Sampling effort and prevalence of CoV from waterbirds at Ottenby, Sweden, 2006–2007.

<p>Sampling effort and prevalence of CoV from waterbirds at Ottenby, Sweden, 2006–2007.</p

Global phylogeny of avian <i>gammacoronavirus</i> partial RdRp.

<p>(a) Radial projection of all current wild bird sequences, including only a few “IBV-like” sequences to root the tree, and (b) the clade containing most of the Mallard CoV sequences generated in this study. Tips are coloured by geographic origin of sequence, Mallard CoV sequences generated in this study are indicated with a filled circle and Scaup CoV sequences with an asterisk. Scale bar represents number of substitutions per site. Traditional projection of panel A with support values is presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150198#pone.0150198.s002" target="_blank">S2 Fig</a>.</p

Gene expression papers in Mallard and Pekin ducks.

<p>This summary is limited to those studies assessing mRNA transcriptional changes of genes of interest in response to infection of live animals with a pathogen followed by qPCR profiling of gene expression.</p

The number of RGs required for data normalisation.

<p>Y-axis represents the GeNorm V value and the X-axis is V_i/j where “<i>i</i>” is V calculated for <i>n</i> genes and “<i>j</i>” is <i>n</i> + 1 genes. If the V value for a given comparison of V_i/j falls below 0.15 (red dashed line), then the “<i>i</i>” number of genes is sufficient for normalisation.</p

Selected reference genes per tissue.

<p>Combined stability value for the best combination of genes as calculated in (A) GeNorm and (B) NormFinder. For GeNorm, the number selected was that required to reach a threshold stability V value of lower than 0.15; for NormFinder the recommended combination of the two best genes are provided. Note that stability values are not directly comparable between GeNorm and NormFinder, as each algorithm uses its own stability index.</p

NormFinder stability rankings of eleven candidate reference genes amongst six mallard tissues.

<p>(A) Blood. (B) Spleen. (C) Liver. (D) GI2 (distal jejunum). (E) GI4 (distal ileum). (F) Colon. Data is plotted from least stable (left) to most stable (right) gene.</p

GeNorm stability rankings (M value) of eleven candidate reference genes amongst six mallard tissues.

<p>(A) Blood. (B) Spleen. (C) Liver. (D) GI2 (distal jejunum). (E) GI4 (distal ileum). (F) Colon. Data is plotted from least stable (left) to most stable (right) gene. Genes with an M value below 0.5 (red dashed line) are considered stable.</p

Spatial distribution of detections of the Atlantic flyway duck AIV sub-lineages in North American flyways.

<p>The box plots show the proportions of detections in each of the flyways for the gene sub-lineages that were identified in the 2006–2011 Atlantic flyway duck AIVs. The solid line in the box is the median. The top and bottom of the box are the first and third quartiles, respectively. The upper and lower horizontal lines represent 1.5X the difference between the first and third quartiles and any values falling outside of those are plotted as points. The detailed results for the each segment are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086999#pone.0086999.s005" target="_blank">Figure S5</a>.</p

Primers used in this study.

<p>F denotes the forward primer and R the reverse primer. Annealing temperature (Ta) expressed in °C and length in base pairs (bp).</p

Expression levels of each putative RG per tissue.

<p>Expression level expressed in terms of Ct value whereby a lower Ct value represents higher expression, of the eleven putative reference genes (RGs) across six mallard tissues. (A) Blood. (B) Spleen. (C) Lung. (D) GI 2 (distal jejunum). (E) GI 4 (distal ileum). (F) Colon. Uninfected individuals are shown with blue triangles, infected individuals with black circles.</p