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

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

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

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

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

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

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

Nuclear clusters detected by Structure.

<p>Neighbor joining tree (A) and distribution of the seven SSR clusters before (B) and after (C) removing presumably non-native genotypes. In (A) each rectangle represents a cluster. In (B) and (C) pie charts represent cluster composition of the 40 presumably native populations and 5 populations sampled outside the range (n°72, 73, 78, 79 and 80) (~24 individuals/population). Individuals with <i>q</i> values > 0.5 are colored, the remaining ones are in white.</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

130224_Larix_sample_info_mt_ha

130224_Larix_sample_info_mt_h