Comparative transcriptome profiling of a desert evergreen shrub, Ammopiptanthus mongolicus, in response to drought and cold stresses

Abstract

BackgroundThe molecular mechanisms involved in plant tolerance to either drought or cold have been extensively studied in many plant species. However, few studies have focused on their comparisons especially using non-model plants with strong tolerance to both stresses. Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f. is the only evergreen broadleaf shrub grown in the central Asian desert and it has very strong cold and drought tolerance. To provide further insights into plant tolerance, the transcriptome profiles of drought- and cold-treated A. mongolicus seedlings were analyzed using Illumina technology and differentially expressed genes (DEGs) were compared.ResultsA comprehensive transcriptome of A. mongolicus was sequenced using pooled mRNA extracted from drought-, cold-stressed and unstressed seedlings as well as leaves from naturally grown shrub. These sequences were assembled into 86058 unigenes, of which 51014 unigenes had an annotated function and 2440 encoded transcription factors (TFs). Transcriptome profiles were analyzed in A. mongolicus seedlings after drought and cold treatments at three time points (2, 8 and 24 h). Between 3917 and 6102 unigenes were identified as DEGs at a single time point in both stresses. Among these DEGs 2028 and 2026 DEGs were common across the three time points of drought and cold treatments respectively, and 971 DEGs were co-regulated by both stresses. Functional enrichment analyses identified many common or specific biological processes and gene sets in response to drought and cold stresses. The most pronounced findings are that flavonoid biosynthesis genes were enriched in the DEGs co-up-regulated by both stresses; while membrane protein genes and genes related to chloroplast were abundant in the DEGs specifically up-regulated by drought or cold, respectively. Furthermore, the DREB, ERF, NAC and WRKY TFs were predominantly co-up-regulated by both stresses.ConclusionsThe present study provides the most comprehensive transcriptome resource and the first dynamic transcriptome profiles of A. mongolicus under drought and cold stresses. This information will deepen our understanding of plant tolerance to drought and cold. The up-regulated DEGs will be valuable for further investigations of key genes and molecular mechanisms involved in the adaptation of A. mongolicus to harsh environments.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-671) contains supplementary material, which is available to authorized users.

Global Transcriptional Analysis Reveals the Complex Relationship between Tea Quality, Leaf Senescence and the Responses to Cold-Drought Combined Stress in Camellia sinensis

“…In sugarcane plants, the drought-resistant genotype could maintain plant growth under cold and drought stress either alone or combined through enhancing the antioxidant capacity, which was not observed in the sensitive genotype (Sales et al, 2013). In the study on A. mongolicus subjected to individual cold and drought stress, genes involved in the flavonoid biosynthesis pathway were highly induced to cope with stress-induced oxidative damage (Wu et al, 2014). Both flavonoids and carotenoids belong to non-enzymatic antioxidants, which not only defend plants from oxidative damage but also show medicinal characteristics especially against human health problems (Nijveldt et al, 2001; Williams et al, 2004; Fiedor and Burda, 2014; Dani et al, 2016).…”

“…For example, exposure to drought or cold stress can cause inactivation of enzymes and lipid peroxidation due to the over-production of ROS. To minimize damage, cells produce antioxidants such as flavonoids to scavenge excessive ROS (Wu et al, 2014). These secondary metabolites also contribute to the specific colors, odors and tastes in plants, and are unique sources for bio-pesticides, food additives, fragrances and pharmaceuticals.…”

Comparing control options for time‐series RNA sequencing experiments in nonmodel organisms: An example from grasses

“…Among the enriched GO terms, common drought‐related terms typically recovered in drought stress experiments (Fracasso et al, ; Wu et al, ; Zhang, Lei, Lai, Zhao, & Song, ) were recovered here using both control types. For up‐regulated genes, “response to water deprivation (GO:0009414)” and “response to water (GO:0009415)” were over‐represented on all days before recovery in both species.…”

Native Plants to Arid Areas: A Genetic Reservoir for Drought-Tolerant Crops

“…The upregulated DEGs included a heavy representation of genes encoding ripening-related proteins, LEA proteins, peroxidases, transporters, enzymes of flavonoid biosynthetic pathways, protein kinases, ethylene receptors, and transcription factors. About 17.2% of the common DEGs had no homology to known functional proteins [82]. Similarly, Pang et al [83] identified 1620 DEGs, including 1106 upregulated DEGs and 514 downregulated DEGs.…”