Of Genes and Genomes: Mosquito Evolution and Diversity

Properties of "Stable" Mosquito Cytochrome P450 Enzymes

The use of insecticides is widespread in the control of debilitating mosquito-borne diseases. P450 enzymes (CYPs) play essential roles in mosquito physiological function but also in the enzymatic detoxification of xenobiotics. Broadly speaking, CYPs can be classified as "stable", meaning those that have no or very few paralogs, and "labile", constituting gene families with many paralogous members. The evolutionary dichotomy between "stable" and "labile" P450 genes is fuzzy and there is not a clear phylogenetic demarcation between P450s involved in detoxification and P450s involved in essential metabolic processes. In this study, bioinformatic methods were used to explore differences in the sequences of "stable" and "labile" P450s that may facilitate their functional classification. Genomic and sequence data of Anopheles gambiae (Agam), Aedes aegypti (Aaeg), and Culex quinquefasciatus (Cqui) CYPs were obtained from public databases. The results of this study show that "stable" CYPs are encoded by longer genes, have longer introns and more exons, and contain a higher proportion of hydrophobic amino acids than "labile" CYPs. Compared to "labile" CYPs, a significantly higher proportion of "stable" CYPs are associated with biosynthetic and developmental processes.

Genome sequences of four Ixodes species expands understanding of tick evolution

BACKGROUND

Ticks, hematophagous Acari, pose a significant threat by transmitting various pathogens to their vertebrate hosts during feeding. Despite advances in tick genomics, high-quality genomes were lacking until recently, particularly in the genus Ixodes, which includes the main vectors of Lyme disease.

RESULTS

Here, we present the genome sequences of four tick species, derived from a single female individual, with a particular focus on the European species Ixodes ricinus, achieving a chromosome-level assembly. Additionally, draft assemblies were generated for the three other Ixodes species, I. persulcatus, I. pacificus, and I. hexagonus. The quality of the four genomes and extensive annotation of several important gene families have allowed us to study the evolution of gene repertoires at the level of the genus Ixodes and of the tick group. We have determined gene families that have undergone major amplifications during the evolution of ticks, while an expression atlas obtained for I. ricinus reveals striking patterns of specialization both between and within gene families. Notably, several gene family amplifications are associated with a proliferation of single-exon genes-most strikingly for fatty acid elongases and sulfotransferases.

CONCLUSIONS

The integration of our data with existing genomes establishes a solid framework for the study of gene evolution, improving our understanding of tick biology. In addition, our work lays the foundations for applied research and innovative control targeting these organisms.

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.

Mosquito species identity matters: unraveling the complex interplay in vector-borne diseases

BACKGROUND

Research on vector-borne diseases has traditionally centred on a limited number of vertebrate hosts and their associated pathogens, often neglecting the broader array of vectors within communities. Mosquitoes, with their vast species diversity, hold a central role in disease transmission, yet their capacity to transmit specific pathogens varies considerably among species. Quantitative modelling of mosquito-borne diseases is essential for understanding transmission dynamics and requires the necessity of incorporating the identity of vector species into these models. Consequently, understanding the role of different species of mosquitoes in modelling vector-borne diseases is crucial for comprehending pathogen amplification and spill-over into humans. This comprehensive overview highlights the importance of considering mosquito identity and emphasises the essential need for targeted research efforts to gain a complete understanding of vector-pathogen specificity.

METHODS

Leveraging the recently published book, 'Mosquitoes of the World', I identified 19 target mosquito species in Europe, highlighting the diverse transmission patterns exhibited by different vector species and the presence of 135 medically important pathogens.

RESULTS

The review delves into the complexities of vector-pathogen interactions, with a focus on specialist and generalist strategies. Furthermore, I discuss the importance of using appropriate diversity indices and the challenges associated with the identification of correct indices.

CONCLUSIONS

Given that the diversity and relative abundance of key species within a community significantly impact disease risk, comprehending the implications of mosquito diversity in pathogen transmission at a fine scale is crucial for advancing the management and surveillance of mosquito-borne diseases.

Unraveling the genomic complexity of sylvatic mosquitoes in changing Neotropical environments

Sylvatic New World mosquitoes (e.g. Old-growth Forest species) can transmit viruses among non-human primates. This could be a continuous source of viral cycling and spillover events from animals to humans, particularly in changing environments. However, most species of Neotropical sylvatic mosquitoes (genera Aedes, Haemagogus, and Sabethes), which include vector and non-vector species, currently lack genomic resources because there is no reliable and accurate approach for creating de novo reference genomes for these insects. This is a major knowledge gap in the biology of these mosquitoes, restricting our ability to predict and mitigate the emergence and spread of novel arboviruses in Neotropical regions. We discuss recent advances and potential solutions for generating hybrid de novo assemblies from vector and non-vector species using pools of consanguineous offspring. We also discussed research opportunities likely to emerge from these genomic resources.

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.

Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification

Total RNA sequencing (RNA-seq) is an important tool in the study of mosquitoes and the RNA viruses they vector as it allows assessment of both host and viral RNA in specimens. However, there are two main constraints. First, as with many other species, abundant mosquito ribosomal RNA (rRNA) serves as the predominant template from which sequences are generated, meaning that the desired host and viral templates are sequenced far less. Second, mosquito specimens captured in the field must be correctly identified, in some cases to the sub-species level. Here, we generate mosquito rRNA datasets which will substantially mitigate both of these problems. We describe a strategy to assemble novel rRNA sequences from mosquito specimens and produce an unprecedented dataset of 234 full-length 28S and 18S rRNA sequences of 33 medically important species from countries with known histories of mosquito-borne virus circulation (Cambodia, the Central African Republic, Madagascar, and French Guiana). These sequences will allow both physical and computational removal of rRNA from specimens during RNA-seq protocols. We also assess the utility of rRNA sequences for molecular taxonomy and compare phylogenies constructed using rRNA sequences versus those created using the gold standard for molecular species identification of specimens-the mitochondrial cytochrome c oxidase I (COI) gene. We find that rRNA- and COI-derived phylogenetic trees are incongruent and that 28S and concatenated 28S+18S rRNA phylogenies reflect evolutionary relationships that are more aligned with contemporary mosquito systematics. This significant expansion to the current rRNA reference library for mosquitoes will improve mosquito RNA-seq metagenomics by permitting the optimization of species-specific rRNA depletion protocols for a broader range of species and streamlining species identification by rRNA sequence and phylogenetics.

In silico identification of multiple conserved motifs within the control region of Culicidae mitogenomes

Mosquitoes are important vectors for human and animal diseases. Genetic markers, like the mitochondrial COI gene, can facilitate the taxonomic classification of disease vectors, vector-borne disease surveillance, and prevention. Within the control region (CR) of the mitochondrial genome, there exists a highly variable and poorly studied non-coding AT-rich area that contains the origin of replication. Although the CR hypervariable region has been used for species differentiation of some animals, few studies have investigated the mosquito CR. In this study, we analyze the mosquito mitogenome CR sequences from 125 species and 17 genera. We discovered four conserved motifs located 80 to 230 bp upstream of the 12S rRNA gene. Two of these motifs were found within all 392 Anopheles (An.) CR sequences while the other two motifs were identified in all 37 Culex (Cx.) CR sequences. However, only 3 of the 304 non-Culicidae Dipteran mitogenome CR sequences contained these motifs. Interestingly, the short motif found in all 37 Culex sequences had poly-A and poly-T stretch of similar length that is predicted to form a stable hairpin. We show that supervised learning using the frequency chaos game representation of the CR can be used to differentiate mosquito genera from their dipteran relatives.

Visualization of the Linear and Spatial Organization of Chromosomes in Mosquitoes

Mosquitoes are vectors of dangerous human diseases such as malaria, dengue, Zika, West Nile fever, and lymphatic filariasis. Visualization of the linear and spatial organization of mosquito chromosomes is important for understanding genome structure and function. Utilization of chromosomal inversions as markers for population genetics studies yields insights into mosquito adaptation and evolution. Cytogenetic approaches assist with the development of chromosome-scale genome assemblies that are useful tools for studying mosquito biology and for designing novel vector control strategies. Fluorescence in situ hybridization is a powerful technique for localizing specific DNA sequences within the linear chromosome structure and within the spatial organization of the cell nucleus. Here, we introduce protocols used in our laboratories for chromosome visualization and their application in mosquitoes.

Exploring new genomic territories with emerging model insects

Improvements in reference genome generation for insects and across the tree of life are extending the concept and utility of model organisms beyond traditional laboratory-tractable supermodels. Species or groups of species with comprehensive genome resources can be developed into model systems for studying a large variety of biological phenomena. Advances in sequencing and assembly technologies are supporting these emerging genome-enabled model systems by producing resources that are increasingly accurate and complete. Nevertheless, quality controls including assessing gene content completeness are required to ensure that these data can be included in expanding catalogues of high-quality references that will greatly advance understanding of insect biology and evolution.

VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms

VectorBase (VectorBase.org) is part of the VEuPathDB Bioinformatics Resource Center, providing free online access to multi-omics and population biology data, focusing on arthropod vectors and invertebrates of importance to human health. VectorBase includes genomics and functional genomics data from bed bugs, biting midges, body lice, kissing bugs, mites, mosquitoes, sand flies, ticks, tsetse flies, stable flies, house flies, fruit flies, and a snail intermediate host. Tools include the Search Strategy system and MapVEu, enabling users to interrogate and visualize diverse 'omics and population-level data using a graphical interface (no programming experience required). Users can also analyze their own private data, such as transcriptomic sequences, exploring their results in the context of other publicly-available information in the database. Help Desk: help@vectorbase.org.

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

BACKGROUND

Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing biodiversity, these data provide the basis for understanding biological function and evolution. Accurate and complete genome assemblies offer a comprehensive and reliable foundation upon which to advance our understanding of organismal biology at genetic, species, and ecosystem levels. However, ever-changing sequencing technologies and analysis methods mean that available data are often heterogeneous in quality. To guide forthcoming genome generation efforts and promote efficient prioritization of resources, it is thus essential to define and monitor taxonomic coverage and quality of the data.

FINDINGS

Here we present an automated analysis workflow that surveys genome assemblies from the United States NCBI, assesses their completeness using the relevant BUSCO datasets, and collates the results into an interactively browsable resource. We apply our workflow to produce a community resource of available assemblies from the phylum Arthropoda, the Arthropoda Assembly Assessment Catalogue. Using this resource, we survey current taxonomic coverage and assembly quality at the NCBI, examine how key assembly metrics relate to gene content completeness, and compare results from using different BUSCO lineage datasets.

CONCLUSIONS

These results demonstrate how the workflow can be used to build a community resource that enables large-scale assessments to survey species coverage and data quality of available genome assemblies, and to guide prioritizations for ongoing and future sampling, sequencing, and genome generation initiatives.

A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus

Anopheles is a diverse genus of mosquitoes comprising over 500 described species, including all known human malaria vectors. While a limited number of key vector species have been studied in detail, the goal of malaria elimination calls for surveillance of all potential vector species. Here, we develop a multilocus amplicon sequencing approach that targets 62 highly variable loci in the Anopheles genome and two conserved loci in the Plasmodium mitochondrion, simultaneously revealing both the mosquito species and whether that mosquito carries malaria parasites. We also develop a cheap, nondestructive, and high-throughput DNA extraction workflow that provides template DNA from single mosquitoes for the multiplex PCR, which means specimens producing unexpected results can be returned to for morphological examination. Over 1000 individual mosquitoes can be sequenced in a single MiSeq run, and we demonstrate the panel's power to assign species identity using sequencing data for 40 species from Africa, Southeast Asia, and South America. We also show that the approach can be used to resolve geographic population structure within An. gambiae and An. coluzzii populations, as the population structure determined based on these 62 loci from over 1000 mosquitoes closely mirrors that revealed through whole genome sequencing. The end-to-end approach is quick, inexpensive, robust, and accurate, which makes it a promising technique for very large-scale mosquito genetic surveillance and vector control.

Functional constraints on insect immune system components govern their evolutionary trajectories

Roles of constraints in shaping evolutionary outcomes are often considered in the contexts of developmental biology and population genetics, in terms of capacities to generate new variants and how selection limits or promotes consequent phenotypic changes. Comparative genomics also recognizes the role of constraints, in terms of shaping evolution of gene and genome architectures, sequence evolutionary rates, and gene gains or losses, as well as on molecular phenotypes. Characterizing patterns of genomic change where putative functions and interactions of system components are relatively well described offers opportunities to explore whether genes with similar roles exhibit similar evolutionary trajectories. Using insect immunity as our test case system, we hypothesize that characterizing gene evolutionary histories can define distinct dynamics associated with different functional roles. We develop metrics that quantify gene evolutionary histories, employ these to characterize evolutionary features of immune gene repertoires, and explore relationships between gene family evolutionary profiles and their roles in immunity to understand how different constraints may relate to distinct dynamics. We identified three main axes of evolutionary trajectories characterized by gene duplication and synteny, maintenance/stability and sequence conservation, and loss and sequence divergence, highlighting similar and contrasting patterns across these axes amongst subsets of immune genes. Our results suggest that where and how genes participate in immune responses limit the range of possible evolutionary scenarios they exhibit. The test case study system of insect immunity highlights the potential of applying comparative genomics approaches to characterize how functional constraints on different components of biological systems govern their evolutionary trajectories.

Aedes species (Diptera: Culicidae) ecological and host feeding patterns in the north-eastern parts of South Africa, 2014-2018

BACKGROUND

There is a paucity of recent data and knowledge on mosquito diversity and potential vectors of arboviruses in South Africa, with most of the available data dating back to the 1950s-1970s. Aedes and Culex species are the major vectors of some of the principal arboviruses which have emerged and re-emerged in the past few decades.

METHODS

In this study we used entomological surveillance in selected areas in the north-eastern parts of South Africa from 2014 to 2018 to assess mosquito diversity, with special emphasis on the Aedes species. The impact of trap types and environmental conditions was also investigated. Identification of the blood meal sources of engorged females collected during the study period was carried out, and DNA barcodes were generated for selected species.

RESULTS

Overall, 18.5% of the total Culicidae mosquitoes collected belonged to the genus Aedes, with 14 species recognised or suspected vectors of arboviruses. Species belonging to the Neomelaniconion subgenus were commonly collected in the Bushveld savanna at conservation areas, especially Aedes mcintoshi and Aedes circumluteolus. Aedes aegypti was present in all sites, albeit in low numbers. Temperature was a limiting factor for the Aedes population, and they were almost exclusively collected at temperatures between 18 °C and 27 °C. The cytochrome oxidase subunit I (COI) barcode fragment was amplified for 21 Aedes species, and for nine of these species it was the first sequence information uploaded on GenBank.

CONCLUSION

This study provides a better understanding of the diversity and relative abundance of Aedes species in the north-east of South Africa. The information provided here will contribute to future arboviral research and implementation of efficient vector control and prevention strategies.

Flavivirus integrations in Aedes aegypti are limited and highly conserved across samples from different geographic regions unlike integrations in Aedes albopictus

Mosquitoes of the genus Aedes are the main vectors of many viruses, e.g. dengue and Zika, which affect millions of people each year and for which there are limited treatment options. Understanding how Aedes mosquitoes tolerate high viral loads may lead to better disease control strategies. Elucidating endogenous viral elements (EVEs) within vector genomes may give exploitable biological insights. Previous studies have reported the presence of a large number of EVEs in Aedes genomes. Here we investigated if flavivirus EVEs are conserved across populations and different Aedes species by using ~ 500 whole genome sequence libraries from Aedes aegypti and Aedes albopictus, sourced from colonies and field mosquitoes across continents. We found that nearly all flavivirus EVEs in the Ae. aegypti reference genome originate from four separate putative viral integration events, and that they are highly conserved across geographically diverse samples. By contrast, flavivirus EVEs in the Ae. albopictus reference genome originate from up to nine distinct integration events and show low levels of conservation, even within samples from narrow geographical ranges. Our analysis suggests that flaviviruses integrated as long sequences and were subsequently fragmented and shuffled by transposable elements. Given that EVEs of Ae. aegypti and Ae. albopictus belong to different phylogenetic clades and have very differing levels of conservation, they may have different evolutionary origins and potentially different functional roles.

The type of blood used to feed Aedes aegypti females affects their cuticular and internal free fatty acid (FFA) profiles

Aedes aegypti, the primary vector of various arthropod-borne viral (arboviral) diseases such as dengue and Zika, is a popular laboratory model in vector biology. However, its maintenance in laboratory conditions is difficult, mostly because the females require blood meals to complete oogenesis, which is often provided as sheep blood. The outermost layer of the mosquito cuticle is consists of lipids which protects against numerous entomopathogens, prevents desiccation and plays an essential role in signalling processes. The aim of this work was to determine how the replacement of human blood with sheep blood affects the cuticular and internal FFA profiles of mosquitoes reared in laboratory culture. The individual FFAs present in cuticular and internal extracts from mosquito were identified and quantified by GC-MS method. The normality of their distribution was checked using the Kolmogorov-Smirnov test and the Student's t-test was used to compare them. GC-MS analysis revealed similar numbers of internal and cuticular FFAs in the female mosquitoes fed sheep blood by membrane (MFSB) and naturally fed human blood (NFHB), however MFSB group demonstrated 3.1 times greater FFA concentrations in the cuticular fraction and 1.4 times the internal fraction than the NFHB group. In the MFSB group, FFA concentration was 1.6 times higher in the cuticular than the internal fraction, while for NFHB, FFA concentration was 1.3 times lower in the cuticular than the internal fraction. The concentration of C18:3 acid was 223 times higher in the internal fraction than the cuticle in the MHSB group but was absent in the NFHB group. MFSB mosquito demonstrate different FFA profiles to wild mosquitoes, which might influence their fertility and the results of vital processes studied under laboratory conditions. The membrane method of feeding mosquitoes is popular, but our research indicates significant differences in the FFA profiles of MFSB and NFHB. Such changes in FFA profile might influence female fertility, as well as other vital processes studied in laboratory conditions, such as the response to pesticides. Our work indicates that sheep blood has potential shortcomings as a substitute feed for human blood, as its use in laboratory studies may yield different results to those demonstrated by free-living mosquitoes.

A Gene-Based Method for Cytogenetic Mapping of Repeat-Rich Mosquito Genomes

Long-read sequencing technologies have opened up new avenues of research on the mosquito genome biology, enabling scientists to better understand the remarkable abilities of vectors for transmitting pathogens. Although new genome mapping technologies such as Hi-C scaffolding and optical mapping may significantly improve the quality of genomes, only cytogenetic mapping, with the help of fluorescence in situ hybridization (FISH), connects genomic scaffolds to a particular chromosome and chromosome band. This mapping approach is important for creating and validating chromosome-scale genome assemblies for mosquitoes with repeat-rich genomes, which can potentially be misassembled. In this study, we describe a new gene-based physical mapping approach that was optimized using the newly assembled Aedes albopictus genome, which is enriched with transposable elements. To avoid amplification of the repetitive DNA, 15 protein-coding gene transcripts were used for the probe design. Instead of using genomic DNA, complementary DNA was utilized as a template for development of the PCR-amplified probes for FISH. All probes were successfully amplified and mapped to specific chromosome bands. The genome-unique probes allowed to perform unambiguous mapping of genomic scaffolds to chromosome regions. The method described in detail here can be used for physical genome mapping in other insects.

Molecular signatures of sexual communication in the phlebotomine sand flies

Phlebotomine sand flies employ an elaborate system of pheromone communication wherein males produce pheromones that attract other males to leks (thus acting as an aggregation pheromone) and females to the lekking males (sex pheromone). In addition, the type of pheromone produced varies among populations. Despite the numerous studies on sand fly chemical communication, little is known of their chemosensory genome. Chemoreceptors interact with chemicals in an organism’s environment to elicit essential behaviors such as the identification of suitable mates and food sources. Thus, they play important roles during adaptation and speciation. Major chemoreceptor gene families, odorant receptors (ORs), gustatory receptors (GRs) and ionotropic receptors (IRs) together detect and discriminate the chemical landscape. Here, we annotated the chemoreceptor repertoire in the genomes of Lutzomyia longipalpis and Phlebotomus papatasi, major phlebotomine vectors in the New World and Old World, respectively. Comparison with other sequenced Diptera revealed a large and unique expansion where over 80% of the ~140 ORs belong to a single, taxonomically restricted clade. We next conducted a comprehensive analysis of the chemoreceptors in 63 L. longipalpis individuals from four different locations in Brazil representing allopatric and sympatric populations and three sex-aggregation pheromone types (chemotypes). Population structure based on single nucleotide polymorphisms (SNPs) and gene copy number in the chemoreceptors corresponded with their putative chemotypes, and corroborate previous studies that identified multiple populations. Our work provides genomic insights into the underlying behavioral evolution of sexual communication in the L. longipalpis species complex in Brazil, and highlights the importance of accounting for the ongoing speciation in central and South American Lutzomyia that could have important implications for vectorial capacity.

Phlebotomine sand flies are the primary vectors of Leishmania parasites, the causative agents of cutaneous and visceral leishmaniasis. Due to the lack of vaccines, control of leishmaniasis relies upon reducing human exposure to sand flies. Sand flies produce sex-aggregation pheromones that elicit robust olfactory behaviors, and the molecular targets for pheromone detection remain unknown. We identified chemoreceptors in the genomes of L. longipalpis and P. papatasi, and used these gene models to explore chemoreceptor evolution in 63 L. longipalpis individuals representing different pheromone types. These analyses identified genomic loci underlying chemosensory behavior in sand flies. This paves the way for understanding the sand fly species diversity at the molecular level, and functional characterization of these candidate genes will isolate and identify chemostimuli that can directly be tested as potential attractants for odor-baited traps.

Chromatin Structure and Function in Mosquitoes

The principles and function of chromatin and nuclear architecture have been extensively studied in model organisms, such as Drosophila melanogaster. However, little is known about the role of these epigenetic processes in transcriptional regulation in other insects including mosquitoes, which are major disease vectors and a worldwide threat for human health. Some of these life-threatening diseases are malaria, which is caused by protozoan parasites of the genus Plasmodium and transmitted by Anopheles mosquitoes; dengue fever, which is caused by an arbovirus mainly transmitted by Aedes aegypti; and West Nile fever, which is caused by an arbovirus transmitted by Culex spp. In this contribution, we review what is known about chromatin-associated mechanisms and the 3D genome structure in various mosquito vectors, including Anopheles, Aedes, and Culex spp. We also discuss the similarities between epigenetic mechanisms in mosquitoes and the model organism Drosophila melanogaster, and advocate that the field could benefit from the cross-application of state-of-the-art functional genomic technologies that are well-developed in the fruit fly. Uncovering the mosquito regulatory genome can lead to the discovery of unique regulatory networks associated with the parasitic life-style of these insects. It is also critical to understand the molecular interactions between the vectors and the pathogens that they transmit, which could hold the key to major breakthroughs on the fight against mosquito-borne diseases. Finally, it is clear that epigenetic mechanisms controlling mosquito environmental plasticity and evolvability are also of utmost importance, particularly in the current context of globalization and climate change.

Radiation with reticulation marks the origin of a major malaria vector

Advances in genomics have led to an appreciation that introgression is common, but its evolutionary consequences are poorly understood. In recent species radiations the sharing of genetic variation across porous species boundaries can facilitate adaptation to new environments and generate novel phenotypes, which may contribute to further diversification. Most Anopheles mosquito species that are of major importance as human malaria vectors have evolved within recent and rapid radiations of largely nonvector species. Here, we focus on one of the most medically important yet understudied anopheline radiations, the Afrotropical Anopheles funestus complex (AFC), to investigate the role of introgression in its diversification and the possible link between introgression and vector potential. The AFC comprises at least seven morphologically similar species, yet only An. funestus sensu stricto is a highly efficient malaria vector with a pan-African distribution. Based on de novo genome assemblies and additional whole-genome resequencing, we use phylogenomic and population genomic analyses to establish species relationships. We show that extensive interspecific gene flow involving multiple species pairs has shaped the evolutionary history of the AFC since its diversification. The most recent introgression event involved a massive and asymmetrical movement of genes from a distantly related AFC lineage into An. funestus, an event that predated and plausibly facilitated its subsequent dramatic geographic range expansion across most of tropical Africa. We propose that introgression may be a common mechanism facilitating adaptation to new environments and enhancing vectorial capacity in Anopheles mosquitoes.

Distinct navigation behaviors in Aedes, Anopheles and Culex mosquito larvae

Mosquitoes spread deadly diseases that impact millions of people every year. Understanding mosquito physiology and behavior is vital for public health and disease prevention. However, many important questions remain unanswered in the field of mosquito neuroethology, particularly in our understanding of the larval stage. In this study, we investigate the innate exploration behavior of six different species of disease vector mosquito larvae. We show that these species exhibit strikingly different movement paths, corresponding to a wide range of exploration behaviors. We also investigated the response of each species to an appetitive food cue, aversive cue or neutral control. In contrast to the large differences in exploration behavior, all species appeared to gather near preferred cues through random aggregation rather than directed navigation, and exhibited slower speeds once encountering food patches. Our results identify key behavioral differences among important disease vector species, and suggest that navigation and exploration among even closely related mosquito species may be much more distinct than previously thought.

Developmental and comparative perspectives on mosquito immunity

Diseases spread by mosquitoes have killed more people than those spread by any other group of arthropod vectors and remain an important factor in determining global health and economic stability. The mosquito innate immune system can act to either modulate infection with human pathogens or fight off entomopathogens and increase the fitness and longevity of infected mosquitoes. While work remains towards understanding the larval immune system and the development of the mosquito immune system, it has recently become clearer that environmental factors heavily shape the developing mosquito immune system and continue to influence the adult immune system as well. The adult immune system has been well-studied and is known to involve multiple tissues and diverse molecular mechanisms. This review summarizes and synthesizes what is currently understood about the development of the mosquito immune system and includes comparisons of immune components unique to mosquitoes among the blood-feeding arthropods as well as important distinguishing factors between the anopheline and culicine mosquitoes. An explanation is included for how mosquito immunity factors into vector competence and vectorial capacity is presented along with a model for the interrelationships between nutrition, microbiome, pathogen interactions and behavior as they relate to mosquito development, immune status, adult female fitness and ultimately, vectorial capacity. Novel discoveries in the fields of mosquito ecoimmunology, neuroimmunology, and intracellular antiviral responses are highlighted.

Evolutionary superscaffolding and chromosome anchoring to improve Anopheles genome assemblies

Background

New sequencing technologies have lowered financial barriers to whole genome sequencing, but resulting assemblies are often fragmented and far from ‘finished’. Updating multi-scaffold drafts to chromosome-level status can be achieved through experimental mapping or re-sequencing efforts. Avoiding the costs associated with such approaches, comparative genomic analysis of gene order conservation (synteny) to predict scaffold neighbours (adjacencies) offers a potentially useful complementary method for improving draft assemblies.

Results

We evaluated and employed 3 gene synteny-based methods applied to 21 Anopheles mosquito assemblies to produce consensus sets of scaffold adjacencies. For subsets of the assemblies, we integrated these with additional supporting data to confirm and complement the synteny-based adjacencies: 6 with physical mapping data that anchor scaffolds to chromosome locations, 13 with paired-end RNA sequencing (RNAseq) data, and 3 with new assemblies based on re-scaffolding or long-read data. Our combined analyses produced 20 new superscaffolded assemblies with improved contiguities: 7 for which assignments of non-anchored scaffolds to chromosome arms span more than 75% of the assemblies, and a further 7 with chromosome anchoring including an 88% anchored Anopheles arabiensis assembly and, respectively, 73% and 84% anchored assemblies with comprehensively updated cytogenetic photomaps for Anopheles funestus and Anopheles stephensi.

Conclusions

Experimental data from probe mapping, RNAseq, or long-read technologies, where available, all contribute to successful upgrading of draft assemblies. Our evaluations show that gene synteny-based computational methods represent a valuable alternative or complementary approach. Our improved Anopheles reference assemblies highlight the utility of applying comparative genomics approaches to improve community genomic resources.

General Visual and Contingent Thermal Cues Interact to Elicit Attraction in Female Aedes aegypti Mosquitoes

Female Aedes aegypti mosquitoes use multiple sensory modalities to hunt human hosts and obtain a blood meal for egg production. Attractive cues include carbon dioxide (CO₂), a major component of exhaled breath [1, 2]; heat elevated above ambient temperature, signifying warm-blooded skin [3, 4]; and dark visual contrast [5, 6], proposed to bridge long-range olfactory and short-range thermal cues [7]. Any of these sensory cues in isolation is an incomplete signal of a human host, and so a mosquito must integrate multimodal sensory information before committing to approaching and biting a person [8]. Here, we study the interaction of visual cues, heat, and CO₂ to investigate the contributions of human-associated stimuli to host-seeking decisions. We show that tethered flying mosquitoes strongly orient toward dark visual contrast, regardless of CO₂ stimulation and internal host-seeking status. This suggests that attraction to visual contrast is general and not contingent on other host cues. In free-flight experiments with CO₂, adding a dark contrasting visual cue to a warmed surface enhanced attraction. Moderate warmth became more attractive to mosquitoes, and mosquitoes aggregated on the cue at all non-noxious temperatures. Gr3 mutants, unable to detect CO₂, were lured to the visual cue at ambient temperatures but fled and did not return when the surface was warmed to host-like temperatures. This suggests that attraction to thermal cues is contingent on the presence of the additional sensory cue CO₂. Our results illustrate that mosquitoes integrate general attractive visual stimuli with context-dependent thermal stimuli to seek promising sites for blood feeding.