Browse
Submit Data
Databases
API
Help

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High-resolution cytogenetic map for the African malaria vector Anopheles gambiae.

ABSTRACT: Cytogenetic and physical maps are indispensible for precise assembly of genome sequences, functional characterization of chromosomal regions, and population genetic and taxonomic studies. We have created a new cytogenetic map for Anopheles gambiae by using a high-pressure squash technique that increases overall band clarity. To link chromosomal regions to the genome sequence, we attached genome coordinates, based on 302 markers of bacterial artificial chromosome, cDNA clones, and PCR-amplified gene fragments, to the chromosomal bands and interbands at approximately a 0.5-1 Mb interval. In addition, we placed the breakpoints of seven common polymorphic inversions on the map and described the chromosomal landmarks for the arm and inversion identification. The map's increased resolution can be used to further enhance physical mapping, improve genome assembly, and stimulate epigenomic studies of malaria vectors.

SUBMITTER: George P

PROVIDER: S-EPMC2970650 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

High-resolution cytogenetic map for the African malaria vector Anopheles gambiae.

George P P Sharakhova M V MV Sharakhov I V IV

Insect molecular biology 20100629 5

Cytogenetic and physical maps are indispensible for precise assembly of genome sequences, functional characterization of chromosomal regions, and population genetic and taxonomic studies. We have created a new cytogenetic map for Anopheles gambiae by using a high-pressure squash technique that increases overall band clarity. To link chromosomal regions to the genome sequence, we attached genome coordinates, based on 302 markers of bacterial artificial chromosome, cDNA clones, and PCR-amplified g ...[more]

PMID: 20609021

Similar Datasets

Genetic diversity of the African malaria vector Anopheles gambiae.

Project description:The sustainability of malaria control in Africa is threatened by the rise of insecticide resistance in Anopheles mosquitoes, which transmit the disease. To gain a deeper understanding of how mosquito populations are evolving, here we sequenced the genomes of 765 specimens of Anopheles gambiae and Anopheles coluzzii sampled from 15 locations across Africa, and identified over 50 million single nucleotide polymorphisms within the accessible genome. These data revealed complex population structure and patterns of gene flow, with evidence of ancient expansions, recent bottlenecks, and local variation in effective population size. Strong signals of recent selection were observed in insecticide-resistance genes, with several sweeps spreading over large geographical distances and between species. The design of new tools for mosquito control using gene-drive systems will need to take account of high levels of genetic diversity in natural mosquito populations.

| S-EPMC6026373 | biostudies-literature

Gene Expression Profiling Data of African Malaria Vector Anopheles gambiae Aging

Project description:Senescence is a biological phenomenon experienced by all living eukaryote organisms. Genome-wide gene expression associated with aging has been explored in model organisms such as Drosophila melanogaster and Caenorhabditis elegans, but this has not been well understood in African malaria vector, Anopheles gambiae. Gene expression profiling using DNA microarray allows for simultaneous study of changes in mRNA levels for thousands of genes. This study examined genome-wide gene expression during aging process in An. gambiae. The influence of blood feeding on gene expression was also examined. The data can be used to further our understanding of mosquito senescence and identify biomarkers for mosquito age grading.

2010-12-31 | GSE19756 | GEO

1.45 A resolution structure of SRPN18 from the malaria vector Anopheles gambiae.

Project description:Serine protease inhibitors (serpins) in insects function within development, wound healing and immunity. The genome of the African malaria vector, Anopheles gambiae, encodes 23 distinct serpin proteins, several of which are implicated in disease-relevant physiological responses. A. gambiae serpin 18 (SRPN18) was previously categorized as non-inhibitory based on the sequence of its reactive-center loop (RCL), a region responsible for targeting and initiating protease inhibition. The crystal structure of A. gambiae SRPN18 was determined to a resolution of 1.45 Å, including nearly the entire RCL in one of the two molecules in the asymmetric unit. The structure reveals that the SRPN18 RCL is extremely short and constricted, a feature associated with noncanonical inhibitors or non-inhibitory serpin superfamily members. Furthermore, the SRPN18 RCL does not contain a suitable protease target site and contains a large number of prolines. The SRPN18 structure therefore reveals a unique RCL architecture among the highly conserved serpin fold.

| S-EPMC5137461 | biostudies-literature

Gene Expression Profiling Data of African Malaria Vector Anopheles gambiae Aging

2010-12-31 | E-GEOD-19756 | biostudies-arrayexpress

Association mapping desiccation resistance within chromosomal inversions in the African malaria vector Anopheles gambiae.

Project description:Inversion polymorphisms are responsible for many ecologically important phenotypes and are often found under balancing selection. However, the same features that ensure their large role in local adaptation-especially reduced recombination between alternate arrangements-mean that uncovering the precise loci within inversions that control these phenotypes is unachievable using standard mapping approaches. Here, we take advantage of long-term balancing selection on a pair of inversions in the mosquito Anopheles gambiae to map desiccation tolerance via pool-GWAS. Two polymorphic inversions on chromosome 2 of this species (denoted 2La and 2Rb) are associated with arid and hot conditions in Africa and are maintained in spatially and temporally heterogeneous environments. After measuring thousands of wild-caught individuals for survival under desiccation stress, we used phenotypically extreme individuals homozygous for alternative arrangements at the 2La inversion to construct pools for whole-genome sequencing. Genomewide association mapping using these pools revealed dozens of significant SNPs within both 2La and 2Rb, many of which neighboured genes controlling ion channels or related functions. Our results point to the promise of similar approaches in systems with inversions maintained by balancing selection and provide a list of candidate genes underlying the specific phenotypes controlled by the two inversions studied here.

| S-EPMC6433559 | biostudies-literature

Viral paratransgenesis in the malaria vector Anopheles gambiae.

Project description:Paratransgenesis, the genetic manipulation of insect symbiotic microorganisms, is being considered as a potential method to control vector-borne diseases such as malaria. The feasibility of paratransgenic malaria control has been hampered by the lack of candidate symbiotic microorganisms for the major vector Anopheles gambiae. In other systems, densonucleosis viruses (DNVs) are attractive agents for viral paratransgenesis because they infect important vector insects, can be genetically manipulated and are transmitted to subsequent generations. However, An. gambiae has been shown to be refractory to DNV dissemination. We discovered, cloned and characterized the first known DNV (AgDNV) capable of infection and dissemination in An. gambiae. We developed a flexible AgDNV-based expression vector to express any gene of interest in An. gambiae using a two-plasmid helper-transducer system. To demonstrate proof-of-concept of the viral paratransgenesis strategy, we used this system to transduce expression of an exogenous gene (enhanced green fluorescent protein; EGFP) in An. gambiae mosquitoes. Wild-type and EGFP-transducing AgDNV virions were highly infectious to An. gambiae larvae, disseminated to and expressed EGFP in epidemiologically relevant adult tissues such as midgut, fat body and ovaries and were transmitted to subsequent mosquito generations. These proof-of-principle data suggest that AgDNV could be used as part of a paratransgenic malaria control strategy by transduction of anti-Plasmodium peptides or insect-specific toxins in Anopheles mosquitoes. AgDNV will also be extremely valuable as an effective and easy-to-use laboratory tool for transient gene expression or RNAi in An. gambiae.

| S-EPMC2500179 | biostudies-literature

Genome-wide patterns of gene expression during aging in the African malaria vector Anopheles gambiae.

Project description:The primary means of reducing malaria transmission is through reduction in longevity in days of the adult female stage of the Anopheles vector. However, assessing chronological age is limited to crude physiologic methods which categorize the females binomially as either very young (nulliparous) or not very young (parous). Yet the epidemiologically relevant reduction in life span falls within the latter category. Age-grading methods that delineate chronological age, using accurate molecular surrogates based upon gene expression profiles, will allow quantification of the longevity-reducing effects of vector control tools aimed at the adult, female mosquito. In this study, microarray analyses of gene expression profiles in the African malaria vector Anopheles gambiae were conducted during natural senescence of females in laboratory conditions. Results showed that detoxification-related and stress-responsive genes were up-regulated as mosquitoes aged. A total of 276 transcripts had age-dependent expression, independently of blood feeding and egg laying events. Expression of 112 (40.6%) of these transcripts increased or decreased monotonically with increasing chronologic age. Seven candidate genes for practical age assessment were tested by quantitative gene amplification in the An. gambiae G3 strain in a laboratory experiment and the Mbita strain in field enclosures set up in western Kenya under conditions closely resembling natural ones. Results were similar between experiments, indicating that senescence is marked by changes in gene expression and that chronological age can be gauged accurately and repeatedly with this method. These results indicate that the method may be suitable for accurate gauging of the age in days of field-caught, female An. gambiae.

| S-EPMC2954169 | biostudies-literature

Genetic differentiation in the African malaria vector, Anopheles gambiae s.s., and the problem of taxonomic status.

Project description:Of the seven recognized species of the Anopheles gambiae complex, A. gambiae s.s. is the most widespread and most important vector of malaria. It is becoming clear that, in parts of West Africa, this nominal species is not a single panmictic unit. We found that the internal transcribed spacer (ITS) of the X-linked rDNA has two distinct sequences with three fixed nucleotide differences; we detected no heterozygotes at these three sites, even in areas of sympatry of the two ITS types. The intergenic spacer (IGS) of this region also displays two distinct sequences that are in almost complete linkage disequilibrium with the distinct ITS alleles. We have designated these two types as S/type I and M/type II. These rDNA types correspond at least partly to the previously recognized chromosomal forms. Here we expand the geographic range of sampling to 251 individuals from 38 populations. Outside of West Africa, a single rDNA type, S/type I, corresponds to the Savanna chromosomal form. In West Africa, both types are often found in a single local sample. To understand if these findings might be due to unusual behavior of the rDNA region, we sequenced the same region for 46 A. arabiensis, a sympatric sibling species. No such distinct discontinuity was observed for this species. Autosomal inversions in one chromosome arm (2R), an insecticide resistance gene on 2L, and this single X-linked region indicate at least two genetically differentiated subpopulations of A. gambiae. Yet, rather extensive studies of other regions of the genome have failed to reveal genetic discontinuity. Evidently, incomplete genetic isolation exists within this single nominal species.

| S-EPMC1462204 | biostudies-other

Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii.

Project description:Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with a high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on the second phase of a project to build an open resource of high-quality data on genome variation among natural populations of the major African malaria vector species Anopheles gambiae and Anopheles coluzzii We analyzed whole genomes of 1142 individual mosquitoes sampled from the wild in 13 African countries, as well as a further 234 individuals comprising parents and progeny of 11 laboratory crosses. The data resource includes high-confidence single-nucleotide polymorphism (SNP) calls at 57 million variable sites, genome-wide copy number variation (CNV) calls, and haplotypes phased at biallelic SNPs. We use these data to analyze genetic population structure and characterize genetic diversity within and between populations. We illustrate the utility of these data by investigating species differences in isolation by distance, genetic variation within proposed gene drive target sequences, and patterns of resistance to pyrethroid insecticides. This data resource provides a foundation for developing new operational systems for molecular surveillance and for accelerating research and development of new vector control tools. It also provides a unique resource for the study of population genomics and evolutionary biology in eukaryotic species with high levels of genetic diversity under strong anthropogenic evolutionary pressures.

| S-EPMC7605271 | biostudies-literature

Dosage Compensation in the African Malaria Mosquito Anopheles gambiae.

Project description:Dosage compensation is the fundamental process by which gene expression from the male monosomic X chromosome and from the diploid set of autosomes is equalized. Various molecular mechanisms have evolved in different organisms to achieve this task. In Drosophila, genes on the male X chromosome are upregulated to the levels of expression from the two X chromosomes in females. To test whether a similar mechanism is operating in immature stages of Anopheles mosquitoes, we analyzed global gene expression in the Anopheles gambiae fourth instar larvae and pupae using high-coverage RNA-seq data. In pupae of both sexes, the median expression ratios of X-linked to autosomal genes (X:A) were close to 1.0, and within the ranges of expression ratios between the autosomal pairs, consistent with complete compensation. Gene-by-gene comparisons of expression in males and females revealed mild female bias, likely attributable to a deficit of male-biased X-linked genes. In larvae, male to female ratios of the X chromosome expression levels were more female biased than in pupae, suggesting that compensation may not be complete. No compensation mechanism appears to operate in male germline of early pupae. Confirmation of the existence of dosage compensation in A. gambiae lays the foundation for research into the components of dosage compensation machinery in this important vector species.

| S-EPMC4779611 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data