The EU and the Catalan Crisis

List of all differentially expressed proteins (n = 45) identified in the study. (XLSX 11 kb

qRT–PCR validation of RNA-Seq results.

<p>Fifteen genes were randomly selected from the DEGs (<i>red columns</i>) from the RNA-Seq data and were analyzed for differential expression changes (<i>blue columns</i>) of the genes. The results were the average of two biological replicate samples in triplicate. <i>Error bars</i> indicate the standard error of two biological replicates in qRT–PCR.</p

GO classifications of genes.

<p>The results are summarized in three main categories: biological processes, molecular functions and cellular components by GO analysis. (A) GO classifications of all genes between the two treatments and all 177 DEGs between the two treatments. <b>(B)</b> GO analysis of the down-regulated genes in A1-vs-A2. <b>(C)</b> GO analysis of the up-regulated genes in A1-vs-A2.</p

Transcriptomic Profiling Analysis of <i>Arabidopsis thaliana</i> Treated with Exogenous <i>Myo</i>-Inositol

<div><p><i>Myo</i>-insositol (MI) is a crucial substance in the growth and developmental processes in plants. It is commonly added to the culture medium to promote adventitious shoot development. In our previous work, MI was found in influencing <i>Agrobacterium</i>-mediated transformation. In this report, a high-throughput RNA sequencing technique (RNA-Seq) was used to investigate differently expressed genes in one-month-old <i>Arabidopsis</i> seedling grown on MI free or MI supplemented culture medium. The results showed that 21,288 and 21,299 genes were detected with and without MI treatment, respectively. The detected genes included 184 new genes that were not annotated in the <i>Arabidopsis thaliana</i> reference genome. Additionally, 183 differentially expressed genes were identified (DEGs, FDR ≤0.05, log₂ FC≥1), including 93 up-regulated genes and 90 down-regulated genes. The DEGs were involved in multiple pathways, such as cell wall biosynthesis, biotic and abiotic stress response, chromosome modification, and substrate transportation. Some significantly differently expressed genes provided us with valuable information for exploring the functions of exogenous MI. RNA-Seq results showed that exogenous MI could alter gene expression and signaling transduction in plant cells. These results provided a systematic understanding of the functions of exogenous MI in detail and provided a foundation for future studies.</p></div

Hierarchical cluster analyses of gene expression based on log ratio RPKM data.

<p>The cluster display expression patterns for a subset of DEGs in two comparisons (A1-vs-A2) between two treatments. The <i>color key</i> represents RPKM normalized log₁₀ transformed counts. <i>Red</i> represents high expression, <i>green</i> represents a low expression. <i>Each column</i> represents an experimental condition, and <i>each row</i> represents a gene. The columns are evenly divided into three groups, I, II and III. Each group contains 61 genes, their order are arranged in accordance with the blue arrow direction. The green box contains 26 genes, which represented the green rows in III group.</p

All 183 DEGs were divided according to the folds of FPKM value between two treatments.

<p>All 183 DEGs were divided according to the folds of FPKM value between two treatments.</p

MapMan overview of cellular function (A) and biotic stress (B) showing all DEGs between the two treatments with exogenous <i>myo</i>-inositol.

<p>The <i>big grey circle</i> is an illustrated map of nucleus. The <i>small grey circle</i> indicate annotated biological process (metabolites). The <i>small squares</i> represent individual genes. The <i>color key</i> represents RPKM normalized log₂ transformed counts. <i>Red</i> represents up-regulation and <i>blue</i> represents down-regulation between two treatments with exogenous <i>myo</i>-inositol.</p

Reads number based on the RNA-Seq data in two libraries of <i>A</i>. <i>thaliana</i> wild-type (Col-0) under exogenous <i>myo</i>-inositol (MI+ or MI-).

<p>Reads number based on the RNA-Seq data in two libraries of <i>A</i>. <i>thaliana</i> wild-type (Col-0) under exogenous <i>myo</i>-inositol (MI+ or MI-).</p

<i>De novo</i> Assembly and Transcriptomic Profiling of the Grazing Response in <i>Stipa grandis</i>

<div><p>Background</p><p><i>Stipa grandis</i> (Poaceae) is one of the dominant species in a typical steppe of the Inner Mongolian Plateau. However, primarily due to heavy grazing, the grasslands have become seriously degraded, and <i>S</i>. <i>grandis</i> has developed a special growth-inhibition phenotype against the stressful habitat. Because of the lack of transcriptomic and genomic information, the understanding of the molecular mechanisms underlying the grazing response of <i>S</i>. <i>grandis</i> has been prohibited.</p><p>Results</p><p>Using the Illumina HiSeq 2000 platform, two libraries prepared from non-grazing (FS) and overgrazing samples (OS) were sequenced. <i>De novo</i> assembly produced 94,674 unigenes, of which 65,047 unigenes had BLAST hits in the National Center for Biotechnology Information (NCBI) non-redundant (nr) database (E-value < 10^-5). In total, 47,747, 26,156 and 40,842 unigenes were assigned to the Gene Ontology (GO), Clusters of Orthologous Group (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. A total of 13,221 unigenes showed significant differences in expression under the overgrazing condition, with a threshold false discovery rate ≤ 0.001 and an absolute value of log₂Ratio ≥ 1. These differentially expressed genes (DEGs) were assigned to 43,257 GO terms and were significantly enriched in 32 KEGG pathways (q-value ≤ 0.05). The alterations in the wound-, drought- and defense-related genes indicate that stressors have an additive effect on the growth inhibition of this species.</p><p>Conclusions</p><p>This first large-scale transcriptome study will provide important information for further gene expression and functional genomics studies, and it facilitated our investigation of the molecular mechanisms of the <i>S</i>. <i>grandis</i> grazing response and the associated morphological and physiological characteristics.</p></div

Identification of the DEGs (differentially expressed genes) between FS and OS.

<p>The DEGs were determined using a threshold of FDR ≤ 0.001 and an absolute value of log₂Ratio ≥ 1. The red, green and blue spots represent the upregulated, the downregulated DEGs and the genes without obvious changes in response to grazing, respectively.</p