Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

Abstract Background Anopheles coluzzii and Anopheles arabiensis belong to the Anopheles gambiae complex and are among the major malaria vectors in sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species. Findings In this study, we produced de novo chromosome-level genome assemblies for A. coluzzii and A. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 and 256.8 Mb of the total assemblies for A. coluzzii and A. arabiensis, respectively. Each assembly consists of 3 chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomic coordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions in A. coluzzii and A. arabiensis. Conclusion The new chromosome-level assemblies will facilitate functional and population genomic studies in A. coluzzii and A. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.

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Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

10.1101/2020.09.29.318477 ◽

2020 ◽

Cited By ~ 1

Author(s):

Anton Zamyatin ◽

Pavel Avdeyev ◽

Jiangtao Liang ◽

Atashi Sharma ◽

Chujia Chen ◽

...

Keyword(s):

De Novo ◽

Mosquito Species ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Anopheles Coluzzii ◽

Reference Quality ◽

Genomic Studies ◽

Sub Saharan ◽

Genome Assemblies ◽

Chromosome Level

AbstractBackgroundAnopheles coluzzii and An. arabiensis belong to the An. gambiae complex and are among the major malaria vectors in Sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species.FindingsIn this study, we produced de novo chromosome-level genome assemblies for An. coluzzii and An. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 Mbp and 265.7 Mbp assemblies for An. coluzzii and An. arabiensis, respectively. Each assembly consists of three chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomic coordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions in An. coluzzii and An. arabiensis.ConclusionThe new chromosome-level assemblies will facilitate functional and population genomic studies in An. coluzzii and An. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.

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Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa

Wellcome Open Research ◽

10.12688/wellcomeopenres.14765.1 ◽

2018 ◽

Vol 3 ◽

pp. 113 ◽

Cited By ~ 3

Author(s):

Claire L. Jeffries ◽

Gena G. Lawrence ◽

George Golovko ◽

Mojca Kristan ◽

James Orsborne ◽

...

Keyword(s):

Control Strategies ◽

Mosquito Species ◽

Amplicon Sequencing ◽

Pathogen Transmission ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Endosymbiotic Bacterium ◽

Prevalence Rates ◽

Republic Of The Congo ◽

Sub Saharan

Background: Wolbachia, a common insect endosymbiotic bacterium that can influence pathogen transmission and manipulate host reproduction, has historically been considered absent from the Anopheles (An.) genera, but has recently been found in An. gambiae s.l. populations. As there are numerous Anopheles species that have the capacity to transmit malaria, we analysed a range of species to determine Wolbachia prevalence rates, characterise novel Wolbachia strains and determine any correlation between the presence of Plasmodium, Wolbachia and the competing endosymbiotic bacterium Asaia. Methods: Anopheles adult mosquitoes were collected from five malaria-endemic countries: Guinea, Democratic Republic of the Congo (DRC), Ghana, Uganda and Madagascar, between 2013 and 2017. Molecular analysis of samples was undertaken using quantitative PCR, Sanger sequencing, Wolbachia multilocus sequence typing (MLST) and high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Results: Novel Wolbachia strains were discovered in five species: An. coluzzii, An. gambiae s.s., An. arabiensis, An. moucheti and An. species ‘A’, increasing the number of Anopheles species known to be naturally infected. Variable prevalence rates in different locations were observed and novel strains were phylogenetically diverse, clustering with Wolbachia supergroup B strains. We also provide evidence for resident strain variants within An. species ‘A’. Wolbachia is the dominant member of the microbiome in An. moucheti and An. species ‘A’, but present at lower densities in An. coluzzii. Interestingly, no evidence of Wolbachia/Asaia co-infections was seen and Asaia infection densities were also shown to be variable and location dependent. Conclusions: The important discovery of novel Wolbachia strains in Anopheles provides greater insight into the prevalence of resident Wolbachia strains in diverse malaria vectors. Novel Wolbachia strains (particularly high-density strains) are ideal candidate strains for transinfection to create stable infections in other Anopheles mosquito species, which could be used for population replacement or suppression control strategies.

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Microsporidia MB is found predominantly associated with Anopheles gambiae s.s and Anopheles coluzzii in Ghana

Scientific Reports ◽

10.1038/s41598-021-98268-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jewelna Akorli ◽

Esinam Abla Akorli ◽

Seraphim Naa Afoley Tetteh ◽

Godwin Kwame Amlalo ◽

Millicent Opoku ◽

...

Keyword(s):

West Africa ◽

Malaria Vector ◽

Sibling Species ◽

Horizontal Transfer ◽

Anopheles Arabiensis ◽

Sub Saharan Africa ◽

Anopheles Coluzzii ◽

Vector Species ◽

Anopheles Gambiae S.S ◽

Sub Saharan

AbstractA vertically transmitted microsporidian, Microsporidia MB, with the ability to disrupt Plasmodium development was reported in Anopheles arabiensis from Kenya, East Africa. To demonstrate its range of incidence, archived DNA samples from 7575 Anopheles mosquitoes collected from Ghana were screened. MB prevalence was observed at 1.8%. An. gambiae s.s constituted 87% of positive mosquitoes while the remaining were from An. coluzzii. Both sibling species had similar positivity rates (24% and 19%; p = 0.42) despite the significantly higher number of An. gambiae s.s analysed (An. gambiae s.s = 487; An. coluzzii = 94; p = 0.0005). The microsporidian was also more prevalent in emerged adults from field-collected larvae than field-caught adults (p < 0.0001) suggestive of an efficient vertical transmission and/or horizontal transfer among larvae. This is the first report of Microsporidia MB in Anopheles mosquitoes in West Africa. It indicates possible widespread among malaria vector species and warrants investigations into the symbiont’s diversity across sub-Saharan Africa.

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Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa

Wellcome Open Research ◽

10.12688/wellcomeopenres.14765.2 ◽

2018 ◽

Vol 3 ◽

pp. 113 ◽

Cited By ~ 27

Author(s):

Claire L. Jeffries ◽

Gena G. Lawrence ◽

George Golovko ◽

Mojca Kristan ◽

James Orsborne ◽

...

Keyword(s):

Control Strategies ◽

Mosquito Species ◽

Amplicon Sequencing ◽

Pathogen Transmission ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Prevalence Rates ◽

Population Replacement ◽

Republic Of The Congo ◽

Sub Saharan

Background: Wolbachia, a common insect endosymbiotic bacterium that can influence pathogen transmission and manipulate host reproduction, has historically been considered absent from the Anopheles (An.) genera, but has recently been found in An. gambiae s.l. populations in West Africa. As there are numerous Anopheles species that have the capacity to transmit malaria, we analysed a range of species across five malaria endemic countries to determine Wolbachia prevalence rates, characterise novel Wolbachia strains and determine any correlation between the presence of Plasmodium, Wolbachia and the competing bacterium Asaia. Methods: Anopheles adult mosquitoes were collected from five malaria-endemic countries: Guinea, Democratic Republic of the Congo (DRC), Ghana, Uganda and Madagascar, between 2013 and 2017. Molecular analysis was undertaken using quantitative PCR, Sanger sequencing, Wolbachia multilocus sequence typing (MLST) and high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Results: Novel Wolbachia strains were discovered in five species: An. coluzzii, An. gambiae s.s., An. arabiensis, An. moucheti and An. species A, increasing the number of Anopheles species known to be naturally infected. Variable prevalence rates in different locations were observed and novel strains were phylogenetically diverse, clustering with Wolbachia supergroup B strains. We also provide evidence for resident strain variants within An. species A. Wolbachia is the dominant member of the microbiome in An. moucheti and An. species A but present at lower densities in An. coluzzii. Interestingly, no evidence of Wolbachia/Asaia co-infections was seen and Asaia infection densities were shown to be variable and location dependent. Conclusions: The important discovery of novel Wolbachia strains in Anopheles provides greater insight into the prevalence of resident Wolbachia strains in diverse malaria vectors. Novel Wolbachia strains (particularly high-density strains) are ideal candidate strains for transinfection to create stable infections in other Anopheles mosquito species, which could be used for population replacement or suppression control strategies.

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Evidence for natural hybridisation and novel Wolbachia strain superinfections in the Anopheles gambiae complex from Guinea

10.1101/772855 ◽

2019 ◽

Cited By ~ 1

Author(s):

Claire L Jeffries ◽

Cintia Cansado-Utrilla ◽

Abdoul H Beavogui ◽

Caleb Stica ◽

Eugene K Lama ◽

...

Keyword(s):

Prevalence Rate ◽

Mosquito Species ◽

Wolbachia Strain ◽

Pathogen Transmission ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Prevalence Rates ◽

Anopheles Gambiae Complex ◽

Natural Hybridisation ◽

Sub Saharan

1.SummaryWolbachia, a widespread bacterium which can influence mosquito-borne pathogen transmission, has recently been detected within Anopheles (An.) species that are malaria vectors in Sub-Saharan Africa. Although studies have reported Wolbachia strains in the An. gambiae complex, apparent low density and prevalence rates require confirmation. In this study, wild Anopheles mosquitoes collected from two regions of Guinea were investigated. In contrast to previous studies, RNA was extracted from adult females (n=516) to increase the chances for detection of actively expressed Wolbachia genes, determine Wolbachia prevalence rates and estimate relative strain densities. Molecular confirmation of mosquito species and Wolbachia Multilocus sequence typing (MLST) were carried out to analyse phylogenetic relationships of mosquito hosts and newly discovered Wolbachia strains. Strains were detected in An. gambiae s.s. (prevalence rates of 0.0-2.8%) from the Faranah region, An. melas (prevalence rate of 11.6% - 16/138) and hybrids between these two species (prevalence rate of 40.0% - 6/15) from Senguelen in the Maferinyah region. Furthermore, a novel high-density strain, termed wAnsX, was found in an unclassified Anopheles species. The discovery of novel Wolbachia strains (particularly in members, and hybrids, of the An. gambiae complex) provides further candidate strains that could be used for future Wolbachia-based malaria biocontrol strategies.

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Associated patterns of insecticide resistance in field populations of malaria vectors across Africa

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1801826115 ◽

2018 ◽

Vol 115 (23) ◽

pp. 5938-5943 ◽

Cited By ~ 24

Author(s):

Penelope A. Hancock ◽

Antoinette Wiebe ◽

Katherine A. Gleave ◽

Samir Bhatt ◽

Ewan Cameron ◽

...

Keyword(s):

Insecticide Resistance ◽

Vector Control ◽

Mosquito Species ◽

Quantitative Information ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Cross Resistance ◽

Resistance Patterns ◽

Geostatistical Models ◽

Sub Saharan

The development of insecticide resistance in African malaria vectors threatens the continued efficacy of important vector control methods that rely on a limited set of insecticides. To understand the operational significance of resistance we require quantitative information about levels of resistance in field populations to the suite of vector control insecticides. Estimation of resistance is complicated by the sparsity of observations in field populations, variation in resistance over time and space at local and regional scales, and cross-resistance between different insecticide types. Using observations of the prevalence of resistance in mosquito species from the Anopheles gambiae complex sampled from 1,183 locations throughout Africa, we applied Bayesian geostatistical models to quantify patterns of covariation in resistance phenotypes across different insecticides. For resistance to the three pyrethroids tested, deltamethrin, permethrin, and λ-cyhalothrin, we found consistent forms of covariation across sub-Saharan Africa and covariation between resistance to these pyrethroids and resistance to DDT. We found no evidence of resistance interactions between carbamate and organophosphate insecticides or between these insecticides and those from other classes. For pyrethroids and DDT we found significant associations between predicted mean resistance and the observed frequency of kdr mutations in the Vgsc gene in field mosquito samples, with DDT showing the strongest association. These results improve our capacity to understand and predict resistance patterns throughout Africa and can guide the development of monitoring strategies.

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Characterization of Anopheles stephensi Odorant Receptor 8, an Abundant Component of the Mouthpart Chemosensory Transcriptome

Insects ◽

10.3390/insects12070593 ◽

2021 ◽

Vol 12 (7) ◽

pp. 593

Author(s):

Zachary Speth ◽

Gurlaz Kaur ◽

Devin Mazolewski ◽

Rayden Sisomphou ◽

Danielle Denise C. Siao ◽

...

Keyword(s):

Host Selection ◽

Odorant Receptor ◽

Mosquito Species ◽

Transcript Abundance ◽

Host Finding ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Host Seeking ◽

High Transcript Abundance ◽

Sub Saharan

Several mosquito species within the genus Anopheles are vectors for human malaria, and the spread of this disease is driven by the propensity of certain species to feed preferentially on humans. The study of olfaction in mosquitoes is important to understand dynamics of host-seeking and host-selection; however, the majority of these studies focus on Anopheles gambiae or An. coluzzii, both vectors of malaria in Sub-Saharan Africa. Other malaria vectors may recognize different chemical cues from potential hosts; therefore, in this study, we investigated An. stephensi, the south Asian malaria mosquito. We specifically focused on the mouthparts (primarily the maxillary palp and labella) that have been much less investigated compared to the antennae but are also important for host-seeking. To provide a broad view of chemoreceptor expression, RNAseq was used to examine the transcriptomes from the mouthparts of host-seeking females, blood-fed females, and males. Notably, AsOr8 had a high transcript abundance in all transcriptomes and was, therefore, cloned and expressed in the Drosophila empty neuron system. This permitted characterization with a panel of odorants that were selected, in part, for their presence in the human odor profile. The responsiveness of AsOr8 to odorants was highly similar to An. gambiae Or8 (AgOr8), except for sulcatone, which was detected by AsOr8 but not AgOr8. Subtle differences in the receptor sensitivity to specific odorants may provide clues to species- or strain-specific approaches to host-seeking and host selection. Further exploration of the profile of An. stephensi chemosensory proteins may yield a better understanding of how different malaria vectors navigate host-finding and host-choice.

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The dominant malaria vector, Anopheles funestus from rural south-eastern Tanzania, is more strongly resistant to insecticides than Anopheles arabiensis

10.21203/rs.3.rs-19762/v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Polius Gerazi Pinda ◽

Claudia Eichenberger ◽

Halfan S Ngowo ◽

Dickson S Msaky ◽

Said Abbasi ◽

...

Keyword(s):

Malaria Transmission ◽

Pyrethroid Resistance ◽

Mosquito Species ◽

Anopheles Funestus ◽

Indoor Residual Spraying ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Insecticide Treated Nets ◽

South Eastern ◽

Sub Saharan

Abstract Background: Long-lasting insecticide-treated nets (LLINs) and indoor residual spraying (IRS) have greatly reduced malaria transmission in sub-Saharan Africa, but are threatened by insecticide resistance in dominant malaria vectors. In south-eastern Tanzania, pyrethroid-resistant Anopheles funestus now transmit more than 80% of malaria infections even in villages where the species occurs at far lower densities than other vectors such as Anopheles arabiensis.Methods: To better understand the dominance of An. funestus in these settings and improve options for its control, this study compared intensities of resistance between females of this species and those of An. arabiensis , using WHO assays with 1×, 5× and 10× insecticide doses. Additional tests were done to assess the reversibility of such resistance using synergists. The mosquitoes were collected from villages across two districts in south-eastern Tanzania.Findings: Both species were resistant to the two pyrethroids (permethrin and deltamethrin) and the organochloride (DDT) but susceptible to the organophosphate (pirimiphos-methyl) at standard baseline doses (1×). However, An. funestus as opposed to An. arabiensis was also resistant to the carbamate (bendiocarb) at standard doses (1×). An. funestus showed strong resistance to pyrethroids, surviving the 5× doses and 10× doses except in one village. Pre-exposure to the synergist, piperonyl butoxide (PBO), reversed the pyrethroid-resistance in both An. arabiensis and An. funestus achieving mortalities >98%, except for An. funestus from two villages for which permethrin-associated mortalities exceeded 90% but not 98%.Conclusions : In these communities where An. funestus now dominates malaria transmission, the species also displays much stronger resistance to pyrethroids than its counterpart, An. arabiensis, and can readily survive more classes of insecticides, including carbamates. The resistance to pyrethroids in both mosquito species appears to be mostly metabolic and can be reversed significantly using synergists such as PBO. These findings may explain the continued persistence and dominance of An. funestus despite widespread use of pyrethroid-treated LLINs, and will also inform future choices of interventions to tackle malaria transmission in this area and other similar settings. Such interventions may include PBO-based LLINs or improved IRS with compounds such as organophosphates against which the vectors are still susceptible.

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Evidence for natural hybridization and novel Wolbachia strain superinfections in the Anopheles gambiae complex from Guinea

Royal Society Open Science ◽

10.1098/rsos.202032 ◽

2021 ◽

Vol 8 (4) ◽

Author(s):

Claire L. Jeffries ◽

Cintia Cansado-Utrilla ◽

Abdoul H. Beavogui ◽

Caleb Stica ◽

Eugene K. Lama ◽

...

Keyword(s):

Prevalence Rate ◽

Mosquito Species ◽

Sensu Stricto ◽

Pathogen Transmission ◽

Sub Saharan Africa ◽

Natural Hybridization ◽

Malaria Vectors ◽

Prevalence Rates ◽

Anopheles Gambiae Complex ◽

Sub Saharan

Wolbachia , a widespread bacterium which can influence mosquito-borne pathogen transmission, has recently been detected within Anopheles ( An .) species that are malaria vectors in Sub-Saharan Africa. Although studies have reported Wolbachia strains in the An. gambiae complex, apparent low density and prevalence rates require confirmation. In this study, wild Anopheles mosquitoes collected from two regions of Guinea were investigated. In contrast with previous studies, RNA was extracted from adult females ( n = 516) to increase the chances for the detection of actively expressed Wolbachia genes, determine Wolbachia prevalence rates and estimate relative strain densities. Molecular confirmation of mosquito species and Wolbachia multilocus sequence typing (MLST) were carried out to analyse phylogenetic relationships of mosquito hosts and newly discovered Wolbachia strains. Strains were detected in An. melas (prevalence rate of 11.6%–16/138) and hybrids between An. melas and An. gambiae sensu stricto (prevalence rate of 40.0%–6/15) from Senguelen in the Maferinyah region. Furthermore, a novel high-density strain, termed w AnsX, was found in an unclassified Anopheles species. The discovery of novel Wolbachia strains (particularly in members, and hybrids, of the An. gambiae complex) provides further candidate strains that could be used for future Wolbachia -based malaria biocontrol strategies.

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Spatial modelling for population replacement of mosquito vectors at continental scale

10.1101/2021.10.06.463299 ◽

2021 ◽

Author(s):

Nicholas J. Beeton ◽

Andrew Wilkins ◽

Adrien Ickowicz ◽

Keith R. Hayes ◽

Geoffrey R. Hosack

Keyword(s):

Anopheles Gambiae ◽

Control Strategies ◽

Drive System ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Anopheles Coluzzii ◽

Gene Drive ◽

Continental Scale ◽

Wide Range ◽

Sub Saharan

AbstractMalaria is one of the deadliest vector-borne diseases in the world. Researchers are developing new genetic and conventional vector control strategies to attempt to limit its burden. To be deployed responsibly and successfully, proposed novel control strategies require detailed safety assessment. Anopheles gambiae sensu stricto (s.s.) and Anopheles coluzzii, two closely related subspecies within the species complex Anopheles gambiae sensu lato (s.l.), are among the dominant malaria vectors in sub-Saharan Africa. These two subspecies readily hybridise and compete in the wild and are also known to have distinct niches, each with spatially and temporally varying carrying capacities driven by precipitation and land use factors.We model the spread and persistence of a population-modifying gene drive system in these subspecies across sub-Saharan Africa, by simulating introductions of genetically modified mosquitoes across the African mainland as well as on some offshore islands. We explore transmission of the gene drive between the subspecies, different hybridisation mechanisms, the effects of both local dispersal and potential wind-aided migration to the spread, and the development of resistance to the gene drive. We find that given best current available knowledge on the subspecies’ life histories, an introduced gene drive system with typical characteristics can plausibly spread from even distant offshore islands to the African mainland with the aid of wind-driven migration, with resistance taking over within a decade. Our model demonstrates a range of realistic dynamics including the effect of prevailing wind on spread and spatio-temporally varying carrying capacities for subspecies. We thus show both the plausibility and importance of accounting for a wide range of mechanisms from regional to continental scales.

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