Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

Abstract

Background: Rose is one of most popular ornamental plants worldwide and is of high economic value and great cultural importance. However, cold damage restricts its planting application in cold areas. To elucidate the metabolic response of rose under low temperature stress, we conducted transcriptome and de novo analysis of Rosa xanthina f. spontanea.

Results: A total of 124,106 unigenes from 9 libraries were generated by de novo assembly, with N50 length was 1470 bp, under 4 °C and - 20 °C stress (23 °C was used as a control). Functional annotation and prediction analyses identified 55,084 unigenes, and 67.72% of these unigenes had significant similarity (BLAST, E ≤ 10^{- 5}) to those in the public databases. A total of 3031 genes were upregulated and 3891 were downregulated at 4 °C compared with 23 °C, and 867 genes were upregulated and 1763 were downregulated at - 20 °C compared with 23 °C. A total of 468 common DEGs were detected under cold stress, and the matched DEGs were involved in three functional categories: biological process (58.45%), cellular component (11.27%) and molecular function (30.28%). Based on KEGG functional annotations, four pathways were significantly enriched: metabolic pathway, response to plant pathogen interaction (32 genes); starch and sucrose metabolism (21 genes); circadian rhythm plant (8 genes); and photosynthesis antenna proteins (7 genes).

Conclusions: Our study is the first to report the response to cold stress at the transcriptome level in R. xanthina f. spontanea. The results can help to elucidate the molecular mechanism of cold resistance in rose and provide new insights and candidate genes for genetically enhancing cold stress tolerance.

Keywords: DEGs; Low-temperature stress; Metabolic pathway; Rose.

Fig. 1

The column and Venn diagrams of DEGs assembled under low-temperature stress across three sets of comparisons expressed as 4 °C vs 23 °C (control), − 20 °C vs 23 °C and 4 °C vs − 20 °C, respectively (P < 0.05)

Fig. 2

GO enrichment analysis of 468 DEGs. The unigenes were classified into three main categories: biological process, cellular component and molecular function

Fig. 3

qRT-PCR analysis of expression levels of randomly selected genes in R. xanthina f. spontanea along with corresponding results under 4 °C, − 20 °C and 23 °C stress, respectively. Standard errors (SE) bars are shown within each of the columns