First record of translocation in Culicidae (Diptera) mitogenomes: evidence from the tribe Sabethini

JW, Vieira DBR, Brandão RCF, Medeiros DBDA, Nunes Neto JP. Sequencing and Description of the Mitochondrial Genome of Orthopodomyia fascipes (Diptera: Culicidae)

The genus Orthopodomyia Theobald, 1904 (Diptera: Culicidae) comprises 36 wild mosquito species, with distribution largely restricted to tropical and temperate areas, most of which are not recognized as vectors of epidemiological importance due to the lack of information related to their bionomy and involvement in the cycle transmission of infectious agents. Furthermore, their evolutionary relationships are not completely understood, reflecting the scarcity of genetic information about the genus. Therefore, in this study, we report the first complete description of the mitochondrial genome of a Neotropical species representing the genus, Orthopodomyia fascipes Coquillet, 1906, collected in the Brazilian Amazon region. Using High Throughput Sequencing, we obtained a mitochondrial sequence of 15,598 bp, with an average coverage of 418.5×, comprising 37 functional subunits and a final portion rich in A + T, corresponding to the control region. The phylogenetic analysis, using Maximum Likelihood and Bayesian Inference based on the 13 protein-coding genes, corroborated the monophyly of Culicidae and its two subfamilies, supporting the proximity between the tribes Orthopodomyiini and Mansoniini, partially disagreeing with previous studies based on the use of molecular and morphological markers. The information generated in this study contributes to a better understanding of the taxonomy and evolutionary history of the genus and other groups of Culicidae.

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.

Unusual rearrangements of mitogenomes in Diptera revealed by comparative analysis of 135 tachinid species (Insecta, Diptera, Tachinidae)

The Tachinidae is one of the most speciose families in Diptera, and the exclusively parasitoid species play an important role in regulating populations of many herbivorous insects in ecosystems, including many agricultural pests. To better comprehend the characteristics and evolution of the mitochondrial genome for the Tachinidae, we are adding a massive amount of new molecular data by assembling the mitogenomes for 71 genera and 135 species from all four tachinid subfamilies through next-generation sequencing, and we are presenting the most comprehensive mitogenomic phylogenetic analysis of this family so far. Extensive rearrangements observed in the mitogenome of Admontia podomyia (Exoristinae) are unique for the entire suborder Cyclorrhapha. The rearrangement pattern suggests that the process involved a tandem duplication of the complete mitogenome, followed by both random and nonrandom loss of one copy of each gene. Additionally, five minor mitogenome rearrangements are discovered and described in three subfamilies. We present the largest species-level phylogenetic hypothesis for Tachinidae to date, based on mitogenomes of 152 species of Tachinidae, representing all four subfamilies and with five non-tachinid outgroups. Our analyses support the monophyly of the Tachinidae and most tribes and genera were recovered with good support, but the higher-level phylogenetic relationships within Tachinidae were poorly resolved, indicating that mitogenome data alone are not enough to unambiguously resolve the deeper phylogenetic relationships within Tachinidae.

Sequencing and Analysis of the Mitochondrial Genome of Aedes aegypti (Diptera: Culicidae) from the Brazilian Amazon Region

Aedes aegypti is a mosquito native to the African continent, which is now widespread in the tropical and subtropical regions of the world. In many regions, it represents a major challenge to public health, given its role in the cycle of transmission of important arboviruses, such as Dengue, Zika, and Chikungunya. Considering the epidemiological importance of Ae. aegypti, the present study sequenced the partial mitochondrial genome of a sample collected in the municipality of Balsas, in the Brazilian state of Maranhão, followed by High Throughput Sequencing and phylogenetic analyses. The mitochondrial sequence obtained here was 15,863 bp long, and contained 37 functional subunits (thirteen PCGs, twenty-two tRNAs and two rRNAs) in addition to a partial final portion rich in A+T. The data obtained here contribute to the enrichment of our knowledge of the taxonomy and evolutionary biology of this prominent disease vector. These findings represent an important advancement in the understanding of the characteristics of the populations of northeastern Brazil and provide valuable insights into the taxonomy and evolutionary biology of this prominent disease vector.

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.

First description of the mitogenome and phylogeny:Aedes vexansand Ochlerotatus caspius of the Tribe Aedini (Diptera: Culicidae)

Culicidae, the mosquito family, includes more than 3600 species subdivided into the subfamilies Anophelinae and Culicinae. One-third of mosquitoes belong to the Aedini tribe, which is subordinate to the subfamily Culicinae, which comprises common vectors of viral zoonoses. The tribe of Aedini is extremely diverse in morphology and geographical distribution and has high ecological and medical significance. However, knowledge about the systematics of the Aedini tribe is still limited owing to its large population and the similar morphological characteristics of its species. This study provides the first description of the complete mitochondrial (mt) genome sequence of Aedes vexans and Ochlerotatus caspius belonging to the Aedini tribe. The mt genomes of A. vexans and O. caspius are circular molecules that are 15,861 bp and 15,954 bp in size, with AT contents of 78.54% and 79.36%, respectively. Both the circular mt genomes comprise 37 functional subunits, including 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes (tRNAs), and a control region (also known as the AT-rich region). The most common start codons are ATT/ATG, apart from cox1 (TCG) and nad5 (GTG), while TAA is the termination codon for all PCGs. All tRNAs have a typical clover leaf structure, except tRNA Ser1. Phylogenetic analysis of the concatenated, aligned amino acid sequences of the 13 PCGs showed that A. vexans gathered with Aedes sp. in a sister taxon, and O. caspius gathered with Ochlerotatus sp. in a sister taxon. The findings from the present study support the concept of monophyly of all groups, ratify the current taxonomic classification, and provide vital molecular marker resources for further studies of the taxonomy, population genetics, and systematics of the Aedini tribe.

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.

Novel tRNA gene rearrangements in the mitochondrial genomes of praying mantises (Mantodea: Mantidae): Translocation, duplication and pseudogenization

Gene rearrangements have been found in several mitochondrial genomes of Mantodea, located in the gene blocks CR-I-Q-M-ND2, COX1-K-D-ATP8 and ND3-A-R-N-S-E-F-ND5. We have sequenced one mitogenome of Amelidae (Yersinia mexicana) and six mitogenomes of Mantidae to discuss the mitochondrial gene rearrangement and the phylogenetic relationship within Mantidae. These mitogenomes showed rearrangements of tRNA genes except for Asiadodis yunnanensis and Hierodula zhangi. These novel gene rearrangements of Mantidae were primarily concentrated in the region of CR-I-Q-M-ND2, including gene translocation, duplication and pseudogenization. For the occurrences of these rearrangements, the tandem duplication-random loss (TDRL) model and slipped-strand mispairing model were suitable to explain. Large non-coding regions (LNCRs) located in the region of CR-I-Q-M-ND2 were detected in most Mantidae species, whereas some LNCRs had high similarity to the control region (CR). Both BI and ML phylogenetic analyses supported the monophyly of Mantidae and the paraphyly of Mantinae. The phylogenetic results with the gene order and the location of NCRs acted as forceful evidence that specific gene rearrangements and special LNCRs may be synapomorphies for several groups of mantises.

Molecular characterization of mosquitoes (Diptera: Culicidae) from the Colombian rainforest

A few studies have carried out the taxonomic and molecular characterization of sylvatic mosquito species in Latin America, where some species have been incriminated as vectors for arboviruses and parasites transmission. The present study reports the molecular characterization of mosquito species in the Sierra Nevada de Santa Marta, a natural ecosystem in the Northern coast of Colombia. Manual capture methods were used to collect mosquitoes, and the specimens were identified via classical taxonomy. The COI marker was used for species confirmation, and phylogenetic analysis was performed using the neighbor-joining method, with the Kimura-2-Parameters model. Aedes serratus , Psorophora ferox , Johnbelkinia ulopus , Sabethes chloropterus , Sabethes cyaneus , Wyeomyia aporonoma , Wyeomyia pseudopecten , Wyeomyia ulocoma and Wyeomyia luteoventralis were identified. We assessed the genetic variability of mosquitoes in this area and phylogenetic reconstructions allowed the identification at the species level. Classical and molecular taxonomy demonstrated to be useful and complementary when morphological characteristics are not well preserved, or the taxonomic group is not represented in public molecular databases.

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.

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.

Novel gene rearrangement pattern in the mitochondrial genomes of Torleya mikhaili and Cincticostella fusca (Ephemeroptera: Ephemerellidae)

The mayfly family Ephemerellidae (Insecta: Ephemeroptera) is distributed around the world and has very high species diversity. However, its evolution pattern of mitogenome and phylogenetic relationships within Ephemeroptera remain unclear. In this study, the complete mitochondrial genomes (mitogenomes) of Torleya mikhaili (15,042 bp) and Cincticostella fusca (15,135 bp) were firstly determined and analyzed. Two ephemerellid mitogenomes shared similar gene organization with 37 typical genes as well as a putative control region. Compared with other reported mitogenomes of mayflies, the unique gene order (I'-CR-Q-M) was found in these two mitogenomes. Although the observed rearrangement pattern is novel within ephemeropteran mitogenomes, it could be explained presumably by the mechanisms of tandem duplication-random loss and recombination. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on four nucleotide datasets placed three ephemerellid species together. Furthermore, the phylogenetic relationships of the three genera were recovered as ((Ephemerella + Cincticostella) + Torleya).

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.

The use of wing shape for characterising macroevolution in mosquitoes (Diptera: Culicidae)

The wing form of culicid mosquitoes shows considerable variation among groups: this phenomenon has been addressed by several studies through space-time analyses in mosquito populations, species, and genera. The observed variation results from a combination of two distinct factors: heredity and phenotypic plasticity. The first is usually related to wing shape, a complex character that may serve as a taxonomic marker in specific cases. We hypothesized that wing shape might be phylogenetically meaningful in Culicidae. In this study, we applied a geometric morphometrical approach based on 18 landmarks in 81 species of mosquitoes, representing 19 different genera, to investigate whether wing shape can help retrieve macroevolutionary patterns or identify any phylogenetic signals. We observed that wing shape differed considerably among groups, especially between Anophelinae and Culicinae subfamilies; thus, some wing shape elements may be synapomorphic. Comparisons among wing consensus after Procrustes superimposition revealed that landmark #1, located between the veins RS and R1, was the most variable. Sabethini tribe was distinguished from other taxa owing to a strong phylogenetic signal of its wings, whereas other culicids presented weaker signals and were not that distinguishable. Evolutionary forces such as natural selection, evolutionary limitation/constraint, or canalization mechanisms might drive the evolution of wing phenotype. These findings suggest that the wing undergoes evolution over long periods, but is not neutral enough to reconstruct the phylogenetic history of these insects. Gene-based studies should be performed to understand the driving forces in wing evolution.