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

Mitogenome-based phylogeny of mosquitoes (Diptera: Culicidae)

Mosquitoes are of great medical significance as vectors of many deadly diseases. Mitogenomes have been widely used in phylogenetic studies, but mitogenome knowledge within the family Culicidae is limited, and Culicidae phylogeny is far from resolved. In this study, we surveyed the mitogenomes of 149 Culicidae species, including 7 newly sequenced species. Comparative analysis of 149 mosquito mitogenomes shows gene composition and order to be identical to that of an ancestral insect, and the AT bias, length variation, and codon usage are all consistent with that of other reported Dipteran mitogenomes. Phylogenetic analyses based on the DNA sequences of the 13 protein-coding genes from the 149 species robustly support the monophyly of the subfamily Anophelinae and the tribes Aedini, Culicini, Mansoniini, Sabethini, and Toxorhynchitini. To resolve ambiguous relationships between clades within the subfamily Culicinae, we performed topological tests and show that Aedini is a sister to Culicini and that Uranotaeniini is a sister to (Mansoniini + (Toxorhynchitini + Sabethini)). In addition, we estimated divergence times using a Bayesian relaxation clock based on the sequence data and 3 fossil calibration points. The results show mosquitoes diverged during the Early Jurassic with massive Culicinae radiations during the Cretaceous, coincident with the emergence of angiosperms and the burst of mammals and birds. Overall, this study, which uses the largest number of Culicidae mitogenomes sequenced to date, comprehensively reveals the mitogenome characteristics and mitogenome-based phylogeny and divergence times of Culicidae, providing information for further studies on the mitogenome, phylogeny, evolution, and taxonomic revision of Culicidae.

Comparative mitochondrial genomic analysis provides new insights into the evolution of the subfamily Lamiinae (Coleoptera: Cerambycidae)

The genus Monochamus within the subfamily Lamiinae is the main vector of Bursaphelenchus xylophilus, which causes pine wilt disease and induces substantial economic and ecological losses. Only three complete mitochondrial genomes of the genus Monochamus have been sequenced to date, and no comparative mitochondrial genomic studies of Lamiinae have been conducted. Here, the mitochondrial genomes of two Monochamus species, M. saltuarius and M. urussovi, were newly sequenced and annotated. The composition and order of genes in the mitochondrial genomes of Monochamus species are conserved. All transfer RNAs exhibit the typical clover-leaf secondary structure, with the exception of trnS1. Similar to other longhorn beetles, Lamiinae mitochondrial genomes have an A + T bias. All 13 protein-coding genes have experienced purifying selection, and tandem repeat sequences are abundant in the A + T-rich region. Phylogenetic analyses revealed congruent topologies among trees inferred from the five datasets, with the monophyly of Acanthocinini, Agapanthiini, Batocerini, Dorcaschematini, Pteropliini, and Saperdini receiving high support. The findings of this study enhance our understanding of mitochondrial genome evolution and will provide a basis for future studies of population genetics and phylogenetic investigations in this group.

Mitochondrial composition of and diffusion limiting factors of three social wasp genera Polistes, Ropalidia, and parapolybia (Hymenoptera: Vespidae)

Background

Social wasps Polistes, Ropalidia, and Parapolybia, belonging to the subfamily Polistinae, have obviously different distribution patterns, yet the factors leading to this difference remain unknown.

Results

The 17 newly sequenced mitogenomes of Polistes, Ropalidia, and Parapolybia contain 37 genes, and there are obvious differences among the compositions of the three genera. The monophyly of the genus Polistes and a monophyletic Ropalidiini: (Ropalidia + Parapolybia) are concordant with previous morphological analysis of the subfamily Polistinae. Our inferred divergence time demonstrates Polistes (at around 69 Ma) was diverged earlier than Ropalidia and Parapolybia (at around 61 Ma). The rearrangement of both trnY and trnL1 are shared by all the Polistinae. In addition, the unique rearrangement of TDRL derived at 69 Ma is detected in Polistes, and Ropalidia contains a Reversal which may derive at 61 Ma. Hereafter, the possibility is elaborated that Polistes originated in Aisa and then dispersed from Africa to South America, and Polistes and Ropalidia spread from Southeast Asia to Australia. At last, continental drift and Quaternary Ice Ages are inferred to be two main limiting factors in the current distributions of the three genera.

Conclusions

Obvious differences occur in the mitochondrial composition of Polistes, Ropalidia, and Parapolybia. According to the reconstructed time-calibrated framework, it is inquired that the continental drifts and the climate are mainly diffusion limiting factors of the three genera.

Supplementary information

The online version contains supplementary material available at 10.1186/s12862-022-02017-6.

The complete mitochondrial genome sequences of the cat flea Ctenocephalides felis felis (Siphonaptera: Pulicidae) support the hypothesis that C. felis isolates from China and USA were the same C. f. felis subspecies

The cat flea Ctenocephalides felis (Siphonaptera: Pulicidae) is the most important ectoparasite in cats and dogs worldwide. Over the years, there has been much dispute regarding the taxonomic and systematic status of C. felis. Mitochondrial (mt) genome sequences are useful genetic markers for the identification and differentiation of ectoparasites, but the mt genome of C. felis and its subspecies has not yet been entirely characterized. In the present study, the entire mt genome of C. f. felis from China was sequenced and compared with that of C. felis from the USA. Both contain 37 genes and a long non-coding region of >6 kbp. The molecular identity between the Chinese and American isolates was 99%, except for the non-coding region. The protein-coding genes showed differences at both the nucleotide (1.2%) and amino acid (1%) levels. Interestingly, the cox1 gene of the Chinese isolate had an unusual putative start codon (TTT). Taken together, our analyses strongly support the hypothesis that C. felis isolates from China and the USA were the same C. f. felis subspecies. The mt genome sequence of the C. f. felis China isolate presented in this study provides useful molecular markers to further address the taxonomy and systematics of C. felis.

Culicidae evolutionary history focusing on the Culicinae subfamily based on mitochondrial phylogenomics

Mosquitoes are insects of medical importance due their role as vectors of different pathogens to humans. There is a lack of information about the evolutionary history and phylogenetic positioning of the majority of mosquito species. Here we characterized the mitogenomes of mosquito species through low-coverage whole genome sequencing and data mining. A total of 37 draft mitogenomes of different species were assembled from which 16 are newly-sequenced species. We datamined additional 49 mosquito mitogenomes, and together with our 37 mitogenomes, we reconstructed the evolutionary history of 86 species including representatives from 15 genera and 7 tribes. Our results showed that most of the species clustered in clades with other members of their own genus with exception of Aedes genus which was paraphyletic. We confirmed the monophyletic status of the Mansoniini tribe including both Coquillettidia and Mansonia genus. The Aedeomyiini and Uranotaeniini were consistently recovered as basal to other tribes in the subfamily Culicinae, although the exact relationships among these tribes differed between analyses. These results demonstrate that low-coverage sequencing is effective to recover mitogenomes, establish phylogenetic knowledge and hence generate basic fundamental information that will help in the understanding of the role of these species as pathogen vectors.

Mitochondrial genome sequencing and phylogeny of Haemagogus albomaculatus, Haemagogus leucocelaenus, Haemagogus spegazzinii, and Haemagogus tropicalis (Diptera: Culicidae)

The genus Haemagogus (Diptera: Culicidae) comprises species of great epidemiological relevance, involved in transmission cycles of the Yellow fever virus and other arboviruses in South America. So far, only Haemagogus janthinomys has complete mitochondrial sequences available. Given the unavailability of information related to aspects of the evolutionary biology and molecular taxonomy of this genus, we report here, the first sequencing of the mitogenomes of Haemagogus albomaculatus, Haemagogus leucocelaenus, Haemagogus spegazzinii, and Haemagogus tropicalis. The mitogenomes showed an average length of 15,038 bp, average AT content of 79.3%, positive AT-skews, negative GC-skews, and comprised 37 functional subunits (13 PCGs, 22 tRNA, and 02 rRNA). The PCGs showed ATN as start codon, TAA as stop codon, and signs of purifying selection. The tRNAs had the typical leaf clover structure, except tRNA^Ser1. Phylogenetic analyzes of Bayesian inference and Maximum Likelihood, based on concatenated sequences from all 13 PCGs, produced identical topologies and strongly supported the monophyletic relationship between the Haemagogus and Conopostegus subgenera, and corroborated with the known taxonomic classification of the evaluated taxa, based on external morphological aspects. The information produced on the mitogenomes of the Haemagogus species evaluated here may be useful in carrying out future taxonomic and evolutionary studies of the genus.

Phylogeny of Anopheles (Kerteszia) (Diptera: Culicidae) Using Mitochondrial Genes

Identification of mosquito species is necessary for determining the entomological components of malaria transmission, but it can be difficult in morphologically similar species. DNA sequences are largely used as an additional tool for species recognition, including those that belong to species complexes. Kerteszia mosquitoes are vectors of human and simian malaria in the Neotropical Region, but there are few DNA sequences of Kerteszia species in public databases. In order to provide relevant information about diversity and improve knowledge in taxonomy of Kerteszia species in Peru, we sequenced part of the mitochondrial genome, including the cytochrome c oxidase I (COI) barcode region. Phylogenetic analyses structured all species of mosquitoes collected in Peru into a single clade, separate from the Brazilian species. The Peruvian clade was composed of two lineages, encompassing sequences from Anopheles (Kerteszia) boliviensis and Anopheles (Kerteszia) pholidotus. An. pholidotus sequences were recorded for the first time in Peru, whereas An. boliviensis sequences were for the first time published in the GenBank database. Sequences generated from specimens morphologically identified as Anopheles (Kerteszia) cruzii clustered into three separate clades according to the collection localities of Serra do Mar, Serra da Mantiqueira, and Serra da Cantareira, confirming An. cruzii as a species complex, composed of at least three putative species.

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.

Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: Identification, characterization and distribution (Diptera: Culicidae)

Simple sequence repeats (SSRs) exist in both eukaryotic and prokaryotic genomes and are the most popular genetic markers, but the SSRs of mosquito genomes are still not well understood. In this study, we identified and analyzed the SSRs in 23 mosquito species using Drosophila melanogaster as reference at the whole-genome level. The results show that SSR numbers (33 076-560 175/genome) and genome sizes (574.57-1342.21 Mb) are significantly positively correlated (R² = 0.8992, P < 0.01), but the correlation in individual species varies in these mosquito species. In six types of SSR, mono- to trinucleotide SSRs are dominant with cumulative percentages of 95.14%-99.00% and densities of 195.65/Mb-787.51/Mb, whereas tetra- to hexanucleotide SSRs are rare with 1.12%-4.22% and 3.76/Mb-40.23/Mb. The (A/T)n, (AC/GT)n and (AGC/GCT)n are the most frequent motifs in mononucleotide, dinucleotide and trinucleotide SSRs, respectively, and the motif frequencies of tetra- to hexanucleotide SSRs appear to be species-specific. The 10-20 bp length of SSRs are dominant with the number of 110 561 ± 93 482 and the frequency of 87.25% ± 5.73% on average, and the number and frequency decline with the increase of length. Most SSRs (83.34% ± 7.72%) are located in intergenic regions, followed by intron regions (11.59% ± 5.59%), exon regions (3.74% ± 1.95%), and untranslated regions (1.32% ± 1.39%). The mono-, di- and trinucleotide SSRs are the main SSRs in both gene regions (98.55% ± 0.85%) and exon regions (99.27% ± 0.52%). An average of 42.52% of total genes contains SSRs, and the preference for SSR occurrence in different gene subcategories are species-specific. The study provides useful insights into the SSR diversity, characteristics and distribution in 23 mosquito species of genomes.

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.

The first divergence time estimation of the subfamily Stenogastrinae (Hymenoptera: Vespidae) based on mitochondrial phylogenomics

In this study, the mitochondrial genomes of three Stenogastrinae species, Eustenogaster scitula, Liostenogaster nitidipennis and Parishnogaster mellyi were sequenced and annotated, and a total of 16 vespid mtgenomes are comparatively analyzed. Our results indicate that codon usage bias is mainly dominated by mutational pressure, and affected only slightly by natural selection. Selective pressure analysis of protein-coding genes (PCGs) shows that the highest evolutionary rate is present in NADH complex I, and the lowest in cox1. Compared with the reported mtgenomes of other Vespidae, in Stenogastrinae, trnH is shifted to a new position. Phylogenetic analyses are performed using Bayesian method and Maximum Parsimony. Phylogenetic analysis further confirms that the Stenogastrinae is the sister group of all remaining Vespidae. Divergence time of Stenogastrinae from other Vespidae is estimated at ~ 166 Mya. Our results also support that eusociality evolved twice in the family Vespidae.

The complete mitochondrial genome of Orancistrocerusaterrimusaterrimus and comparative analysis in the family Vespidae (Hymenoptera, Vespidae, Eumeninae)

To date, only one mitochondrial genome (mitogenome) in the Eumeninae has been reported in the world and this is the first report in China. The mitogenome of O.a.aterrimus is 17 972 bp long, and contains 38 genes, including 13 protein coding genes (PCGs), 23 tRNA genes, two rRNA genes, a long non-coding region (NCR), and a control region (CR). The mitogenome has 79.43% A + T content, its 13 PCGs use ATN as the initiation codon except for cox1 using TTG, and nine genes used complete translation termination TAA and four genes have incomplete stop codon T (cox2, cox3, nad4, and cytb). Twenty-two of 23 tRNAs can form the typical cloverleaf secondary structure except for trnS1. The CR is 1 078 bp long with 84.69% A+T content, comprising 28 bp tandem repeat sequences and 13 bp T-strech. There are two gene rearrangements which are an extra trnM2 located between trnQ and nad2 and the trnL2 in the upstream of nad1. Within all rearrangements of these mitogenomes reported in the family Vespidae, the translocation between trnS1 and trnE genes only appears in Vespinae, and the translocation of trnY in Polistinae and Vespinae. The absent codons of 13 PCGs in Polistinae are more than those both in Vespinae and Eumeninae in the family Vespidae. The study reports the complete mitogenome of O.a.aterrimus, compares the characteristics and construct phylogenetic relationships of the mitogenomes in the family Vespidae.

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.

Complete Anopheles funestus mitogenomes reveal an ancient history of mitochondrial lineages and their distribution in southern and central Africa

Anopheles funestus s.s. is a primary vector of malaria in sub-Saharan Africa. Despite its important role in human Plasmodium transmission, evolutionary history, genetic diversity, and population structure of An. funestus in southern and central Africa remains understudied. We deep sequenced, assembled, and annotated the complete mitochondrial genome of An. funestus s.s. for the first time, providing a foundation for further genetic research of this important malaria vector species. We further analyzed the complete mitochondrial genomes of 43 An. funestus s.s. from three sites in Zambia, Democratic Republic of the Congo, and Tanzania. From these 43 mitogenomes we identified 41 unique haplotypes that comprised 567 polymorphic sites. Bayesian phylogenetic reconstruction confirmed the co-existence of two highly divergent An. funestus maternal lineages, herein defined as lineages I and II, in Zambia and Tanzania. The estimated coalescence time of these two mitochondrial lineages is ~500,000 years ago (95% HPD 426,000–594,000 years ago) with subsequent independent diversification. Haplotype network and phylogenetic analysis revealed two major clusters within lineage I, and genetic relatedness of samples with deep branching in lineage II. At this time, data suggest that the lineages are partially sympatric. This study illustrates that accurate retrieval of full mitogenomes of Anopheles vectors enables fine-resolution studies of intraspecies genetic relationships, population differentiation, and demographic history. Further investigations on whether An. funestus mitochondrial lineages represent biologically meaningful populations and their potential implications for malaria vector control are warranted.

The mitochondrial genomes of two walnut pests, Gastrolina depressa depressa and G. depressa thoracica (Coleoptera: Chrysomelidae), and phylogenetic analyses

In this study, the mitochondrial genomes (mitogenomes) of two walnut leaf insect pests, Gastrolina depressa depressa and G. depressa thoracica, were sequenced by Sanger sequencing technology. The mitogenome of G. depressa thoracica was complete at 16,109 bp in length, while the mitogenome of G. depressa depressa (14,277 bp) was partial. The genomic analyses indicated that both mitogenomes have the typical gene content and arrangement. The formerly identified elements, 'TAGTA' between trnSer(UCN) and nad2, and 'ATGATAA' between atp8 and atp6, were more conserved than that between nad4L and nad4, which was 'ATGTTAA' in Coleoptera excluding Polyphaga. Phylogenetic analyses of the 13 protein-coding genes from 36 coleopteran species well supported a close affinity between the subfamily Chrysomelinae including G. depressa thoracica and G. depressa depressa and Galerucinae, as well as a sister relationship of ((Eumolpinae + Cryptocephalinae) + Cassidinae) within Chrysomelidae.

Sequencing and analysis of the complete mitochondrial genome in Anopheles sinensis (Diptera: Culicidae)

Background

Anopheles sinensis (Diptera: Culicidae) is a primary vector of Plasmodium vivax and Brugia malayi in most regions of China. In addition, its phylogenetic relationship with the cryptic species of the Hyrcanus Group is complex and remains unresolved. Mitochondrial genome sequences are widely used as molecular markers for phylogenetic studies of mosquito species complexes, of which mitochondrial genome data of An. sinensis is not available.

Methods

An. sinensis samples was collected from Shandong, China, and identified by molecular marker. Genomic DNA was extracted, followed by the Illumina sequencing. Two complete mitochondrial genomes were assembled and annotated using the mitochondrial genome of An. gambiae as reference. The mitochondrial genomes sequences of the 28 known Anopheles species were aligned and reconstructed phylogenetic tree by Maximum Likelihood (ML) method.

Findings

The length of complete mitochondrial genomes of An. sinensis was 15,076 bp and 15,138 bp, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and an AT-rich control region. As in other insects, most mitochondrial genes are encoded on the J strand, except for ND5, ND4, ND4L, ND1, two rRNA and eight tRNA genes, which are encoded on the N strand. The bootstrap value was set as 1000 in ML analyses. The topologies restored phylogenetic affinity within subfamily Anophelinae. The ML tree showed four major clades, corresponding to the subgenera Cellia, Anopheles, Nyssorhynchus and Kerteszia of the genus Anopheles.

Conclusions

The complete mitochondrial genomes of An. sinensis were obtained. The number, order and transcription direction of An. sinensis mitochondrial genes were the same as in other species of family Culicidae.

Electronic supplementary material

The online version of this article (10.1186/s40249-017-0362-7) contains supplementary material, which is available to authorized users.