Dataset Information

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

ABSTRACT:

Background

The 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.

Results

A 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.

Conclusions

The 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.

SUBMITTER: Wu Y

PROVIDER: S-EPMC4143566 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Wu Yaqi Y Wei Wei W Pang Xinyue X Wang Xuefeng X Zhang Huiling H Dong Bo B Xing Yanping Y Li Xinguo X Wang Maoyan M

BMC genomics 20140809

<h4>Background</h4>The 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 tolera ...[more]

PMID: 25108399

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Project description:BACKGROUND: Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f., an evergreen broadleaf legume shrub, is distributed in Mid-Asia where the temperature can be as low as -30°C during the winter. Although A. mongolicus is an ideal model to study the plant response to cold stress, insufficient genomic resources for this species are available in public databases. To identify genes involved in cold acclimation (a phenomenon experienced by plants after low temperature stress), a high-throughput sequencing technology was applied. RESULTS: We sequenced cold-treated and control (untreated) samples of A. mongolicus, and obtained 65,075,656 and 67,287,120 high quality reads, respectively. After de novo assembly and quantitative assessment, 82795 all-unigenes were finally generated with an average length of 816 bp. We then obtained functional annotations by aligning all-unigenes with public protein databases including NR, SwissProt, KEGG and COG. Differentially expressed genes (DEGs) were investigated using the RPKM method. Overall, 9309 up-regulated genes and 23419 down-regulated genes were identified. To increase our understanding of these DEGs, we performed GO enrichment and metabolic pathway enrichment analyses. Based on these results, a series of candidate genes involved in cold responsive pathways were selected and discussed. Moreover, we analyzed transcription factors, and found 720 of them are differentially expressed. Finally, 20 of the candidate genes that were up-regulated and known to be associated with cold stress were examined using qRT-PCR. CONCLUSIONS: In this study, we identified a large set of cDNA unigenes from A. mongolicus. This is the first transcriptome sequencing of this non-model species under cold-acclimation using Illumina/Solexa, a next-generation sequencing technology. We sequenced cold-treated and control (untreated) samples of A. mongolicus and obtained large numbers of unigenes annotated to public databases. Studies of differentially expressed genes involved in cold-related metabolic pathways and transcription factors facilitate the discovery of cold-resistance genes.

Project description:BACKGROUND: Ammopiptanthus mongolicus is the only evergreen broadleaf shrub in the northwest desert of China, which can survive long-term aridity and extremely cold environments. In order to understand the genetic mechanisms underlying stress tolerance and adaptation to unfavorable environments of woody plants, an EST approach was used to investigate expression patterns of A. mongolicus in response to abiotic stresses. RESULTS: ESTs were generated from a cDNA library constructed from A. mongolicus seedlings subjected to cold and drought stresses. Analysis of 5,637 cDNA sequences led to the identification of 5,282 ESTs and 1,594 unigenes, which were denoted as the AmCDUnigene set. Of these, 70% of unigenes were annotated and classified into 12 functional categories according to Gene Ontology, and 30% of unigenes encoded unknown function proteins, suggesting some of them were novel or A. mongolicus specific genes. Using comparative analysis with the reported genes from other plants, 528 (33%) unigenes were identified as stress-responsive genes. The functional classification of the 528 genes showed that a majority of them are associated with scavenging reactive oxygen species, stress response, cellular transport, signal transduction and transcription. To further identify candidate abiotic stress-tolerance genes, the 528 stress-responsive genes were compared with reported abiotic stress genes in the Comparative Stress Genes Catalog of GCP. This comparative analysis identified 120 abiotic stress-responsive genes, and their expression in A. mongolicus seedlings under cold or drought stress were characterized by qRT-PCR. Significantly, 82 genes responded to cold and/or drought stress. These cold- and/or drought-inducible genes confirmed that the ROS network, signal transduction and osmolyte accumulation undergo transcriptional reorganization when exposed to cold or drought stress treatments. Additionally, among the 1,594 unigenes sequences, 155 simple sequence repeats (SSRs) were identified. CONCLUSION: This study represents a comprehensive analysis of cold and/or drought stress-responsive transcriptiome of A. mongolicus. The newly characterized genes and gene-derived markers from the AmCDUnigene set are valuable resources for a better understanding of the mechanisms that govern stress tolerance in A. mongolicus and other related species. Certain up-regulated genes characterizing these processes are potential targets for breeding for cold and/or drought tolerance of woody plants.

Dataset Information

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

Background

Results

Conclusions

Publications

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

Similar Datasets

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