Summary of read statistics from RNA-sequencing of <i>Crossostephium chinensis</i>.

<p>Summary of read statistics from RNA-sequencing of <i>Crossostephium chinensis</i>.</p

Changes in the physiological parameters of <i>C</i>. <i>chinensis</i> leaves during NaCl stress.

<p>A, B, C, and D show the changes in proline content, the K+/Na+ ratio, SOD activity, and POD activity, respectively, after 0, 1, 3, 6, 9, 12, 24, and 72 hours of 360 mM NaCl stress. Values in each column with the same letter are not significantly different (p = 0.05) as described by Duncan’s test.</p

Validation of RNA-seq results by qRT-PCR.

<p>Twelve unigenes were randomly selected from among the salt-response-related genes for verification by qRT-PCR. The red bar indicates the RNA-seq results, and the blue bar represents the qRT-PCR outcomes.</p

Top 20 enriched KEGG pathways among DEGs from ‘ST3 vs ST0’, ‘ST9 vs ST3’, and ‘ST9 vs ST0’.

<p>The number of DEGs in each pathway is positively related to the size of the plots. The padj values shown in red are positive.</p

GO enrichment of DEGs in the three compared groups.

<p>DEGs in ‘ST3 vs ST0’, ‘ST9 vs ST3’, and ‘ST9 vs ST0’ were enriched for 15, 21, and 7 GO terms, respectively.</p

qRT-PCR analysis of 12 DEGs during periods of salt stress.

<p>Twelve unigenes used for verification by qRT-PCR were randomly selected from among salt-response-related genes. The qRT-PCR results are the means ± standard deviations (± SDs) of three replicates.</p

Differential expression patterns of all unigenes among three libraries (ST0, ST3 and ST9).

<p>A, B, and C show volcano plot analyses of DEGs in ‘ST3 vs ST0’, ‘ST9 vs ST3’ and ‘ST9 vs ST0’, respectively. The x-axis indicates the expression ratio of the different samples, and the y-axis indicates the significance of the differential gene expression, which is positive in relation to the -log₁₀(padj) value and negative in relation to the padj value. Red plots represent up-regulated genes; green plots represent down-regulated genes; and blue plots represent no significant difference. D indicates the number of DEGs shared among different groups.</p

Unigene annotation results from seven databases.

<p>Unigene annotation results from seven databases.</p

Expression of salt-responsive gene families.

<p>Expression of salt-responsive gene families.</p

Transcriptome analysis of <i>Crossostephium chinensis</i> provides insight into the molecular basis of salinity stress responses

<div><p>Soil salinization is becoming a limitation to the utilization of ornamental plants worldwide. <i>Crossostephium chinensis</i> (Linnaeus) Makino is often cultivated along the southeast coast of China for its desirable ornamental qualities and high salt tolerance. However, little is known about the genomic background of the salt tolerance mechanism in <i>C</i>. <i>chinensis</i>. In the present study, we used Illumina paired-end sequencing to systematically investigate leaf transcriptomes derived from <i>C</i>. <i>chinensis</i> seedlings grown under normal conditions and under salt stress. A total of 105,473,004 bp of reads were assembled into 163,046 unigenes, of which 65,839 (40.38% of the total) and 54,342 (33.32% of the total) were aligned in Swiss-Prot and Nr protein, respectively. A total of 11,331 (6.95%) differentially expressed genes (DEGs) were identified among three comparisons, including 2,239 in ‘ST3 vs ST0’, 5,880 in ‘ST9 vs ST3’ and 9,718 in ‘ST9 vs ST0’, and they were generally classified into 26 Gene Ontology terms and 58 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway terms. Many genes encoding important transcription factors (e.g., <i>WRKY</i>, <i>MYB</i>, and <i>AP2/EREBP</i>) and proteins involved in starch and sucrose metabolism, arginine and proline metabolism, plant hormone signal transduction, amino acid biosynthesis, plant-pathogen interactions and carbohydrate metabolism, among others, were substantially up-regulated under salt stress. These genes represent important candidates for studying the salt-response mechanism and molecular biology of <i>C</i>. <i>chinensis</i> and its relatives. Our findings provide a genomic sequence resource for functional genetic assignments in <i>C</i>. <i>chinensis</i>. These transcriptome datasets will help elucidate the molecular mechanisms responsible for salt-stress tolerance in <i>C</i>. <i>chinensis</i> and facilitate the breeding of new stress-tolerant cultivars for high-saline areas using this valuable genetic resource.</p></div