Transcriptome sequencing and de novo analysis of Rosa multiflora under cold stress

Rose is one of most popular ornamental plants in the world. The plant is of high economical value and great cultural importance. Low temperature exerts strong influence on the cultivation and commercial value of rose. The negative impacts could be genetically reduced through elucidating the mechanisms underlying plant cold tolerance. The Illumina Hiseq™ 2000 RNA-seq is a promising approach in gene expression analysis at the transcriptome level. With the transcriptome and DEG analysis, we investigated the gene expression profiles in response to cold stress of Rosa multiflora. The results shed light on the underlying molecular mechanisms of plant cold resistance. In the study, clean data that were generated from three samples of Rosa multiflora under different cold stress (i.e., CK, CT1 and CT2). A total of 61,864 unigenes with an average length of 1216 bp were obtained by assembling the data. A total of 42,553 complete and 1246 partial coding sequences (CDSs) were determined by protein database alignments and ESTScan prediction, respectively. Subsequently, we obtained functional annotations by aligning all unigenes with public protein databases (i.e., NR, Swiss-Prot, KEGG and COG). DEG analysis was performed to assess the changes in gene expression in cold condition (4 and 25 °C) using the FPKM method. The results indicated that there were 4966 up-regulated genes and 4592 down-regulated genes between CK and CT1, and 7915 up-regulated genes and 10,912 down-regulated genes between CK and CT2. We then performed GO enrichment and metabolic pathway enrichment analyses. A series of candidate genes that are involved in cold responsive pathways and a number of transcription factors were selected and discussed. We selected 15 up-regulated and five down-regulated unigenes in Rosa multiflora were quantified using qRT-PCR. The study provides a comprehensive overview of transcriptome response and gene expression profiling of Rosa multiflora in response to cold stress. The large number of transcriptomic sequences obtained in the study provides sufficient resources for molecular markers and gene cloning. The study facilities the understanding of the underlying mechanisms of cold resistance in Rosa multiflora.