Hoban_EvolApps_microsat_Data_For_Dryad

The genotypes for trees used in this study for all analyses, after clones, etc. have been removed. The data are referred to in the publication as "1515 unique genotypes for analysis: 79 J. ailantifolia reference, 7 hybrid 231 reference, 66 J. cinerea reference, and 1363 naturally occurring trees." The names of the populations are as in table one, or similar abbreviation. File format is Convert, tab delimited. All 12 microsatellite loci. Missing data with a '?'. Details about collections are in the manuscript

Comparative Expression Profiles of Midgut Genes in Dengue Virus Refractory and Susceptible <em>Aedes aegypti</em> across Critical Period for Virus Infection

<div><h3>Background</h3><p><em>Aedes aegypti</em> is the primary mosquito vector for dengue virus (DENV) worldwide. Infectivity of dengue virus varies among natural populations of this mosquito. How <em>A. aegypti</em> responds to DENV infection relative to which genes and associated pathways contribute to its differential susceptibility as a vector is not well defined.</p> <h3>Methods/Principal Findings</h3><p>Here, we used custom cDNA microarrays to identify groups of genes that were differentially expressed in midgut tissues between susceptible and refractory strains in a highly time specific manner. While genes involved in protein processing in the endoplasmic reticulum, mRNA surveillance, and the proteasome were significantly up-regulated in the susceptible strain, several metabolic processes including glycolysis, glycan biosynthesis and Wnt pathway were active in the refractory strain. In addition, several key signaling genes were expressed as common responsive genes in both susceptible and refractory mosquitoes that may be necessary for signal transduction to trigger the appropriate host response to the viral infection. These are coordinately expressed in the form of tight gene networks and expression clusters that may be necessary to differentially contribute to the progression of dengue infection between the two strains.</p> <h3>Conclusions</h3><p>Our data show that highly correlated differential expression of responsive genes throughout the post infection period in <em>A. aegypti</em> midgut tissues is necessary for a coordinated transcriptional response of the mosquito genes to host or defend the viral infection.</p> </div

Cluster analysis and self organizing maps of DETs.

<p>Four groups (I–IV) are shown that represent similar patterns of gene expression. For each group, the expression patterns of DETs (Moyo-D relative to Moyo-S) are shown at the 5 time points. In each graph, the y-axis represents the k-means of expression of transcripts and x-axis represents the post-infection time points. The blue line shows the mean expression values of the transcripts (number of genes showing that pattern is listed on the top of each graph) and the two red lines above and below the blue line shows the level of variance of transcript expression at each time point. The c# is the cluster number. The higher mean values indicate the genes are expressed at significantly higher levels in Moyo-D than in Moyo-S. The self organizing maps are shown to the right of the corresponding cluster graphs. Red and green colors represent up-regulation and down-regulation of genes in Moyo-D relative to Moyo-S, respectively.</p

List of significant genes identified from the microarray experiment which are related to endocytosis, peroxisome and ribosome functions.

<p>The time points at which the gene (gene ID, the gene name and the cDNA shown) are significantly differentially expressed between the two strains are shown. The fold changes of expression with respect to the control are shown in both the strains. The genes are activated in antagonistic manner between the two strains suggesting possible role of coordinated action of these three groups of genes in the mosquito after dengue virus infection.</p

Number of differentially expressed genes at each post-infection time point.

<p>The 2^nd column shows the total number of significant genes which are up-regulated in the Moyo-S strain but down-regulated in the Moyo-D strain at the corresponding time point. The 3^rd column shows the total number of significant genes which are up-regulated in the Moyo-R strain but down-regulated in the Moyo-S strain at the corresponding time point.</p

Hierarchical cluster of transcript expression among DENV susceptible (S) and DENV refractory (R) strains based on differential expression among post infection time points after DENV infection.

<p>The time points and strains within the box show higher correlated expression after DENV infection than other time points.</p

Number and distribution of DETs at different post infection time points.

<p>The thick horizontal arrow shows the progression of dengue infection with the time points marked in hours (hr). In the boxes above each time point, the numbers of transcripts that are up-regulated in the susceptible strain or down-regulated in the refractory strain are shown in red. Numbers of transcripts that are up-regulated in the refractory strain or down-regulated in the susceptible strain are shown in blue. The numbers in each box corresponding to ‘Time-specific Expression’ represent DETs which are differentially regulated exclusively at the specified post-infection time. On the other hand, entries in the boxes corresponding to ‘Overlapping Expression’ show numbers of DETs which are differentially expressed at more than one time point after infection (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0047350#pone.0047350.s004" target="_blank">Table S1</a>). The downward arrows show specificity of expression of the genes to time point(s). The genes showing differential expressions at each time point represent specific pathways genes. The top three representative pathways specific to each infection time point are shown below the time points.</p

Differential distribution of KEGG pathway genes in susceptible versus refractory strains.

<p>Pathways where the number of significant genes are significantly higher in susceptible than refractory strain are shown specific to ‘susceptible’ and pathways where the significant genes that show the opposite distribution pattern are shown specific to ‘refractory’. Several pathways were found commonly activated in both the strains without statistically significant bias and they are listed as ‘common’ pathways.</p

Examples of highly correlated gene expression throughout post-infection times.

<p>(A) Transcripts that had higher levels of expression in the DENV susceptible strain than the DENV refractory strain and (B) Transcripts that had higher levels of expression in the refractory strain than the susceptible strain. The expression levels are shown as stacked line graphs where the x-axis shows strains and time points and y-axis shows the cumulative values of fold-changes in expression of the responsive genes.</p

List of signal transduction genes that show differential expression (up-regulation in one and down-regulation in the other) between MS and MD strains in response to DENV infection.

<p>The fold-change values of expression are shown for each transcript and time of observation.</p