A multipurpose high throughput SNP chip for the dengue and yellow fever mosquito, Aedes aegypti
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR776402_1.fastq.gz | Fastqsanger.gz | |||
| ERR776402_2.fastq.gz | Fastqsanger.gz | |||
| ERR776403_1.fastq.gz | Fastqsanger.gz | |||
| ERR776403_2.fastq.gz | Fastqsanger.gz | |||
| ERR776404_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 96 |
Similar Datasets
Project description:Dengue fever is among the most widespread vector-borne infectious diseases. The primary vector of dengue is the Aedes aegypti mosquito. Ae. aegypti is prevalent in the tropics and sub-tropics and is closely associated with human habitats outside its native range of Africa. While long established in the southeastern United States of America where dengue is re-emerging, breeding populations have never been reported from California until the summer of 2013. Using 12 highly variable microsatellite loci and a database of reference populations, we have determined that the likely source of the California introduction is the southeastern United States, ruling out introductions from abroad, from the geographically closer Arizona or northern Mexico populations, or an accidental release from a research laboratory. The power to identify the origin of new introductions of invasive vectors of human disease relies heavily on the availability of a panel of reference populations. Our work demonstrates the importance of generating extensive reference databases of genetically fingerprinted human-disease vector populations to aid public health efforts to prevent the introduction and spread of vector-borne diseases.
| S-EPMC4117443 | biostudies-literature
Project description:Aedes aegypti mosquitoes infect hundreds of millions of people each year with dangerous viral pathogens including dengue, yellow fever, Zika, and chikungunya. Progress in understanding the biology of this insect, and developing tools to fight it, depends on the availablity of a high-quality genome assembly. Here we use DNA proximity ligaton (Hi-C) and Pacific Biosciences long reads to create AaegL5 - a highly contiguous A. aegypti reference.
2018-08-23 | GSE113256 | GEO
Project description:MicroRNAs (miRNA) have alternative forms known as isomiRs, which differ from each other by a few nucleotides. Next generation sequencing platforms facilitate identification of these isomiRs and recent discoveries regarding their functional importance have increased our understandings of the regulatory complexities of the microRNAome. Observed changes in the miRNA profiles in mosquitoes infected with flaviviruses have implicated small RNAs in the interactions between viruses and their vectors. Here we analysed the isomiR profiles of both uninfected and infected blood fed Aedes aegypti mosquitoes with a major human pathogen, Dengue virus at two time points post-infection. We found noticeable changes to the isomiR expression profile in response to infection and aging. Data analysis revealed a distinct bias towards isomiR production in the mature miRNA as opposed to the star strand. Furthermore, we noticed that only in 40% of Ae. aegypti miRNAs, the most abundant reads for each particular miRNA match the exact sequence reported in the miRbase. The isomiR expression variations between an Ae. aegypti embryonic cell line (Aag2) and whole mosquitoes demonstrated a tissue-specific pattern of isomiR production. Our results illustrated a bias for certain types of isomiRs for each miRNA. The findings presented in this study also provide evidence that isomiR production is not a random phenomenon and may be important in DENV colonisation of its vector. Examination of isomiR production rate in DENV infected and non infected mosquitoes
2015-11-05 | E-GEOD-59516 | biostudies-arrayexpress
Project description:MicroRNAs (miRNA) have alternative forms known as isomiRs, which differ from each other by a few nucleotides. Next generation sequencing platforms facilitate identification of these isomiRs and recent discoveries regarding their functional importance have increased our understandings of the regulatory complexities of the microRNAome. Observed changes in the miRNA profiles in mosquitoes infected with flaviviruses have implicated small RNAs in the interactions between viruses and their vectors. Here we analysed the isomiR profiles of both uninfected and infected blood fed Aedes aegypti mosquitoes with a major human pathogen, Dengue virus at two time points post-infection. We found noticeable changes to the isomiR expression profile in response to infection and aging. Data analysis revealed a distinct bias towards isomiR production in the mature miRNA as opposed to the star strand. Furthermore, we noticed that only in 40% of Ae. aegypti miRNAs, the most abundant reads for each particular miRNA match the exact sequence reported in the miRbase. The isomiR expression variations between an Ae. aegypti embryonic cell line (Aag2) and whole mosquitoes demonstrated a tissue-specific pattern of isomiR production. Our results illustrated a bias for certain types of isomiRs for each miRNA. The findings presented in this study also provide evidence that isomiR production is not a random phenomenon and may be important in DENV colonisation of its vector.
2015-11-05 | GSE59516 | GEO
Project description:BackgroundThe mosquito Aedes aegypti was recently transinfected with a life-shortening strain of the endosymbiont Wolbachia pipientis (wMelPop) as the first step in developing a biocontrol strategy for dengue virus transmission. In addition to life-shortening, the wMelPop-infected mosquitoes also exhibit increased daytime activity and metabolic rates. Here we sought to quantify the blood-feeding behaviour of Wolbachia-infected females as an indicator of any virulence or energetic drain associated with Wolbachia infection.Methodology/principal findingsIn a series of blood-feeding trials in response to humans, we have shown that Wolbachia-infected mosquitoes do not differ in their response time to humans, but that as they age they obtain fewer and smaller blood meals than Wolbachia-uninfected controls. Lastly, we observed a behavioural characteristic in the Wolbachia infected mosquitoes best described as a "bendy" proboscis that may explain the decreased biting success.Conclusions/significanceTaken together the evidence suggests that wMelPop infection may be causing tissue damage in a manner that intensifies with mosquito age and that leads to reduced blood-feeding success. These behavioural changes require further investigation with respect to a possible physiological mechanism and their role in vectorial capacity of the insect. The selective decrease of feeding success in older mosquitoes may act synergistically with other Wolbachia-associated traits including life-shortening and viral protection in biocontrol strategies.
| S-EPMC2734393 | biostudies-literature
Project description:Controlled sex-, stage- and tissue-specific expression of antipathogen effector molecules is important for genetic engineering strategies to control mosquito-borne diseases. Adult female salivary glands are involved in pathogen transmission to human hosts and are target sites for expression of antipathogen effector molecules. The Aedes aegypti 30K a and 30K b genes are expressed exclusively in adult female salivary glands and are transcribed divergently from start sites separated by 263 nucleotides. The intergenic, 5'- and 3'-end untranslated regions of both genes are sufficient to express simultaneously two different transgene products in the distal-lateral lobes of the female salivary glands. An antidengue effector gene, membranes no protein (Mnp), driven by the 30K b promoter, expresses an inverted-repeat RNA with sequences derived from the premembrane protein-encoding region of the dengue virus serotype 2 genome and reduces significantly the prevalence and mean intensities of viral infection in mosquito salivary glands and saliva.
| S-EPMC2976824 | biostudies-literature
Project description:Although anthropogenic impacts are often considered harmful to species, human modifications to the landscape can actually create novel niches to which other species can adapt. These "domestication" processes are especially important in the context of arthropod disease vectors, where ecological overlap of vector and human populations may lead to epidemics. Here, we present results of a global genetic study of one such species, the dengue and yellow fever mosquito, Aedes aegypti, whose evolutionary history and current distribution have been profoundly shaped by humans. We used DNA sequences of four nuclear genes and 1504 single nucleotide polymorphism (SNP) markers developed with restriction-site associated DNA (RAD) sequencing to test the hypothesis that Ae. aegypti originated in Africa, where a domestic form arose and spread throughout the tropical and subtropical world with human trade and movement. Results confirmed African ancestry of the species, and supported a single subspeciation event leading to the pantropical domestic form. In addition, genetic data strongly supported the hypothesis that human trade routes first moved domestic Ae. aegypti out of Africa into the New World, followed by a later invasion from the New World into Southeast Asia and the Pacific. These patterns of domestication and invasion are relevant to many species worldwide, as anthropogenic forces increasingly impact evolutionary processes.
| S-EPMC3946797 | biostudies-literature
Project description:BackgroundThe mosquito Aedes aegypti (L.) is a major vector of viral diseases like dengue fever, Zika and chikungunya. Aedes aegypti exhibits high morphological and behavioral variation, some of which is thought to be of epidemiological significance. Globally distributed domestic Ae. aegypti have often been grouped into (i) the very pale variety queenslandensis and (ii) the type form. Because the two color forms co-occur across most of their range, there is interest in understanding how freely they interbreed. This knowledge is particularly important for control strategies that rely on mating compatibilities between the release and target mosquitoes, such as Wolbachia releases and SIT. To address this question, we analyzed nuclear and mitochondrial genome-wide variation in the co-occurring pale and type Ae. aegypti from northern Queensland (Australia) and Singapore.Methods/findingsWe typed 74 individuals at a 1170 bp-long mitochondrial sequence and at 16,569 nuclear SNPs using a customized double-digest RAD sequencing. 11/29 genotyped individuals from Singapore and 11/45 from Queensland were identified as var. queenslandensis based on the diagnostic scaling patterns. We found 24 different mitochondrial haplotypes, seven of which were shared between the two forms. Multivariate genetic clustering based on nuclear SNPs corresponded to individuals' geographic location, not their color. Several family groups consisted of both forms and three queenslandensis individuals were Wolbachia infected, indicating previous breeding with the type form which has been used to introduce Wolbachia into Ae. aegypti populations.ConclusionAedes aegypti queenslandensis are genomically indistinguishable from the type form, which points to these forms freely interbreeding at least in Australia and Singapore. Based on our findings, it is unlikely that the presence of very pale Ae. aegypti will affect the success of Aedes control programs based on Wolbachia-infected, sterile or RIDL mosquitoes.
| S-EPMC5091912 | biostudies-literature
Project description:The dengue and yellow fever mosquito, Aedes aegypti, contributes significantly to global disease burden. Genetic study of Aedes aegypti is essential to understanding its evolutionary history, competence as a disease vector, and the effects and efficacy of vector control methods. The prevalence of repeats and transposable elements in the Aedes aegypti genome complicates marker development and makes genome-wide genetic study challenging. To overcome these challenges, we developed a high-throughput genotyping chip, Axiom_aegypti1. This chip screens for 50,000 single-nucleotide polymorphisms present in Aedes aegypti populations from around the world. The array currently used genotypes 96 samples simultaneously. To ensure that these markers satisfy assumptions commonly made in many genetic analyses, we tested for Mendelian inheritance and linkage disequilibrium in laboratory crosses and a wild population, respectively. We have validated more than 25,000 of these markers to date, and expect this number to increase with more sampling. We also present evidence of the chip's efficacy in distinguishing populations throughout the world. The markers on this chip are ideal for applications ranging from population genetics to genome-wide association studies. This tool makes rapid, cost-effective, and comparable genotype data attainable to diverse sets of Aedes aegypti researchers, from those interested in potential range shifts due to climate change to those characterizing the genetic underpinnings of its competence to transmit disease.
| S-EPMC4426360 | biostudies-literature
Project description:Our previous findings [Hazelton & Lang (1978) Fed. Proc. Fed. Am. Soc. Exp. Biol. 37(6), 2378 (abstr.)] demonstrated a senescence-specific decrease in glutathione (GSH) concentration in the yellow-fever mosquito Aedes aegypti (Louisville)]. As a possible mechanism for this change, GSH biosynthesis was investigated in adult mosquitoes of different ages through the life-span. Biosynthesis was measured as the incorporation rate of [14C]glycine or [14C]cystine into glutathione. Essential information to validate the procedure was also obtained on the precursor-amino-acid pool sizes and kinetic parameters such as lag-time and time course of incorporation. Also, synthesis de novo rather than exchange was verified using buthionine sulphoximine, a specific inhibitor of GSH biosynthesis. The synthetic rates with either amino acid precursor varied throughout the adult life-span, but the patterns for both precursors were essentially identical. Biosynthesis was high in the newly emerged adult and decreased 62-70% (P less than 0.005) to a plateau during maturity. From the mature value there was a decrease of 36-41% (P less than 0.005) to a new plateau during senescence. Glutathione biosynthesis and concentration were correlated throughout maturity and senescence (r = 0.982) and thus biosynthesis was proportional to glutathione content. On this basis we concluded that impaired biosynthesis is the major and perhaps sole mechanism for the aging decrease in glutathione content.
| S-EPMC1154223 | biostudies-other