitochondrial genomes (mitogenomes) in the subfamily Steganinae (Diptera: Drosophilidae), we assembled 12 complete mitogenomes for six representative species in the genus Amiota and six representative species in the genus Phortica. We performed a series of comparative and phylogenetic analyses for these 12 Steganinae mitogenomes, paying special attention to the commonalities and differences in the D-loop sequences. Primarily determined by the lengths of the D-loop regions, the sizes of the Amiota and Phortica mitogenomes ranged from 16,143-16,803 bp and 15,933-16,290 bp, respectively. Our results indicated that the sizes of genes and intergenic nucleotides (IGNs), codon usage and amino acid usage, compositional skewness levels, evolutionary rates of protein-coding genes (PCGs), and D-loop sequence variability all showed unambiguous genus-specific characteristics and provided novel insights into the evolutionary implications between and within Amiota and Phortica. Most of the consensus motifs were found downstream of the D-loop regions, and some of them showed distinct genus-specific patterns. In addition, the D-loop sequences were phylogenetically informative as the data sets of PCGs and/or rRNAs, especially within the genus Phortica.

Phylogeny and Evolutionary Timescale of Muscidae (Diptera: Calyptratae) Inferred from Mitochondrial Genomes

House flies (Muscidae) comprise the most species-rich family of the muscoid grade with over 5000 described species worldwide, and they are abundant in various terrestrial and aquatic ecosystems. The high number of species, varied appearances, complex feeding habits, and wide distributions have hindered researchers from understanding their phylogeny and evolutionary history. Here, we newly sequenced fifteen mitochondrial genomes and reconstructed the phylogenetic relationships and divergence time among eight subfamilies of Muscidae (Diptera). The best phylogenetic tree, which was inferred by IQ-Tree, recovered the monophyly for seven out of eight subfamilies (except for Mydaeinae). Based on phylogenetic analyses and morphological characteristics, we prefer the subfamily status of Azeliinae and Reinwardtiinae, and separate Stomoxyinae from Muscinae. Genus Helina Robineau-Desvoidy, 1830 was synonymized with Phaonia Robineau-Desvoidy, 1830. The divergence time estimation indicated Muscidae originated at 51.59 Ma (early Eocene). Most subfamilies had originated around 41 Ma. We provided a mtgenomic viewpoint on the phylogenetic relationships and divergence time estimation of Muscidae.

The first complete mitochondrial genome sequences for Ulidiidae and phylogenetic analysis of Diptera

BACKGROUND

Tetanops sintenisi is a pest that mainly damages the root of quinoa (Chenopodium quinoa) and it is first discovered in China in 2018.

METHODS AND RESULTS

Here, the complete mitochondrial genome (mitogenome) of T. sintenisi was sequenced and compared with the mitogenomes of other Diptera species. The results revealed that the mitogenome of T. sintenisi is 15,763 bp in length (GenBank accession number: MT795181) and is comprised of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA genes, and a non-coding A + T-rich region (959 bp). The highly conserved gene arrangement of the mitogenome of T. sintenisi was identical to that of other Diptera insects. Twelve PCGs contained the typical insect start codon ATN, while cox1 had CGA as the start codon. The genes cox2, nad4, and nad1 contained an incomplete termination codon T; nad3, nad5, and cob contained the complete termination codon TAG; and the remaining seven PCGs contained the termination codon TAA. All tRNA genes were predicted to fold into the typical cloverleaf secondary structure. Phylogenetic analysis of 48 species based on the mitogenome sequence revealed that T. sintenisi clustered with the Tephritidae family, indicating that T. sintenisi and Tephritidae have a close phylogenetic relationship.

CONCLUSIONS

The phylogenetic relationship of T. sintenisi based on the mitogenome is consistent with the traditional morphological taxonomy, according to which T. sintenisi belongs to the family Otitidae, which is closely related to the family Muscidae.

Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.

Complete mitogenomes of Anopheles peditaeniatus and Anopheles nitidus and phylogenetic relationships within the genus Anopheles inferred from mitogenomes

BACKGROUND

Despite the medical importance of mosquitoes of the genus Anopheles in the transmission of malaria and other human diseases, its phylogenetic relationships are not settled, and the characteristics of mitochondrial genome (mitogenome) are not thoroughly understood.

METHODS

The present study sequenced and analyzed the complete mitogenomes of An. peditaeniatus and An. nitidus, investigated genome characteristics, and inferred the phylogenetic relationships of 76 Anopheles spp.

RESULTS

The complete mitogenomes of An. peditaeniatus and An. nitidus are 15,416 and 15,418 bp long, respectively, and both include 13 PCGs, 22 tRNAs, two tRNAs and one control region (CR). Mitogenomes of Anopheles spp. are similar to those of other insects in general characteristics; however, the trnR and trnA have been reversed to "trnR-trnA," as has been reported in other mosquito genera. Genome variations mainly occur in CR length (493-886 bp) with six repeat unit types identified for the first time that demonstrate an evolutionary signal. The subgenera Lophopodomyia, Stethomyia, Kerteszia, Nyssorhynchus, Anopheles and Cellia are inferred to be monophyletic, and the phylogenetic analyses support a new phylogenetic relationship among the six subgenera investigated, in that subgenus Lophopodomyia is the sister to all other five subgenera, and the remaining five subgenera are divided into two clades, one of which is a sister-taxon subgenera Stethomyia + Kerteszia, and the other consists of subgenus Nyssorhynchus as the sister to a sister-group subgenera Anopheles + Cellia. Four series (Neomyzomyia, Pyretophorus, Neocellia and Myzomyia) of the subgenus Cellia, and two series (Arribalzagia and Myzorhynchus) of the subgenus Anopheles were found to be monophyletic, whereas three sections (Myzorhynchella, Argyritarsis and Albimanus) and their subdivisions of the subgenus Nyssorhynchus were polyphyletic or paraphyletic.

CONCLUSIONS

The study comprehensively uncovered the characteristics of mitogenome and the phylogenetics based on mitogenomes in the genus Anopheles, and provided information for further study on the mitogenomes, phylogenetics and taxonomic revision of the genus.

Mitochondrial genes associated with pyrethroid resistance revealed by mitochondrial genome and transcriptome analyses in the malaria vector Anopheles sinensis (Diptera: Culicidae)

BACKGROUND

Insecticides are still the main method of mosquito control, but mosquito resistance presents a large obstacle. The function of mitochondrial genes in the evolution of insecticide resistance is still poorly understood. Pyrethroid is the most commonly used insecticide, and Anopheles sinensis is an important malaria vector in China and Southeast Asia. In this study, we investigated the mitochondrial genes associated with pyrethroid resistance through their genetic and expression variation based on analyses of transcriptomes and 36 individuals with resequencing in three geographical populations in China.

RESULTS

The nucleotide diversity (Pi) in 18 resistant individuals was much lower than that in 18 susceptible individuals, which suggests that some sites experienced purifying selection subject to pyrethroid stress. Ka/Ks and amino acid analyses showed that ND4 experienced positive selection and had 23 amino acid mutations due to pyrethroid stress. These mutations might change the ND4 structure and function and thus alter the efficiency of the respiratory chain. ND5 was significantly upregulated, and ATP8 was significantly downregulated in these three pyrethroid resistant populations, which suggests that these two genes function in the production and maintenance of pyrethroid resistance. There are differences in mitochondrial genes involved in pyrethroid resistance among these three populations.

CONCLUSION

This is the first study to reveal the association of mitochondrial genes in the evolution of insecticide resistance through amino acid mutation and expression patterns and can help us further understand insecticide resistance mechanisms. © 2019 Society of Chemical Industry.

The complete mt genomes of Lutzia halifaxia, Lt. fuscanus and Culex pallidothorax (Diptera: Culicidae) and comparative analysis of 16 Culex and Lutzia mt genome sequences

BACKGROUND

Despite the medical importance of the genus Culex, the mitochondrial genome (mt genome) characteristics of Culex spp. are not well understood. The phylogeny of the genus and particularly the generic status of the genus Lutzia and the subgenus Culiciomyia remain unclear.

METHODS

The present study sequenced and analyzed the complete mt genomes of Lutzia halifaxia, Lutzia fuscanus and Cx. (Culiciomyia) pallidothorax and assessed the general characteristics and phylogenetics of all known 16 mt genome sequences for species in the genera Culex and Lutzia.

RESULTS

The complete mt genomes of Lt. halifaxia, Lt. fuscanus and Cx. pallidothorax are 15,744, 15,803 and 15,578 bp long, respectively, including 13 PCGs, 22 tRNAs, two tRNAs and a control region (CR). Length variations in the Culex and Lutzia mt genomes involved mainly the CR, and gene arrangements are the same as in other mosquitoes. We identified four types of repeat units in the CR sequences, and the poly-T stretch exists in all of these mt genomes. The repeat units of CR are conserved to different extent and provide information on their evolution. Phylogenetic analyses demonstrated that the Coronator and Sitiens groups are each monophyletic, whereas the monophyletic status of the Pipiens Group was not supported; Cx. pallidothorax is more closely related to the Sitiens and Pipiens groups; and both phylogenetics analysis and repeat unit features in CR show that Lutzia is a characteristic monophyletic entity, which should be an independent genus.

CONCLUSIONS

To our knowledge, this is the first comprehensive review of the mt genome sequences and taxonomic discussion based on the mt genomes of Culex spp. and Lutzia spp. The research provides general information on the mt genome of these two genera, and the phylogenetic and taxonomic status of Lutzia and Culiciomyia.

Complete mitogenome of Anopheles sinensis and mitochondrial insertion segments in the nuclear genomes of 19 mosquito species

Anopheles sinensis is a major malarial vector in China and Southeast Asia. The mitochondria is involved in many important biological functions. Nuclear mitochondrial DNA segments (NUMTs) are common in eukaryotic organisms, but their characteristics are poorly understood. We sequenced and analyzed the complete mitochondrial (mt) genome of An. sinensis. The mt genome is 15,418 bp long and contains 13 protein-coding genes (PCGs), two rRNAs, 22 tRNAs and a large non-coding region. Its gene arrangement is similar to previously published mosquito mt genomes. We identified and analyzed the NUMTs of 19 mosquito species with both nuclear genomes and mt genome sequences. The number, total length and density of NUMTs are significantly correlated with genome size. About half of NUMTs are short (< 200 bp), but larger genomes can house longer NUMTs. NUMTs may help explain genome size expansion in mosquitoes. The expansion due to mitochondrial insertion segments is variable in different insect groups. PCGs are transferred to nuclear genomes at a higher frequency in mosquitoes, but NUMT origination is more different than in mammals. Larger-sized nuclear genomes have longer mt genome sequences in both mosquitoes and mammals. The study provides a foundation for the functional research of mitochondrial genes in An. sinensis and helps us understand the characteristics and origin of NUMTs and the potential contribution to genome expansion.

Comparative analysis of the Liriomyza chinensis mitochondrial genome with other Agromyzids reveals conserved genome features

Liriomyza chinensis is a serious pest of onions in many countries, especially in East Asia. We sequenced the complete mitochondrial genome of this species and compared it with five other Agromyzidae species. The L. chinensis mitogenome is a double-stranded 16,175 bp circular molecule with an A + T content of 78.3%. It contains 37 genes and a control region as do the sequenced Liriomyza species. The mitogenomes of L. chinensis and other Agromyzidae species showed a clear bias in nucleotide composition with a positive AT-skew. Most PCGs used standard ATN as start codons, and TAN as termination codons. The tRNAs exhibited the typical clover-leaf structure, except for tRNASer^(AGN) and the two rRNA genes are conserved with those of other Agromyzids. The L. chinensis mitogenome control region included several conserved regions, including a poly-T, two (TA)n and one poly-A stretch, which are considered important replication and transcription. The 13 PCGs were used to study the phylogeny of L. chinensis and five related Agromyzids. Analysis by maximum likelihood, Bayesian inference and genetic distance suggest congruent phylogenetic relationships in Liriomyza spp. and provide a useful supplement to taxonomic classification by morphology.

The complete mitochondrial genome of the bazaar fly, Musca sorbens Wiedemann (Diptera: Muscidae)

The bazaar fly, Musca sorbens (Diptera: Muscidae) Wiedemann, 1830 is a world-wide species with sanitary, medical, and veterinary importance. The complete mitochondrial genome of M. sorbens is sequenced to better understand the mitogenomic characteristics and phylogeny of this species. The circular mitogenome is 16,120 bp in length, contains 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), two rRNA genes, and an AT-rich control region. The mitogenome comprises an A + T content of 77.4%. All PCGs start with "ATN" codons except for COI which starts with TCG, and terminate with the common stop codons TNN. A phylogenetic tree, including six Muscidae species, is reconstructed based on the whole mitogenome sequences. The interspecific distances of mitogenomes between the six Muscidae species range from 0.059 to 0.168.

The complete mitochondrial genome of Anopheles minimus (Diptera: Culicidae) and the phylogenetics of known Anopheles mitogenomes

Anopheles minimus is an important vector of human malaria in southern China and Southeast Asia. The phylogenetics of mosquitoes has not been well resolved, and the mitochondrial genome (mtgenome) has proven to be an important marker in the study of evolutionary biology. In this study, the complete mtgenome of An. minimus was sequenced for the first time. It is 15 395 bp long and encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and a non-coding region. The gene organization is consistent with those of known Anopheles mtgenomes. The mtgenome performs a clear bias in nucleotide composition with a positive AT-skew and a negative GC-skew. All 13 PCGs prefer to use the codon UUA (Leu), ATN as initiation codon but cytochrome-oxidase subunit 1 (COI) and ND5, with TCG and GTG, and TAA as termination codon, but COI, COII, COIII and ND4, all with the incomplete T. tRNAs have the typical clover-leaf structure, but tRNA(Ser(AGN)) is consistent with known Anopheles mtgenomes. The control region includes a conserved T-stretch and a (TA)n stretch, and has the highest A+T content at 93.1%. The phylogenetics of An. minimus with 18 other Anopheles species was constructed by maximum likelihood and Bayesian inference, based on concatenated PCG sequences. The subgenera, Cellia and Anopheles, and Nyssorhynchus and Kerteszia have mutually close relationships, respectively. The Punctulatus group and Leucosphyrus group of Neomyzomyia Series, and the Albitarsis group of Albitarsis Series were suggested to be monophyletic. The monophyletic status of the subgenera, Cellia, Anopheles, Nyssorhynchus and Kerteszia need to be further elucidated.