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.

A comparative transcriptomic analysis reveals a coordinated mechanism activated in response to cold acclimation in common vetch (Vicia sativa L.)

“…The circadian clock of plants provides them with a competitive advantage in their living environment by regulating their physiological and metabolic rhythms. Circadian clocks are composed of transcription-translation feedback loops that are influenced by signals such as external temperature and light to adjust biological rhythms to match the environment [33,34]. In this study, 25 DEGs were enriched in the KEGG pathway "circadian rhythm-plant"; in the CA treatment group, Lanjian No.…”

Comparative physiology and transcriptome response patterns in cold-tolerant and cold-sensitive varieties of Solanum melongena

“…The advent of high-throughput sequencing has facilitated the comprehensive exploration of the entire genome’s expression at the transcriptional level. Transcriptome sequencing has been conducted on various plants under low-temperature stress, encompassing model plants [ 21 – 24 ], horticultural plants [ 25 ], vegetable crops [ 20 ], and trees [ 26 ]. These studies offer insights into how transcriptional changes respond to cold stress, leading to the identification of numerous cold response genes across different crops.…”

Genome-Wide Identification of the Rose SWEET Gene Family and Their Different Expression Profiles in Cold Response between Two Rose Species

“…Our previous study found that the significantly higher freezing tolerance in the shoot of R. beggeriana than that of R. fortuneana , which originated in southeastern China, might be due to the stronger ability of the spatial transfer of soluble sugars from leaves to shoots and consequently the storage of soluble sugars as starch in the shoots during overwintering [ 44 ]. The transcriptome analyses in R. multiflora and R. xanthina further indicated that the pathways of starch and sucrose metabolism were activated during cold stress [ 42 , 45 ]. However, it is not clear whether and which members of the SWEET gene family may participate in the cold response of a rose.…”