Transcript Assembly and Quantification by RNA-Seq Reveals Significant Differences in Gene Expression and Genetic Variants in Mosquitoes of the Culex pipiens (Diptera: Culicidae) Complex

RNA-Seq-Pop: Exploiting the sequence in RNA sequencing-A Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae

We provide a reproducible and scalable Snakemake workflow, called RNA-Seq-Pop, which provides end-to-end analysis of RNA sequencing data sets. The workflow allows the user to perform quality control, perform differential expression analyses and call genomic variants. Additional options include the calculation of allele frequencies of variants of interest, summaries of genetic variation and population structure, and genome-wide selection scans, together with clear visualizations. RNA-Seq-Pop is applicable to any organism, and we demonstrate the utility of the workflow by investigating pyrethroid resistance in selected strains of the major malaria mosquito, Anopheles gambiae. The workflow provides additional modules specifically for An. gambiae, including estimating recent ancestry and determining the karyotype of common chromosomal inversions. The Busia laboratory colony used for selections was collected in Busia, Uganda, in November 2018. We performed a comparative analysis of three groups: a parental G24 Busia strain; its deltamethrin-selected G28 offspring; and the susceptible reference strain Kisumu. Measures of genetic diversity reveal patterns consistent with that of laboratory colonization and selection, with the parental Busia strain exhibiting the highest nucleotide diversity, followed by the selected Busia offspring, and finally, Kisumu. Differential expression and variant analyses reveal that the selected Busia colony exhibits a number of distinct mechanisms of pyrethroid resistance, including the Vgsc-995S target-site mutation, upregulation of SAP genes, P450s and a cluster of carboxylesterases. During deltamethrin selections, the 2La chromosomal inversion rose in frequency (from 33% to 86%), supporting a previous link with pyrethroid resistance. RNA-Seq-Pop is hosted at: github.com/sanjaynagi/rna-seq-pop. We anticipate that the workflow will provide a useful tool to facilitate reproducible, transcriptomic studies in An. gambiae and other taxa.

The chemical code for attracting Culex mosquitoes

Mosquitoes use chemical codes to locate and discriminate among vertebrate hosts to obtain a blood meal. Recent advances have allowed for the identification of the chemical codes used by mosquitoes to locate and discriminate humans from other vertebrate hosts. Humans are incidental “dead-end” hosts for the West Nile virus, which is maintained in an enzootic cycle, primarily through its transmission between infected birds by Culex mosquitoes. Host-seeking Culex mosquitoes are attracted to the odor of chicken, which are used in sentinel traps to monitor West Nile virus transmission. Using combined gas chromatography and electroantennography and mass spectrometry we identify a blend of volatile organic compounds present in chicken emanates, including mostly salient bioactive compounds previously identified in human emanates. When released at their identified ratios, this blend elicits behavioral responses of Culex pipiens molestus and Culex quinquefasciatus similar to that to the natural chicken odor. Tested under field conditions, this blend attract Culex spp. and other species of mosquitoes using birds among their hosts. This study provides evidence for conserved chemical codes for resource location by mosquitoes, and highlights the intricate role of CO2 for host-seeking mosquitoes. The identification of conserved chemical codes, which drive innate preference behaviors that are fundamental for survival and reproduction, provides important substrates for future control interventions targeting disease vector mosquitoes.

Random Forest Analysis of Impact of Abiotic Factors on Culex pipiens and Culex quinquefasciatus Occurrence

The Culex pipiens complex of mosquitoes are significant vectors of several pathogens resulting in infectious human diseases in North America, including but not limited to West Nile encephalitis, Rift Valley Fever, and Lymphatic filariasis. Among this complex are C. pipiens form pipiens and Culex quinquefasciatus. While morphologically similar, the mosquitoes exhibit unique life histories that suit them uniquely to divergent niches, wherein C. pipiens can thrive despite the cold winters of the northern United States and C. quinquefasciatus is able to survive periods of drought typical in the southern states. Here, Random Forests machine-learning algorithms were employed to model and explore which environmental parameters best explain mosquito occurrence in historical trapping data across the continental United States of America, and test correlation with abundance data. The models explained between 71 and 97% of the presence or absence of the two mosquitoes based on historical climatic data. The results of this study will improve vector management programs by explaining which environmental variables will provide the most accurate predictions of mosquito presence at a given site.

The urban-adapted underground mosquito Culex pipiens form molestus maintains exogenously influenceable circadian rhythms

Genes known to affect circadian rhythms (i.e. 'clock genes') also influence the photoperiodic induction of overwintering reproductive diapause in the northern house mosquito, Culex pipiens f. pipiens. This suggests that molecular changes in one or more clock genes could contribute to the inability to diapause in a second form of this mosquito, Culex pipiens f. molestus. Temperate populations of Cx. pipiens f. molestus inhabit underground locations generally devoid of predictable photoperiods. For this reason, there could be limited fitness consequences if the hypothesized molecular changes to its clock genes also eliminated this mosquito's ability to regulate circadian rhythms in response to photoperiod variation. Here, we demonstrate that in contrast to this prediction, underground derived Cx. pipiens f. molestus retain exogenously influenceable circadian rhythms. Nonetheless, our genetic analyses indicate that the gene Helicase domino (dom) has a nine-nucleotide, in-frame deletion specific to Cx. pipiens f. molestus. Previous work has shown that splice variants in this gene differentially influence circadian behavior in Drosophila melanogaster. We also find derived, non-synonymous single nucleotide polymorphisms (SNPs) in eight genes that may also affect circadian rhythms and/or diapause induction in Cx. pipiens f. molestus. Finally, four putative circadian genes were found to have no quantifiable expression during any examined life stage, suggesting potential regulatory effects. Collectively, our findings indicate that the distinct, but molecularly interconnected life-history traits of diapause induction and circadian rhythms are decoupled in Cx. pipiens f. molestus and suggest this taxon may be a valuable tool for exploring exogenously influenced phenotypes in mosquitoes more broadly.

Suppressed expression of oxidoreductin-like protein, Oxidor, increases follicle degeneration and decreases survival during the overwintering diapause of the mosquito Culex pipiens

Throughout diapause in mosquitoes, stress resistance and subsequent prolonged lifespan are a few important features of diapause that are crucial for overwintering success. In the mosquito Culex pipiens, we suggest that oxidoreductin-like protein is involved with these diapause characteristics for overwintering survival. Expression of oxidor was more than two-fold higher in early stage diapausing females compared to their non-diapausing counterparts. Suppression of the gene that encodes oxidoreductin-like protein by RNAi significantly increased the proportion of degenerating follicles in early-stage adult diapausing females. Inhibition of oxidor also significantly reduced the survivability of diapausing females which indicates that this protein plays a key role in protecting multiple tissues during early diapause.