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

Phylogenetic Analysis of Some Species of the Anopheles hyrcanus Group (Diptera: Culicidae) in China Based on Complete Mitochondrial Genomes

Some species of the Hyrcanus group are vectors of malaria in China. However, the member species are difficult to identify accurately by morphology. The development of sequencing technologies offers the possibility of further studies based on the complete mitochondrial genome. In this study, samples of mosquitoes of the Hyrcanus group were collected in China between 1997 and 2015. The mitochondrial genomes of ten species of the Hyrcanus group were analyzed, including the structure and base composition, codon usage, secondary structure of tRNA, and base difference sites in protein coding regions. Phylogenetic analyses using maximum-likelihood and Bayesian inference were performed based on mitochondrial genes and complete mitochondrial genomes The mitochondrial genome of 10 Hyrcanus group members ranged from 15,403 bp to 15,475 bp, with an average 78.23% (A + T) content, comprising of 13 PCGs (protein coding genes), 22 tRNAs, and 2 rRNAs. Site differences between some closely related species in the PCGs were small. There were only 36 variable sites between Anopheles sinensis and Anopheles belenrae for a variation ratio of 0.32% in all PCGs. The pairwise interspecies distance based on 13 PCGs was low, with an average of 0.04. A phylogenetic tree constructed with the 13 PCGs was consistent with the known evolutionary relationships. Some phylogenetic trees constructed by single coding regions (such as COI or ND4) or combined coding regions (COI + ND2 + ND4 + ND5 or ND2 + ND4) were consistent with the phylogenetic tree constructed using the 13 PCGs. The phylogenetic trees constructed using some coding genes (COII, ND5, tRNAs, 12S rRNA, and 16S rRNA) differed from the phylogenetic tree constructed using PCGs. The difference in mitochondrial genome sequences between An. sinensis and An. belenrae was very small, corresponding to intraspecies difference, suggesting that the species was in the process of differentiation. The combination of all 13 PCG sequences was demonstrated to be optimal for phylogenetic analysis in closely related species.

Contribution to the Knowledge of Dicranoptychini (Diptera, Tipuloidea, Limoniidae) in China, with the First Mitochondrial Genome of the Tribe and Its Phylogenetic Implications

Dicranoptychini is a tribe in the subfamily Limoniinae (Diptera, Tipuloidea, and Limoniidae) and includes only the genus Dicranoptycha Osten Sacken, 1860. However, the species diversity of the tribe in China was seriously underestimated, and the taxonomic status of Dicranoptycha has long been controversial. In this study, types of Chinese Dicranoptycha species and specimens collected from several localities in China were examined, and the first mitochondrial (mt) genome of the tribe Dicranoptychini is presented. Two Dicranoptycha species, D. jiufengshana sp. nov. and D. shandongensis sp. nov., from China, are described and illustrated as new to science. A Palaearctic species, D. prolongata Alexander, 1938, is recorded in China for the first time. In addition, the complete mt genome of D. shandongensis sp. nov. is sequenced and annotated, indicating that it is a typical circular DNA molecule with a length of 16,157 bp and shows a similar gene order, nucleotide composition, and codon usage to mt genomes of other Tipuloidea species. The two pairs of repeat elements are found in its control region. Phylogenetic results confirm the sister-group relationship between Cylindrotomidae and Tipulidae, question the position of the genus Epiphragma Osten Sacken, 1860 in Limoniidae, and indicate that Dicranoptychini may be a basal lineage within Limoniinae.

Sequencing and description of the complete mitochondrial genome of Limatus durhamii (Diptera: Culicidae)

The genus Limatus (Diptera: Culicidae) are wild mosquitoes belonging to the Sabethini tribe that occurs in tropical countries and is related to transmission cycles of Orthobunyavirus (Bunyaviridae), particularly in the Amazon region. Given the unavailability of information related to evolutionary biology and molecular taxonomy aspects of this genus, we report here the first complete sequencing of the mitochondrial genome of Limatus durhamii Theobald, 1901. The NextSeq 500 platform was used for sample sequencing, and the mitochondrial sequence obtained was 14,875 bp long, comprising 37 functional subunits (13 PCGs, 22 tRNA and 02 rRNA). The phylogeny reconstructed by maximum likelihood based on the concatenation of all 13 PCGs corroborated the known taxonomic classification based most on aspects of the external morphology and few molecular studies. The data and information produced here may be useful in the future development of taxonomic and evolutionary studies for the genus, as well as the Culicidae family itself.

Description of mitochon genome and phylogenetic considerations of Sabethes bipartipes, Sabethes cyaneus, Sabethes quasicyaneus, and Sabethes tarsopus (Diptera: Culicidae)

The genus Sabethes (Diptera: Culicidae) comprises species of great epidemiological relevance, particularly involved in transmission cycles of the Yellow fever virus in South America. Given the unavailability of information related to aspects of evolutionary biology and molecular taxonomy of species of this genus of mosquitoes, we report here the first sequencing of the mitochondrial genomes of Sabethes bipartipes, Sabethes cyaneus, Sabethes tarsopus, and Sabethes quasicyaneus. The sequences obtained showed an average length of 14,920 bp, comprising 37 functional genes (13 PCGs, 22 tRNA, and 02 rRNA). The phylogenies reconstructed by Maximum likelihood and Bayesian inference methods, based on the concatenated sequences of all 13 PCGs, produced similar topologies and strongly supported the monophyletic relationship between the Sabethes subgenera, corroborating the known taxonomic classification based on aspects of the external morphology of the taxa assessed. The data and information produced from the Sabethes species evaluated here may be useful for future taxonomic and evolutionary studies of the genus, as well as the Culicidae family.

Description of the mitogenome and phylogeny of Aedes spp. (Diptera: Culicidae) from the Amazon region

The genus Aedes (Diptera: Culicidae) includes species of great epidemiological relevance, particularly involved in transmission cycles of leading arboviruses in the Brazilian Amazon region, such as the Zika virus (ZIKV), Dengue virus (DENV), Yellow fever virus (YFV), and Chikungunya virus (CHIKV). We report here the first putatively complete sequencing of the mitochondrial genomes of Brazilian populations of the species Aedes albopictus, Aedes scapularis and Aedes serratus. The sequences obtained showed an average length of 14,947 bp, comprising 37 functional subunits, typical in animal mitochondria (13 PCGs, 22 tRNA, and 2 rRNA). The phylogeny reconstructed by Maximum likelihood method, based on the concatenated sequences of all 13 PCGs produced at least two non-directly related groupings, composed of representatives of the subgenus Ochlerotatus and Stegomyia of the genus Aedes. The data and information produced here may be useful for future taxonomic and evolutionary studies of the genus Aedes, as well as the Culicidae family.

The complete mitochondrial genome of major malaria vector Anopheles anthropophagus (Diptera: Culicidae) in China

Anopheles anthropophagus (Xu and Feng 1975) is the major vector of malaria in Eastern and Southern China. The species An. anthropophagus is considered a synonym of An. lesteri (Baisas & Hu, 1936), although they differ in several key biological characteristics. Here, we report the complete mitochondrial genome of An. anthropophagus for the first time. The mitogenome of An. anthropophagus is a typical circular, double-stranded molecule with a total length of 15,413 base pairs, and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and an AT-rich control region. A phylogenetic analysis of the complete mitogenomes of 16 species of Anopheles (Culicidae) revealed that An. anthropophagus is closely related to An. sinensis (Wiedemann 1828), in the family Culicidae. The An. anthropophagus mitogenome provides new data for further taxonomic and phylogenetic studies of the genus Anopheles.

First Description of the Mitogenome and Phylogeny of Culicinae Species from the Amazon Region

The Culicidae family is distributed worldwide and comprises about 3587 species subdivided into the subfamilies Anophelinae and Culicinae. This is the first description of complete mitochondrial DNA sequences from Aedes fluviatilis, Aedeomyia squamipennis, Coquillettidia nigricans, Psorophora albipes, and Psorophora ferox. The mitogenomes showed an average length of 15,046 pb and 78.02% AT content, comprising 37 functional subunits (13 protein coding genes, 22 tRNAs, and two rRNAs). The most common start codons were ATT/ATG, and TAA was the stop codon for all PCGs. The tRNAs had the typical leaf clover structure, except tRNA^Ser1. Phylogeny was inferred by analyzing the 13 PCGs concatenated nucleotide sequences of 48 mitogenomes. Maximum likelihood and Bayesian inference analysis placed Ps. albipes and Ps. ferox in the Janthinosoma group, like the accepted classification of Psorophora genus. Ae. fluviatilis was placed in the Aedini tribe, but was revealed to be more related to the Haemagogus genus, a result that may have been hampered by the poor sampling of Aedes sequences. Cq. nigricans clustered with Cq. chrysonotum, both related to Mansonia. Ae. squamipennis was placed as the most external lineage of the Culicinae subfamily. The yielded topology supports the concept of monophyly of all groups and ratifies the current taxonomic classification.

Phylogenetic analysis of the Neotropical Albitarsis Complex based on mitogenome data

BACKGROUND

Some of the most important malaria vectors in South America belong to the Albitarsis Complex (Culicidae; Anophelinae; Anopheles). Understanding the origin, nature, and geographical distribution of species diversity in this important complex has important implications for vector incrimination, control, and management, and for modelling future responses to climate change, deforestation, and human population expansion. This study attempts to further explore species diversity and evolutionary history in the Albitarsis Complex by undertaking a characterization and phylogenetic analysis of the mitogenome of all 10 putative taxa in the Albitarsis Complex.

METHODS

Mitogenome assembly and annotation allowed for feature comparison among Albitarsis Complex and Anopheles species. Selection analysis was conducted across all 13 protein-coding genes. Maximum likelihood and Bayesian inference methods were used to construct gene and species trees, respectively. Bayesian methods were also used to jointly estimate species delimitation and species trees.

RESULTS

Gene composition and order were conserved across species within the complex. Unique signatures of positive selection were detected in two species-Anopheles janconnae and An. albitarsis G-which may have played a role in the recent and rapid diversification of the complex. The COI gene phylogeny does not fully recover the mitogenome phylogeny, and a multispecies coalescent-based phylogeny shows that considerable uncertainty exists through much of the mitogenome species tree. The origin of divergence in the complex dates to the Pliocene/Pleistocene boundary, and divergence within the distinct northern South American clade is estimated at approximately 1 million years ago. Neither the phylogenetic trees nor the delimitation approach rejected the 10-species hypothesis, although the analyses could not exclude the possibility that four putative species with scant a priori support (An. albitarsis G, An. albitarsis H, An. albitarsis I, and An. albitarsis J), represent population-level, rather than species-level, splits.

CONCLUSION

The lack of resolution in much of the species tree and the limitations of the delimitation analysis warrant future studies on the complex using genome-wide data and the inclusion of additional specimens, particularly from two putative species, An. albitarsis I and An. albitarsis J.

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.

Phylogeny of certain members of Hyrcanus group (Diptera: Culicidae) in China based on mitochondrial genome fragments

Background

Species of the Anopheles hyrcanus group are widely distributed in Palearctic and Oriental regions and some of them are important malaria vectors. The cryptic species of An. hyrcanus group was almost impossible to identify based only on their morphology. The phylogenetic relationship of An. hyrcanus group was also not clear.

Methods

Five members of An. hyrcanus group were identified by rDNA ITS2 sequencing as An. yatsushiroensis, An. belenrae, An. kleini, An. lesteri and An. sineroides. The mitochondrial genome fragments were sequenced and annotated using the mitochondrial genome of An. sinensis as reference. Based on the four segments and Joint Data sequences of these species, and other four anopheline species downloaded from GenBank, intraspecific as well as interspecific genetic distances were calculated and the phylogenetic trees were reconstructed by the methods of neighbor joining, maximum parsimony, minimum evolution and maximum likelihood.

Findings

Four parts of mitochondrial genomes, which were partial fragments COI + tRNA + COII (F5), ATP6 + COIII(F7 + F8), ND1(F19) and lrRNA (F21), were obtained. All fragments were connected as one sequence (referred as Joint Data), which had a total length of 3393 bp. All fragment sequences were highly conservative within species, with the maximum p distance (0.026) calculated by F19 of An. belenrae. The pairwise interspecific p distance calculated by each fragment showed minor or even no difference among An. sinensis, An. kleini and An. belenrae. However, interspecific p distances calculated by the Joint Data sequence ranged from 0.004 (An. belenrae vs An. kleini) to 0.089 (An. sineroides vs An. minimus), and the p distances of the six members of An. hyrcanus group were all less than 0.029. The phylogenetic tree showed two major clades: all subgenus Anopheles species (including six members of An. hyrcanus group, An. atroparvus and An. quadrimaculatus A) and subgenus Cellia (including An. dirus and An. minimus). The An. hyrcanus group was divided into two clusters as ((An. lesteri, An. sineroides) An. yatsushiroensis) and ((An. belenrae, An. sinensis) An. kleini)).

Conclusions

The An. hyrcanus group in this study could be divided into two clusters, in one of which An. belenrae, An. sinensis and An. kleini were most closely related. More molecular markers would make greater contribution to phylogenetic analysis.

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.