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.
Highlights
The molecular mechanisms involved in plant tolerance to either drought or cold have been extensively studied in many plant species
Sequencing, de novo assembly and functional annotation of the A. mongolicus transcriptome Illumina sequencing of the pooled mRNA generated 47.29 million (M) clean paired-end reads with Q20 over 98%
By searching against the PlantTFDB (E-value ≤ 1e-5) in combination with annotations in the NR and Swiss-Prot databases, 2440 unigenes were annotated as transcription factors (TFs), representing 4.8% of the annotated unigenes and covering 57 Transcription factor (TF) families (Table 2)
Summary
The molecular mechanisms involved in plant tolerance to either drought or cold have been extensively studied in many plant species. Drought and low temperature are two major environmental stresses that greatly affect plant growth and crop production worldwide. This is the case in arid and cold areas. Thousands of genes and dozens of metabolic and signaling pathways have been identified in plants during drought and cold stresses [1,2,3,4]. Similar studies are very limited in other plants, and the molecular mechanisms controlling plant tolerance to both drought and cold remain largely unknown
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