GO enrichment of DEGs in response to NO.

<p>The analysis was performed using agriGO.</p

Summary of the hormone related genes in response to NO.

<p>Summary of the hormone related genes in response to NO.</p

Analysis of the DEGs in response to NO.

<p><b>A,</b> Number of DEGs compared with the control. <b>B,</b> Comparison of gene expression for 25 DEGs. Data generated using qPCR (<i>y</i>-axis) and DGE (<i>x</i>-axis) are shown.</p

Overview of the transcriptome analysis of NO responsive genes in plants.

<p>Overview of the transcriptome analysis of NO responsive genes in plants.</p

Transcriptome analysis of nitric oxide-responsive genes in upland cotton (<i>Gossypium hirsutum</i>)

<div><p>Nitric oxide (NO) is an important signaling molecule with diverse physiological functions in plants. It is therefore important to characterize the downstream genes and signal transduction networks modulated by NO. Here, we identified 1,932 differentially expressed genes (DEGs) responding to NO in upland cotton using high throughput tag sequencing. The results of quantitative real-time polymerase chain reaction (qRT-PCR) analysis of 25 DEGs showed good consistency. Gene Ontology (GO) and KEGG pathway were analyzed to gain a better understanding of these DEGs. We identified 157 DEGs belonging to 36 transcription factor (TF) families and 72 DEGs related to eight plant hormones, among which several TF families and hormones were involved in stress responses. Hydrogen peroxide and malondialdehyde (MDA) contents were increased, as well related genes after treatment with sodium nitroprusside (SNP) (an NO donor), suggesting a role for NO in the plant stress response. Finally, we compared of the current and previous data indicating a massive number of NO-responsive genes at the large-scale transcriptome level. This study evaluated the landscape of NO-responsive genes in cotton and identified the involvement of NO in the stress response. Some of the identified DEGs represent good candidates for further functional analysis in cotton.</p></div

Summary of the TFs in response to NO.

<p>Summary of the TFs in response to NO.</p

NO is involved in the stress response.

<p><b>A,</b> Changes in hydrogen peroxide content after treatment with SNP. <b>B,</b> Changes in malondialdehyde content after treatment with SNP. <b>C-L,</b> Expression level of DEGs related to stress responses and defense process.</p

Expression levels of candidate DEGs related to hormone biosynthesis and signaling pathways.

<p>Expression levels of candidate DEGs related to hormone biosynthesis and signaling pathways.</p

Correlation between NBS-encoding resistance genes and disease resistance QTL, as well as their locations in <i>G. raimondii</i>.

<p>Correlation between NBS-encoding resistance genes and disease resistance QTL, as well as their locations in <i>G. raimondii</i>.</p

Phylogenetic tree derived from NBS-encoding resistance genes in <i>G. raimondii</i>.

<p>The neighbor-joining tree was constructed using the sequences of 163 regular NBS containing proteins in <i>G. raimondii</i>. Bootstrap values are indicated on the branches. Each <i>G. raimondii</i> protein is encoded by its name, and then followed by its type (CNL, TNL, TN and so on) and location (chromosomes or scaffolds). Blue clades are genes with TIR domain, while pink and green clades are genes with CC domain.</p