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Abstract
BackgroundChrysanthemum is one kind of ornamental plant well-known and widely used in the world. However, its quality and production were severely affected by low temperature conditions in winter and early spring periods. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze chrysanthemum (Dendranthema grandiflorum) transcription response to low temperature.ResultsUsing Illumina sequencing technology, a total of 86,444,237 high-quality clean reads and 93,837 unigenes were generated from four libraries: T01, controls; T02, 4 °C cold acclimation (CA) for 24 h; T03, − 4 °C freezing treatments for 4 h with prior CA; and T04, − 4 °C freezing treatments for 4 h without prior CA. In total, 7583 differentially expressed genes (DEGs) of 36,462 annotated unigenes were identified. We performed GO and KEGG pathway enrichment analyses, and excavated a group of important cold-responsive genes related to low temperature sensing and signal transduction, membrane lipid stability, reactive oxygen species (ROS) scavenging and osmoregulation. These genes encode many key proteins in plant biological processes, such as protein kinases, transcription factors, fatty acid desaturase, lipid-transfer proteins, antifreeze proteins, antioxidase and soluble sugars synthetases. We also verified expression levels of 10 DEGs using quantitative real-time polymerase chain reaction (qRT-PCR). In addition, we performed the determination of physiological indicators of chrysanthemum treated at low temperature, and the results were basically consistent with molecular sequencing results.ConclusionIn summary, our study presents a genome-wide transcript profile of Dendranthema grandiflorum var. jinba and provides insights into the molecular mechanisms of D. grandiflorum in response to low temperature. These data contributes to our deeper relevant researches on cold tolerance and further exploring new candidate genes for chilling-tolerance and freezing-tolerance chrysanthemum molecular breeding.
Highlights
Chrysanthemum is one kind of ornamental plant well-known and widely used in the world
The proportion of mapped reads per library ranged from 71.71% to 73.77%, and unique mapped reads ranged from 47.49% to 51.43% (Table 2)
We found 3, 12 and 9 differentially expressed genes (DEGs) of calcium-dependent protein kinase (CDPK) family and 7, 5 and 4 DEGs of CBL-interacting protein kinase (CIPK) family were all up regulated in CP1, CP2 and CP3
Summary
Chrysanthemum is one kind of ornamental plant well-known and widely used in the world. We used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze chrysanthemum (Dendranthema grandiflorum) transcription response to low temperature. Plants will make a series of physiological and biochemical changes as defense systems in response to chilling (0–15 °C) and freezing (< 0 °C) injury [1]. Understanding the mechanism of chilling and freezing stress responses and improving the cold tolerance of chrysanthemum by gene transfer are of great importance. Illumina RNA-Seq technology has been successfully applied to many plant species, such as Beta vulgaris [5], Spartina pectinata [6], Camellia sinensis [7], Lilium lancifolium [8], and Camellia japonica [9], for its high accuracy and sensitivity of gene discovery
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