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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

Global dynamics of gene expression. The number of expressed (FPKM > 1) AAEL genes (blue) and AAEL and AAEL-NIP transcripts (red) and NTR gene (green), and NTR transcripts (purple) were plotted across all 42 developmental time points (A). Correlation matrix of all 42 poly (A+) RNA seq time points throughout development for AAEL genes and NTRs. Each developmental stage is most highly correlated with its adjacent time point across all embryogenesis. A decrease in correlation is observable in the 36−48hr ovary and 60−72hr ovary, 52−56hr to 56−60hr embryo. The scale bar indicates the coefficient of variation value between samples 0−1 (B). The expression heat map indicates the number of AAEL genes and NTRs that are fivefold upregulated between each sample. The number of AAEL genes and NTRs that are 5 fold up-regulated can be determined by matching the criteria with respect to the sequence of the row tissue (left) to the column tissue (top). For example, there are 10,762 (yellow, highest number of expressed genes and this value is 1) genes and NTRs that have 5-fold more transcriptional activity in the 24hr BF ovary tissue (left) compared with the NBF ovary tissue (top). In addition, there are 4302 (0.399 value in chart) genes and NTRs (blue), which have 5-fold more transcriptional activity in the NBF ovary tissue (left) compared with the 24-hr BF ovary tissue (top). These two statements are mutually exclusive and therefore each cell represents a different set of genes (C). Hierarchical clustering heat map of AAEL genes and NTRs, illustrating the various patterns of gene expression across all developmental time points. Scale bar indicates the FPKM z scores (D). For A−D, The major developmental groups are indicated by color bars and are organized left to right, as follows: M (brown, male testes, male carcass), Fc (purple, NBF Female Carcass, and multiple time points PBM: 12hr, 24hr, 36hr, 48hr, 60hr, and 72hr), O (red, NBF ovaries, and multiple ovarian time points PBM: 12hr, 24hr, 36hr, 48hr, 60hr and 72hr), E (green, embryo, 0-2hr, 2-4hr, 4-8hr, 8-12hr, 12-16hr, 16-20hr, 20-24hr, 24-28hr, 28-32hr, 32-36hr, 36-40hr, 40-44hr, 44-48hr, 48-52hr, 52-56hr, 56-60hr, 60-64hr, 64-68hr, 68-72hr and 72-76hr embryos), L (light blue, larvae, 1st, 2nd, 3rd and 4th instar larvae stages), and P (light orange, male and female pupae).
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fig1: Global dynamics of gene expression. The number of expressed (FPKM > 1) AAEL genes (blue) and AAEL and AAEL-NIP transcripts (red) and NTR gene (green), and NTR transcripts (purple) were plotted across all 42 developmental time points (A). Correlation matrix of all 42 poly (A+) RNA seq time points throughout development for AAEL genes and NTRs. Each developmental stage is most highly correlated with its adjacent time point across all embryogenesis. A decrease in correlation is observable in the 36−48hr ovary and 60−72hr ovary, 52−56hr to 56−60hr embryo. The scale bar indicates the coefficient of variation value between samples 0−1 (B). The expression heat map indicates the number of AAEL genes and NTRs that are fivefold upregulated between each sample. The number of AAEL genes and NTRs that are 5 fold up-regulated can be determined by matching the criteria with respect to the sequence of the row tissue (left) to the column tissue (top). For example, there are 10,762 (yellow, highest number of expressed genes and this value is 1) genes and NTRs that have 5-fold more transcriptional activity in the 24hr BF ovary tissue (left) compared with the NBF ovary tissue (top). In addition, there are 4302 (0.399 value in chart) genes and NTRs (blue), which have 5-fold more transcriptional activity in the NBF ovary tissue (left) compared with the 24-hr BF ovary tissue (top). These two statements are mutually exclusive and therefore each cell represents a different set of genes (C). Hierarchical clustering heat map of AAEL genes and NTRs, illustrating the various patterns of gene expression across all developmental time points. Scale bar indicates the FPKM z scores (D). For A−D, The major developmental groups are indicated by color bars and are organized left to right, as follows: M (brown, male testes, male carcass), Fc (purple, NBF Female Carcass, and multiple time points PBM: 12hr, 24hr, 36hr, 48hr, 60hr, and 72hr), O (red, NBF ovaries, and multiple ovarian time points PBM: 12hr, 24hr, 36hr, 48hr, 60hr and 72hr), E (green, embryo, 0-2hr, 2-4hr, 4-8hr, 8-12hr, 12-16hr, 16-20hr, 20-24hr, 24-28hr, 28-32hr, 32-36hr, 36-40hr, 40-44hr, 44-48hr, 48-52hr, 52-56hr, 56-60hr, 60-64hr, 64-68hr, 68-72hr and 72-76hr embryos), L (light blue, larvae, 1st, 2nd, 3rd and 4th instar larvae stages), and P (light orange, male and female pupae).

Mentions: To examine the dynamics of gene expression, we quantified expression changes of AAEL, NTR, and AAEL-NIP gene/transcript models across all developmental samples (Figure 1A, Table S8, and Table S9). NBF ovaries express the lowest number of genes (8400) with close to 1.1 isoform per gene. An increase in isoform complexity, which increases to 1.6 transcripts per gene, the highest in the dataset, is seen upon a blood meal. The number of expressed genes and isoforms gradually rises through embryogenesis, reaching a peak at 60 hr and decreasing afterward. Analysis of pair-wise correlations in expression levels of AAEL and NTR genes revealed that almost every developmental stage is most highly correlated with its adjacent stage, particularly during embryogenesis (Figure 1B). Notable exceptions to this trend occur between 36−48 hr and 60−72 hr ovaries, and between the 52−56 hr and 56−60 hr embryo stages, suggesting that these represent important points at which developmental and/or physiological transitions occur.


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)

Global dynamics of gene expression. The number of expressed (FPKM > 1) AAEL genes (blue) and AAEL and AAEL-NIP transcripts (red) and NTR gene (green), and NTR transcripts (purple) were plotted across all 42 developmental time points (A). Correlation matrix of all 42 poly (A+) RNA seq time points throughout development for AAEL genes and NTRs. Each developmental stage is most highly correlated with its adjacent time point across all embryogenesis. A decrease in correlation is observable in the 36−48hr ovary and 60−72hr ovary, 52−56hr to 56−60hr embryo. The scale bar indicates the coefficient of variation value between samples 0−1 (B). The expression heat map indicates the number of AAEL genes and NTRs that are fivefold upregulated between each sample. The number of AAEL genes and NTRs that are 5 fold up-regulated can be determined by matching the criteria with respect to the sequence of the row tissue (left) to the column tissue (top). For example, there are 10,762 (yellow, highest number of expressed genes and this value is 1) genes and NTRs that have 5-fold more transcriptional activity in the 24hr BF ovary tissue (left) compared with the NBF ovary tissue (top). In addition, there are 4302 (0.399 value in chart) genes and NTRs (blue), which have 5-fold more transcriptional activity in the NBF ovary tissue (left) compared with the 24-hr BF ovary tissue (top). These two statements are mutually exclusive and therefore each cell represents a different set of genes (C). Hierarchical clustering heat map of AAEL genes and NTRs, illustrating the various patterns of gene expression across all developmental time points. Scale bar indicates the FPKM z scores (D). For A−D, The major developmental groups are indicated by color bars and are organized left to right, as follows: M (brown, male testes, male carcass), Fc (purple, NBF Female Carcass, and multiple time points PBM: 12hr, 24hr, 36hr, 48hr, 60hr, and 72hr), O (red, NBF ovaries, and multiple ovarian time points PBM: 12hr, 24hr, 36hr, 48hr, 60hr and 72hr), E (green, embryo, 0-2hr, 2-4hr, 4-8hr, 8-12hr, 12-16hr, 16-20hr, 20-24hr, 24-28hr, 28-32hr, 32-36hr, 36-40hr, 40-44hr, 44-48hr, 48-52hr, 52-56hr, 56-60hr, 60-64hr, 64-68hr, 68-72hr and 72-76hr embryos), L (light blue, larvae, 1st, 2nd, 3rd and 4th instar larvae stages), and P (light orange, male and female pupae).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig1: Global dynamics of gene expression. The number of expressed (FPKM > 1) AAEL genes (blue) and AAEL and AAEL-NIP transcripts (red) and NTR gene (green), and NTR transcripts (purple) were plotted across all 42 developmental time points (A). Correlation matrix of all 42 poly (A+) RNA seq time points throughout development for AAEL genes and NTRs. Each developmental stage is most highly correlated with its adjacent time point across all embryogenesis. A decrease in correlation is observable in the 36−48hr ovary and 60−72hr ovary, 52−56hr to 56−60hr embryo. The scale bar indicates the coefficient of variation value between samples 0−1 (B). The expression heat map indicates the number of AAEL genes and NTRs that are fivefold upregulated between each sample. The number of AAEL genes and NTRs that are 5 fold up-regulated can be determined by matching the criteria with respect to the sequence of the row tissue (left) to the column tissue (top). For example, there are 10,762 (yellow, highest number of expressed genes and this value is 1) genes and NTRs that have 5-fold more transcriptional activity in the 24hr BF ovary tissue (left) compared with the NBF ovary tissue (top). In addition, there are 4302 (0.399 value in chart) genes and NTRs (blue), which have 5-fold more transcriptional activity in the NBF ovary tissue (left) compared with the 24-hr BF ovary tissue (top). These two statements are mutually exclusive and therefore each cell represents a different set of genes (C). Hierarchical clustering heat map of AAEL genes and NTRs, illustrating the various patterns of gene expression across all developmental time points. Scale bar indicates the FPKM z scores (D). For A−D, The major developmental groups are indicated by color bars and are organized left to right, as follows: M (brown, male testes, male carcass), Fc (purple, NBF Female Carcass, and multiple time points PBM: 12hr, 24hr, 36hr, 48hr, 60hr, and 72hr), O (red, NBF ovaries, and multiple ovarian time points PBM: 12hr, 24hr, 36hr, 48hr, 60hr and 72hr), E (green, embryo, 0-2hr, 2-4hr, 4-8hr, 8-12hr, 12-16hr, 16-20hr, 20-24hr, 24-28hr, 28-32hr, 32-36hr, 36-40hr, 40-44hr, 44-48hr, 48-52hr, 52-56hr, 56-60hr, 60-64hr, 64-68hr, 68-72hr and 72-76hr embryos), L (light blue, larvae, 1st, 2nd, 3rd and 4th instar larvae stages), and P (light orange, male and female pupae).
Mentions: To examine the dynamics of gene expression, we quantified expression changes of AAEL, NTR, and AAEL-NIP gene/transcript models across all developmental samples (Figure 1A, Table S8, and Table S9). NBF ovaries express the lowest number of genes (8400) with close to 1.1 isoform per gene. An increase in isoform complexity, which increases to 1.6 transcripts per gene, the highest in the dataset, is seen upon a blood meal. The number of expressed genes and isoforms gradually rises through embryogenesis, reaching a peak at 60 hr and decreasing afterward. Analysis of pair-wise correlations in expression levels of AAEL and NTR genes revealed that almost every developmental stage is most highly correlated with its adjacent stage, particularly during embryogenesis (Figure 1B). Notable exceptions to this trend occur between 36−48 hr and 60−72 hr ovaries, and between the 52−56 hr and 56−60 hr embryo stages, suggesting that these represent important points at which developmental and/or physiological transitions occur.

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