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The developmental transcriptome of the mosquito Aedes aegypti, an invasive species and major arbovirus vector.

Akbari OS, Antoshechkin I, Amrhein H, Williams B, Diloreto R, Sandler J, Hay BA - G3 (Bethesda) (2013)

Bottom Line: Altogether these results increase the annotated fraction of the transcribed genome into long polyA+ RNAs by more than twofold.Expression profiles of small RNAs in ovaries, early embryos, testes, and adult male and female somatic tissues also were determined, resulting in the identification of 38 new Aedes-specific miRNAs, and ~291,000 small RNA new transcribed regions, many of which are likely to be endogenous small-interfering RNAs and Piwi-interacting RNAs.Our data have been incorporated into a user-friendly genome browser located at www.Aedes.caltech.edu, with relevant links to Vectorbase (www.vectorbase.org).

View Article: PubMed Central - PubMed

Affiliation: Division of Biology, MC 156-29, California Institute of Technology, Pasadena, California 91125.

ABSTRACT
Mosquitoes are vectors of a number of important human and animal diseases. The development of novel vector control strategies requires a thorough understanding of mosquito biology. To facilitate this, we used RNA-seq to identify novel genes and provide the first high-resolution view of the transcriptome throughout development and in response to blood feeding in a mosquito vector of human disease, Aedes aegypti, the primary vector for Dengue and yellow fever. We characterized mRNA expression at 34 distinct time points throughout Aedes development, including adult somatic and germline tissues, by using polyA+ RNA-seq. We identify a total of 14,238 novel new transcribed regions corresponding to 12,597 new loci, as well as many novel transcript isoforms of previously annotated genes. Altogether these results increase the annotated fraction of the transcribed genome into long polyA+ RNAs by more than twofold. We also identified a number of patterns of shared gene expression, as well as genes and/or exons expressed sex-specifically or sex-differentially. Expression profiles of small RNAs in ovaries, early embryos, testes, and adult male and female somatic tissues also were determined, resulting in the identification of 38 new Aedes-specific miRNAs, and ~291,000 small RNA new transcribed regions, many of which are likely to be endogenous small-interfering RNAs and Piwi-interacting RNAs. Genes of potential interest for transgene-based vector control strategies also are highlighted. Our data have been incorporated into a user-friendly genome browser located at www.Aedes.caltech.edu, with relevant links to Vectorbase (www.vectorbase.org).

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Related in: MedlinePlus

Soft clustering, principal component analysis, and totals. Twenty AAEL gene expression profile clusters were identified through soft clustering. Each gene is assigned a line color corresponding to its membership value, with red (1) indicating high association. The major developmental groups are indicated by symbols on the X axis, and are organized as in Figure 1, B−D (A). Principal component analysis shows relationships between the 20 clusters, with thickness of the blue lines between any two clusters reflecting the fraction of genes that are shared (B, thickness of blue lines). n, the number of genes in each cluster.
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fig2: Soft clustering, principal component analysis, and totals. Twenty AAEL gene expression profile clusters were identified through soft clustering. Each gene is assigned a line color corresponding to its membership value, with red (1) indicating high association. The major developmental groups are indicated by symbols on the X axis, and are organized as in Figure 1, B−D (A). Principal component analysis shows relationships between the 20 clusters, with thickness of the blue lines between any two clusters reflecting the fraction of genes that are shared (B, thickness of blue lines). n, the number of genes in each cluster.

Mentions: A global view of annotated AAEL and NTR gene expression is shown in the hierarchical clustering heat map in Figure 1D. To better visualize the major patterns of co-regulated gene expression for the AAEL genes we used a soft clustering algorithm, and identified 20 distinct patterns that included from 151 to 1293 genes (Figure 2, Table S10, and Table S30). Many of these patterns correspond to specific developmental stages and transitions. For instance cluster 5 includes genes specifically expressed in the NBF ovary. It is highly enriched in genes involved in translation, including 92 tRNA and 12 rRNA genes. Seventy-one percent (n = 47) of the annotated snRNAs present in the Aedes genome also are found in this cluster, suggesting that mRNA splicing and maturation are also particularly important during this stage. Genes involved in mitochondrial biogenesis and RNA polymerase function are also over represented. Perhaps most strikingly, cluster 5 also expresses a large number of putative olfactory and gustatory receptors, raising the interesting possibility that environmental cues sensed by the ovary PBM may be important in initiating ovarian development. The dramatic switch from low to high transcriptome complexity following this life stage (Figure 1A), and the accumulation of genes required for response to stimuli and RNA processing, suggest that NBF ovary is poised for rapid transcriptional response and growth that occurs PBM. Cluster 6 includes genes predominantly expressed somewhat later in oogenesis. These include many genes involved in polysaccharide or carbohydrate binding, as well as peroxidases and oxireductases, which are likely involved in chorion and vitelline membrane biosynthesis. Interestingly, cluster 6 is also highly enriched in odorant-binding proteins. Other genes that are induced in response to a blood meal are grouped in clusters 7, 8, 9, and 11. Cluster 7 includes strictly ovary-specific genes, whereas the others include genes whose expression initiates PBM and extends into embryogenesis. Cluster 8 in particular, the largest cluster produced, includes maternally expressed genes deposited into the embryo, and is enriched in genes involved in response to stimuli, signal transduction, and protein modification among others. Clusters 12 through 16 identify genes with increased expression during early, mid and late embryogenesis; clusters 17, 18, and 19 include larvae-specific genes, while cluster 20 contains genes preferentially expressed in pupae.


The developmental transcriptome of the mosquito Aedes aegypti, an invasive species and major arbovirus vector.

Akbari OS, Antoshechkin I, Amrhein H, Williams B, Diloreto R, Sandler J, Hay BA - G3 (Bethesda) (2013)

Soft clustering, principal component analysis, and totals. Twenty AAEL gene expression profile clusters were identified through soft clustering. Each gene is assigned a line color corresponding to its membership value, with red (1) indicating high association. The major developmental groups are indicated by symbols on the X axis, and are organized as in Figure 1, B−D (A). Principal component analysis shows relationships between the 20 clusters, with thickness of the blue lines between any two clusters reflecting the fraction of genes that are shared (B, thickness of blue lines). n, the number of genes in each cluster.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3755910&req=5

fig2: Soft clustering, principal component analysis, and totals. Twenty AAEL gene expression profile clusters were identified through soft clustering. Each gene is assigned a line color corresponding to its membership value, with red (1) indicating high association. The major developmental groups are indicated by symbols on the X axis, and are organized as in Figure 1, B−D (A). Principal component analysis shows relationships between the 20 clusters, with thickness of the blue lines between any two clusters reflecting the fraction of genes that are shared (B, thickness of blue lines). n, the number of genes in each cluster.
Mentions: A global view of annotated AAEL and NTR gene expression is shown in the hierarchical clustering heat map in Figure 1D. To better visualize the major patterns of co-regulated gene expression for the AAEL genes we used a soft clustering algorithm, and identified 20 distinct patterns that included from 151 to 1293 genes (Figure 2, Table S10, and Table S30). Many of these patterns correspond to specific developmental stages and transitions. For instance cluster 5 includes genes specifically expressed in the NBF ovary. It is highly enriched in genes involved in translation, including 92 tRNA and 12 rRNA genes. Seventy-one percent (n = 47) of the annotated snRNAs present in the Aedes genome also are found in this cluster, suggesting that mRNA splicing and maturation are also particularly important during this stage. Genes involved in mitochondrial biogenesis and RNA polymerase function are also over represented. Perhaps most strikingly, cluster 5 also expresses a large number of putative olfactory and gustatory receptors, raising the interesting possibility that environmental cues sensed by the ovary PBM may be important in initiating ovarian development. The dramatic switch from low to high transcriptome complexity following this life stage (Figure 1A), and the accumulation of genes required for response to stimuli and RNA processing, suggest that NBF ovary is poised for rapid transcriptional response and growth that occurs PBM. Cluster 6 includes genes predominantly expressed somewhat later in oogenesis. These include many genes involved in polysaccharide or carbohydrate binding, as well as peroxidases and oxireductases, which are likely involved in chorion and vitelline membrane biosynthesis. Interestingly, cluster 6 is also highly enriched in odorant-binding proteins. Other genes that are induced in response to a blood meal are grouped in clusters 7, 8, 9, and 11. Cluster 7 includes strictly ovary-specific genes, whereas the others include genes whose expression initiates PBM and extends into embryogenesis. Cluster 8 in particular, the largest cluster produced, includes maternally expressed genes deposited into the embryo, and is enriched in genes involved in response to stimuli, signal transduction, and protein modification among others. Clusters 12 through 16 identify genes with increased expression during early, mid and late embryogenesis; clusters 17, 18, and 19 include larvae-specific genes, while cluster 20 contains genes preferentially expressed in pupae.

Bottom Line: Altogether these results increase the annotated fraction of the transcribed genome into long polyA+ RNAs by more than twofold.Expression profiles of small RNAs in ovaries, early embryos, testes, and adult male and female somatic tissues also were determined, resulting in the identification of 38 new Aedes-specific miRNAs, and ~291,000 small RNA new transcribed regions, many of which are likely to be endogenous small-interfering RNAs and Piwi-interacting RNAs.Our data have been incorporated into a user-friendly genome browser located at www.Aedes.caltech.edu, with relevant links to Vectorbase (www.vectorbase.org).

View Article: PubMed Central - PubMed

Affiliation: Division of Biology, MC 156-29, California Institute of Technology, Pasadena, California 91125.

ABSTRACT
Mosquitoes are vectors of a number of important human and animal diseases. The development of novel vector control strategies requires a thorough understanding of mosquito biology. To facilitate this, we used RNA-seq to identify novel genes and provide the first high-resolution view of the transcriptome throughout development and in response to blood feeding in a mosquito vector of human disease, Aedes aegypti, the primary vector for Dengue and yellow fever. We characterized mRNA expression at 34 distinct time points throughout Aedes development, including adult somatic and germline tissues, by using polyA+ RNA-seq. We identify a total of 14,238 novel new transcribed regions corresponding to 12,597 new loci, as well as many novel transcript isoforms of previously annotated genes. Altogether these results increase the annotated fraction of the transcribed genome into long polyA+ RNAs by more than twofold. We also identified a number of patterns of shared gene expression, as well as genes and/or exons expressed sex-specifically or sex-differentially. Expression profiles of small RNAs in ovaries, early embryos, testes, and adult male and female somatic tissues also were determined, resulting in the identification of 38 new Aedes-specific miRNAs, and ~291,000 small RNA new transcribed regions, many of which are likely to be endogenous small-interfering RNAs and Piwi-interacting RNAs. Genes of potential interest for transgene-based vector control strategies also are highlighted. Our data have been incorporated into a user-friendly genome browser located at www.Aedes.caltech.edu, with relevant links to Vectorbase (www.vectorbase.org).

Show MeSH
Related in: MedlinePlus