Introgression data

The file was produced using the command 'save()' from the R software. This resulted in the file “introgression.RData”, which includes two dataframes: (1) intro.rates.paper and (2) tree.data. The first dataframe comprises the empirical introgression rates recorded by Bialozyt et al. (2012). The columns are the individual tree number followed by the percentage of introgression for year 2006 and 2007 respectively. The second dataframe (tree.data) comprises the name, coordinates, sex and taxa of all trees used in the simulation. In the column 'SEX' females are coded '0' and males are coded '1'. In the column 'SPECIES' Populus nigra are coded '0' and the hybrids (Populus × canadenis) are coded '1'

Venn diagram of the overlapping DE transcripts from the DEGseq, DESeq and NOISeq analyses.

<p>The amount of up- and down-regulated transcripts is given for each segment.</p

Log₂ fold changes of the four specifically amplified genes for validation resulting from the MACE analysis and RT-qPCR (calculated using REST with correction of amplification efficiencies).

<p>SE = standard error.</p><p>Log₂ fold changes of the four specifically amplified genes for validation resulting from the MACE analysis and RT-qPCR (calculated using REST with correction of amplification efficiencies).</p

Properties of the sense-tag-filtered consensus transcripts identified by the three different Seq-analyses.

<p>PUP: Putative uncharacterized protein; UP: Uncharacterized protein.</p><p>^a‘Database hit’ refers to transcripts with database accession number or similarity to a UniProt Reference Cluster (UniRef) sequence.</p><p>Properties of the sense-tag-filtered consensus transcripts identified by the three different Seq-analyses.</p

Characteristics of the MACE libraries constructed from the drought stressed and the well-watered seedlings.

<p>Shown is the amount of total tags analyzed for the library, the amount of unique tags and the amount of tags for each treatment pool (drought stressed and well-watered).</p><p>S: sense direction; AS: antisense direction.</p><p>Characteristics of the MACE libraries constructed from the drought stressed and the well-watered seedlings.</p

Genes for validation derived from the DEGseq analysis; sorted by log₂ fold change in descending order.

<p>Gene names according to UniProt Protein Knowledgebase (<a href="http://www.uniprot.org/" target="_blank">http://www.uniprot.org/</a>) with the corresponding database accession number.</p><p>- No gene name available or abbreviation assigned;</p><p>* Validated via RT-qPCR;</p><p>^<i>a</i> Not identified as DE by DESeq.</p><p>Genes for validation derived from the DEGseq analysis; sorted by log₂ fold change in descending order.</p

Differentially expressed transcripts resulting from the MACE and DEGseq analyses, filtered by log₂ fold change and minimum different sense tags (≥ 50).

<p>Shown is the amount of transcripts with and without database hit and significant assignment to the GO domain biological process (enrichment-<i>p</i>-value < 1e-10).</p><p>^a‘Database hit’ refers to transcripts with database accession number or similarity to a UniProt Reference Cluster (UniRef) sequence.</p><p>Differentially expressed transcripts resulting from the MACE and DEGseq analyses, filtered by log₂ fold change and minimum different sense tags (≥ 50).</p

Log-log plot of up- and down-regulated transcripts in response to drought stress on GO-level 4 in silver fir seedlings.

<p>Transcripts are differentiated by their GO ancestor: metabolic process (GO:0008152), response to stimulus (GO:0050896) or other ancestor. Most obvious GO terms associated with drought stress, as well as photosynthesis, are highlighted and labeled specifically.</p

Scatter plots of the MACE results and subsequent analyses of differential expression for DEGseq (A), NOISeq (B) and DESeq (C).

<p>Each plot contains all identified transcripts (grey dots), as well as the analysis-specific DE transcripts (red dots). Further, the candidate genes validated via RT-qPCR are shown, as well as the corresponding stably expressed reference genes. The x- and y-axis give the transcript count in the well-watered and the drought stressed pool, respectively. Counts are normalized differently for the three analyses: tags per million (TPM) for DEGseq, trimmed mean of M-values (TMM) for NOISeq and hitcount/size factor (hc/fc) for DESeq. Transcripts falling on the straight line (90° bisecting line) are equally expressed in both pools. Transcripts above the line are up-regulated in response to drought stress, while those below the line are down-regulated.</p

Main effects of species, soil moisture and soil composition on the survival rate (living cuttings) and growth performance (n° of sprouts, longest sprouts, shoot biomass, root biomass) after 84 days (three-way ANOVAs; response variables were square-root-transformed to improve the diagnostic plots) and general linear mixed models of the number of sprouts and the longest sprout over time.

<p>Values are F-values. Levels of significance (p) are denoted with *p<0.05, **p<0.01 and ***p<0.001.</p