Complex Modulation of the Aedes aegypti Transcriptome in Response to Dengue Virus Infection

Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, United States of America.
PLoS ONE (Impact Factor: 3.23). 11/2012; 7(11):e50512. DOI: 10.1371/journal.pone.0050512
Source: PubMed


Dengue fever is the most important arboviral disease world-wide, with Aedes aegypti being the major vector. Interactions between the mosquito host and dengue viruses (DENV) are complex and vector competence varies among geographically-distinct Ae. aegypti populations. Additionally, dengue is caused by four antigenically-distinct viral serotypes (DENV1-4), each with multiple genotypes. Each virus genotype interacts differently with vertebrate and invertebrate hosts. Analyses of alterations in mosquito transcriptional profiles during DENV infection are expected to provide the basis for identifying networks of genes involved in responses to viruses and contribute to the molecular-genetic understanding of vector competence. In addition, this knowledge is anticipated to support the development of novel disease-control strategies. RNA-seq technology was used to assess genome-wide changes in transcript abundance at 1, 4 and 14 days following DENV2 infection in carcasses, midguts and salivary glands of the Ae. aegypti Chetumal strain. DENV2 affected the expression of 397 Ae. aegypti genes, most of which were down-regulated by viral infection. Differential accumulation of transcripts was mainly tissue- and time-specific. Comparisons of our data with other published reports reveal conservation of functional classes, but limited concordance of specific mosquito genes responsive to DENV2 infection. These results indicate the necessity of additional studies of mosquito-DENV interactions, specifically those focused on recently-derived mosquito strains with multiple dengue virus serotypes and genotypes.

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Available from: Mariangela Bonizzoni,
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    • "It is particularly effective when a reference genome is not available [23]. NGS transcriptome sequencing has also been successfully applied to mosquito species Anopheles gambiae[11,24], Aedies aegypti[25,26], Culex quinquefasciatus[27], Anopheles funestus[28] and Anopheles albimanus[29], which clearly demonstrated its utility for functional and evolutionary studies [30,31]. "
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    ABSTRACT: Background Anopheles sinensis is the major malaria vector in China and Southeast Asia. Vector control is one of the most effective measures to prevent malaria transmission. However, there is little transcriptome information available for the malaria vector. To better understand the biological basis of malaria transmission and to develop novel and effective means of vector control, there is a need to build a transcriptome dataset for functional genomics analysis by large-scale RNA sequencing (RNA-seq). Methods To provide a more comprehensive and complete transcriptome of An. sinensis, eggs, larvae, pupae, male adults and female adults RNA were pooled together for cDNA preparation, sequenced using the Illumina paired-end sequencing technology and assembled into unigenes. These unigenes were then analyzed in their genome mapping, functional annotation, homology, codon usage bias and simple sequence repeats (SSRs). Results Approximately 51.6 million clean reads were obtained, trimmed, and assembled into 38,504 unigenes with an average length of 571 bp, an N50 of 711 bp, and an average GC content 51.26%. Among them, 98.4% of unigenes could be mapped onto the reference genome, and 69% of unigenes could be annotated with known biological functions. Homology analysis identified certain numbers of An. sinensis unigenes that showed homology or being putative 1:1 orthologues with genomes of other Dipteran species. Codon usage bias was analyzed and 1,904 SSRs were detected, which will provide effective molecular markers for the population genetics of this species. Conclusions Our data and analysis provide the most comprehensive transcriptomic resource and characteristics currently available for An. sinensis, and will facilitate genetic, genomic studies, and further vector control of An. sinensis.
    Parasites & Vectors 07/2014; 7(1):314. DOI:10.1186/1756-3305-7-314 · 3.43 Impact Factor
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    • "Intersection of genes common to RNA-Seq datasets and predicted protein interaction network. (A) Venn diagram shows genes common to three recent transcriptome reports of DENV2-infected Aedes (Behura et al. 2011; Colpitts et al. 2011; Bonizzoni et al. 2012). (B) Genes common to transcriptome reports shown in 1A and protein interaction prediction network of Guo et al. (2010). "
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    ABSTRACT: To define microRNA (miRNA) involvement during arbovirus infection of Aedes aegypti, we mined deep sequencing libraries of Dengue type 2 (DENV2)-exposed mosquitoes. Three biological replicates for each timepoint [2, 4 and 9 days post-exposure (dpe)] and treatment group allowed us to remove the outliers associated with sample-to-sample variability. Using edgeR (R Bioconductor), designed for use with replicate deep sequencing data, we determined the log fold-change (logFC) of miRNA levels [18-23 nucleotides (nt)]. The number of significantly modulated miRNAs increased from ≤5 at 2 and 4 dpe to 23 unique miRNAs by 9 dpe. Putative miRNA targets were predicted by aligning miRNAs to the transcriptome, and the list was reduced to include the intersection of hits found using the Miranda, PITA, and TargetScan algorithms. To further reduce false-positives, putative targets were validated by cross-checking them with mRNAs reported in recent DENV2 host response transcriptome reports; 4076 targets were identified. Of these, 464 gene targets have predicted miRNA-binding sites in 3' untranslated regions. Context-specific target functional groups include proteins involved in transport, transcriptional regulation, mitochondrial function, chromatin modification and signal transduction processes known to be required for viral replication and dissemination. The miRNA response is placed in context with other vector host response studies by comparing the predicted targets with those of transcriptome studies. Together, these data are consistent with the hypothesis that profound and persistent changes to gene expression occur in DENV2-exposed mosquitoes.
    Insect Molecular Biology 11/2013; 23(1). DOI:10.1111/imb.12070 · 2.59 Impact Factor
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    • "Eight highly differentially regulated genes were chosen for validation using an independently prepared BR L17 sample pair (Figure 7). The number of transcripts chosen for validating the RNA-sequencing results is consistent with previous studies [26] and validation results corroborated with the RNA-sequencing data. Detectable differentially expressed transcripts reported by the array were approximately 3x fewer than those by RNA-sequencing (1.66% vs. 5.01%). "
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    BMC Genomics 11/2013; 14(1):763. DOI:10.1186/1471-2164-14-763 · 3.99 Impact Factor
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