A Draft Genome Assembly of Culex pipiens pallens (Diptera: Culicidae) Using PacBio Sequencing

From macro to micro: De novo genomes of Aedes mosquitoes enable comparative genomics among close and distant relatives

The yellow fever mosquito (Aedes aegypti) is an organism of high medical importance because it is the primary vector for diseases such as yellow fever, Zika, dengue, and chikungunya. Its medical importance has made it a subject of numerous efforts to understand their biology. One such effort, was the development of a high-quality reference genome (AaegL5). However, this reference genome was sourced from a highly inbred laboratory strain with unknown geographic origin. Thus, the reference is not representative of a wild mosquito, let alone one from its native range in sub-Saharan Africa. To better understand the genetic architecture of Ae. aegypti and their sister species, we developed two de novo chromosome-scale genomes with sequences sourced from single individuals: one of Ae. aegypti formosus (Aaf) from Burkina Faso and one of Ae. mascarensis (Am) from Mauritius. Both genomes exhibit high contiguity and gene completeness, comparable to AaegL5. While Aaf exhibits high degree of synteny to AaegL5, it also exhibits several large inversions. We further conducted comparative genomic analyses using our genomes and other publicly available culicid reference genomes to find extensive chromosomal rearrangements between major lineages. Overrepresentation analysis of expanded genes in Aaf, AaegL5, and Am revealed that while the overarching category of genes that have expanded are similar, the specific genes that have expanded differ. Our findings elucidate novel insights into chromosome evolution at both microevolutionary and macroevolutionary scales. The genomic resources we present are additions to the arsenal of biologists in understanding mosquito biology and genome evolution.

Evolutionary adaptation under climate change: Aedes sp. demonstrates potential to adapt to warming

Climate warming is expected to shift the distributions of mosquitoes and mosquito-borne diseases, promoting expansions at cool range edges and contractions at warm range edges. However, whether mosquito populations could maintain their warm edges through evolutionary adaptation remains unknown. Here, we investigate the potential for thermal adaptation in Aedes sierrensis, a congener of the major disease vector species that experiences large thermal gradients in its native range, by assaying tolerance to prolonged and acute heat exposure, and its genetic basis in a diverse, field-derived population. We found pervasive evidence of heritable genetic variation in mosquito heat tolerance, and phenotypic trade-offs in tolerance to prolonged versus acute heat exposure. Further, we found genomic variation associated with prolonged heat tolerance was clustered in several regions of the genome, suggesting the presence of larger structural variants such as chromosomal inversions. A simple evolutionary model based on our data estimates that the maximum rate of evolutionary adaptation in mosquito heat tolerance will exceed the projected rate of climate warming, implying the potential for mosquitoes to track warming via genetic adaptation.

Genetic characterization of immune adaptor molecule MyD88 in Culex pipiens complex (Diptera: Culicidae) mosquitoes from China

Mosquitoes of the Culex (Cx.) pipiens complex are vectors of severe diseases including West Nile fever by West Nile virus, Japanese encephalitis by Japanese encephalitis virus, and Lymphatic filariasis by filarial nematode Wuchereria bancrofti. As a major portion of mosquito immune system, the Toll pathway implicates in response against infections of mosquito-borne pathogens and biocontrol agents. The genetic diversity of immune-related molecules is expected to be a feasible and effective introduction to expand our knowledge of the mosquito-microbe interplay. However, a comprehensive description is currently lacking regarding the genetic characteristic of the Toll pathway molecules in Cx. pipiens complex mosquitoes. In the present study, genetic changes in Cx. pipiens complex MyD88 (Myeloid differentiation primary response protein 88) were analyzed as a precedent for the Toll pathway molecules in this taxon. MyD88 is a critical adaptor of the pathway transducing signals from TIR-containing receptors to downstream death domain-containing molecules. Our results revealed that adaptive selection has influenced the genetic changes of the molecule, giving rise to acceleration of diversity at a number of amino acid sites. The adaptively selected sites lie in the death domain, intermediate domain, and C-terminal extension. The characteristics of the genetic changes shed insights into the prominent molecular-level structural basis and the involvement strategy of the adaptor in the arms race against exogenous challenges. This finding would be beneficial for further exploration and deeper understanding of the mosquitoes' vectorial capacity and facilitating the effectiveness and sustainability of the biocontrol agents.

Evolutionary adaptation under climate change: Aedes sp. demonstrates potential to adapt to warming

Climate warming is expected to shift the distributions of mosquitoes and mosquito-borne diseases, facilitating expansions at cool range edges and contractions at warm range edges. However, whether mosquito populations could maintain their warm edges through evolutionary adaptation remains unknown. Here, we investigate the potential for thermal adaptation in Aedes sierrensis, a congener of the major disease vector species that experiences large thermal gradients in its native range, by assaying tolerance to prolonged and acute heat exposure, and its genetic basis in a diverse, field-derived population. We found pervasive evidence of heritable genetic variation in acute heat tolerance, which phenotypically trades off with tolerance to prolonged heat exposure. A simple evolutionary model based on our data shows that the estimated maximum rate of evolutionary adaptation in mosquito heat tolerance typically exceeds that of projected climate warming under idealized conditions. Our findings indicate that natural mosquito populations may have the potential to track projected warming via genetic adaptation. Prior climate-based projections may thus underestimate the range of mosquito and mosquito-borne disease distributions under future climate conditions.

Population-specific thermal responses contribute to regional variability in arbovirus transmission with changing climates

Temperature is increasing globally, and vector-borne diseases are particularly responsive to such increases. While it is known that temperature influences mosquito life history traits, transmission models have not historically considered population-specific effects of temperature. We assessed the interaction between Culex pipiens population and temperature in New York State (NYS) and utilized novel empirical data to inform predictive models of West Nile virus (WNV) transmission. Genetically and regionally distinct populations from NYS were reared at various temperatures, and life history traits were monitored and used to inform trait-based models. Variation in Cx. pipiens life history traits and population-dependent thermal responses account for a predicted 2.9°C difference in peak transmission that is reflected in regional differences in WNV prevalence. We additionally identified genetic signatures that may contribute to distinct thermal responses. Together, these data demonstrate how population variation contributes to significant geographic variability in arbovirus transmission with changing climates.

Consuming royal jelly alters several phenotypes associated with overwintering dormancy in mosquitoes

Introduction

Females of the Northern house mosquito, Culex pipiens, enter an overwintering dormancy, or diapause, in response to short day lengths and low environmental temperatures that is characterized by small egg follicles and high starvation resistance. During diapause, Culex pipiens Major Royal Jelly Protein 1 ortholog (CpMRJP1) is upregulated in females of Cx. pipiens. This protein is highly abundant in royal jelly, a substance produced by honey bees (Apis mellifera), that is fed to future queens throughout larval development and induces the queen phenotype (e.g., high reproductive activity and longer lifespan). However, the role of CpMRJP1 in Cx. pipiens is unknown.

Methods

We first conducted a phylogenetic analysis to determine how the sequence of CpMRJP1 compares with other species. We then investigated how supplementing the diets of both diapausing and nondiapausing females of Cx. pipiens with royal jelly affects egg follicle length, fat content, protein content, starvation resistance, and metabolic profile.

Results

We found that feeding royal jelly to females reared in long-day, diapause-averting conditions significantly reduced the egg follicle lengths and switched their metabolic profiles to be similar to diapausing females. In contrast, feeding royal jelly to females reared in short-day, diapause-inducing conditions significantly reduced lifespan and switched their metabolic profile to be similar nondiapausing mosquitoes. Moreover, RNAi directed against CpMRJPI significantly increased egg follicle length of short-day reared females, suggesting that these females averted diapause.

Discussion

Taken together, our data show that consuming royal jelly reverses several key seasonal phenotypes of Cx. pipiens and that these responses are likely mediated in part by CpMRJP1.

Chromosome-level assembly of Culex pipiens molestus and improved reference genome of Culex pipiens pallens (Culicidae, Diptera)

Culex pipiens molestus and Culex pipiens pallens are two distinct bioforms in the Culex pipiens complex that are important vectors of several pathogens and are widely distributed around the world. In the current study, we present a high-quality chromosome-level genome of Cx. pipiens f. molestus and describe the genetic characteristics of this genome. The assembly genome was 559.749 Mb with contig and scaffold N50 values of 200.952 Mb and 0.370 Mb, and more than 94.78% of the assembled bases were located on 3 chromosomes. A total of 19,399 protein-coding genes were predicted. Many gene families were expanded in the genome of Cx. pipiens f. molestus, particularly those of the chemosensory protein (CSP) and gustatory receptor (GR) gene families. In addition, utilizing Hi-C data, we improved the previously assembled draft genome of Cx. pipiens f. pallens, with scaffold N50 of 186.195 Mb and contig N50 of 0.749 Mb, and more than 97.02% of the assembled bases were located on three chromosomes. This reference genome provides a foundation for genome-based investigations of the unique ecological and evolutionary characteristics of Cx. pipiens f. molestus, and the findings in this study will help to elucidate the mechanisms involved in species divergence in the Culex pipiens complex.

An insight into the female and male Sabethes cyaneus mosquito salivary glands transcriptome

Mosquitoes are responsible for the death and debilitation of millions of people every year due to the pathogens they can transmit while blood feeding. While a handful of mosquitoes, namely those in the Aedes, Anopheles, and Culex genus, are the dominant vectors, many other species belonging to different genus are also involved in various pathogen cycles. Sabethes cyaneus is one of the many poorly understood mosquito species involved in the sylvatic cycle of Yellow Fever Virus. Here, we report the expression profile differences between male and female of Sa.cyaneus salivary glands (SGs). We find that female Sa.cyaneus SGs have 165 up-regulated and 18 down-regulated genes compared to male SGs. Most of the up-regulated genes have unknown functions, however, odorant binding proteins, such as those in the D7 protein family, and mucins were among the top 30 genes. We also performed various in vitro activity assays of female SGs. In the activity analysis we found that female SG extracts inhibit coagulation by blocking factor Xa and has endonuclease activity. Knowledge about mosquitoes and their physiology are important for understanding how different species differ in their ability to feed on and transmits pathogens to humans. These results provide us with an insight into the Sabethes SG activity and gene expression that expands our understanding of mosquito salivary glands.

Isolation of a novel rhabdovirus and detection of multiple novel viral sequences in Culex species mosquitoes in the United States

To increase our understanding of the diversity of the mosquito virome, 6956 mosquitoes of five species (Culex erraticus, Culex pipiens, Culex restuans, Culex tarsalis, and Culex territans) collected in Iowa in the United States in 2017 and 2020 were assayed for novel viruses by performing polyethylene glycol precipitation, virus isolation in cell culture, and unbiased high-throughput sequencing. A novel virus, provisionally named "Walnut Creek virus", was isolated from Cx. tarsalis, and its genomic sequence and organization are characteristic of viruses in the genus Hapavirus (family Rhabdoviridae). Replication of Walnut Creek virus occurred in avian, mammalian, and mosquito, but not tick, cell lines. A novel virus was also isolated from Cx. restuans, and partial genome sequencing revealed that it is distantly related to an unclassified virus of the genus Phytoreovirus (family Sedoreoviridae). Two recognized viruses were also isolated: Culex Y virus (family Birnaviridae) and Houston virus (family Mesoniviridae). We also identified sequences of eight novel viruses from six families (Amalgaviridae, Birnaviridae, Partitiviridae, Sedoreoviridae, Tombusviridae, and Totiviridae), two viruses that do not belong to any established families, and many previously recognized viruses. In summary, we provide evidence of multiple novel and recognized viruses in Culex spp. mosquitoes in the United States.

Special Collection: Highlights of Medical, Urban and Veterinary Entomology. Highlights in Medical Entomology, 2021

Life remained far from normal as we completed the first year of the Covid-19 pandemic and entered a second year. Despite the challenges faced worldwide, together we continue to move the field of Medical Entomology forward. Here, I reflect on parallels between control of Covid-19 and vector-borne disease control, discuss the advantages and caveats of using new genotyping technologies for the study of invasive species, and proceed to highlight papers that were published between 2020 and 2021 with a focus on those related to mosquito surveillance and population genetics of mosquito vectors.

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.

A gene-based capture assay for surveying patterns of genetic diversity and insecticide resistance in a worldwide group of invasive mosquitoes

Understanding patterns of diversification, genetic exchange, and pesticide resistance in arthropod disease vectors is necessary for effective population management. With the availability of next-generation sequencing technologies, one of the best approaches for surveying such patterns involves the simultaneous genotyping of many samples for a large number of genetic markers. To this end, the targeting of gene sequences of known function can be a cost-effective strategy. One insect group of substantial health concern are the mosquito taxa that make up the Culex pipiens complex. Members of this complex transmit damaging arboviruses and filariae worms to humans, as well as other pathogens such as avian malaria parasites that are detrimental to birds. Here we describe the development of a targeted, gene-based assay for surveying genetic diversity and population structure in this mosquito complex. To test the utility of this assay, we sequenced samples from several members of the complex, as well as from distinct populations of the relatively under-studied Culex quinquefasciatus. The data generated was then used to examine taxonomic divergence and population clustering between and within these mosquitoes. We also used this data to investigate genetic variants present in our samples that had previously been shown to correlate with insecticide-resistance. Broadly, our gene capture approach successfully enriched the genomic regions of interest, and proved effective for facilitating examinations of taxonomic divergence and geographic clustering within the Cx. pipiens complex. It also allowed us to successfully survey genetic variation associated with insecticide resistance in Culex mosquitoes. This enrichment protocol will be useful for future studies that aim to understand the genetic mechanisms underlying the evolution of these ubiquitous and increasingly damaging disease vectors.

The mosquito taxa that make up the Culex pipiens complex are important vectors of the agents of several human diseases such as West Nile and St. Louis encephalitides, and lymphatic filariasis. They are also important vectors of avian malaria, which impacts livestock and wildlife. The development of effective strategies for the control of these mosquitoes requires knowledge of their origins, distribution, dispersal patterns, and the extent to which discreet taxonomic entities within the complex interbreed. To achieve these objectives, it is necessary to compare patterns of genetic diversity across many mosquito samples, which can be cost-prohibitive. To address this limitation, we developed a targeted, gene-based assay that allowed us to cost-effectively genotype a large number of genetic variants from a representative global sampling of individual Cx. pipiens complex mosquitoes. We show that this assay is a powerful tool for examining genetic structure and hybridization among populations. We also explore its utility for surveying alleles previously shown to be associated with insecticide resistance. Future use of this enrichment assay and the bioinformatics methods described here will allow researchers to study evolutionary patterns across the Cx. pipiens complex as well as monitor the presence of genetic variation that could affect control efforts.