Abstract
BackgroundDrought and soil salinity are major abiotic stresses. The mechanisms of stress tolerance have been studied extensively in model plants. Caragana korshinskii is characterized by high drought and salt tolerance in northwestern China; unique patterns of gene expression allow it to tolerate the stress imposed by dehydration and semi-desert saline soil. There have, however, been no reports on the differences between C. korshinskii and model plants in the mechanisms underlying their drought and salt tolerance and regulation of gene expression.ResultsThree sequencing libraries from drought and salt-treated whole-seedling- plants and the control were sequenced to investigate changes in the C. korshinskii transcriptome in response to drought and salt stresses. Of the 129,451 contigs, 70,662 (54.12 %) were annotated with gene descriptions, gene ontology (GO) terms, and metabolic pathways, with a cut-off E-value of 10−5. These annotations included 56 GO terms, 148 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and 25 Clusters of Orthologous Groups (COG). On comparison of the transcriptomes of the control, drought- and salt-treated plants, 1630 and 1521 contigs showed significant differences in transcript abundance under drought and salt stresses. Compared to the differentially expressed genes (DEGs) in drought- or salt-treated Arabidopsis in the database, 542 DEGs in drought-treated C. korshinskii and 529 DEGs in salt-treated samples were presumably unique to C. korshinskii. The transcription profiles revealed that genes related to transcription factors, protein kinases, and antioxidant enzymes are relevant to the tolerance of drought and salt stress in this species. The expression patterns of 38 randomly selected DEGs were confirmed by quantitative real-time PCR and were essentially consistent with the changes in transcript abundance identified by RNA-seq.ConclusionsThe present study identified potential genes involved in drought and salt tolerance in C. korshinskii, as well as many DEGs uniquely expressed in drought- or salt-treated C. korshinskii samples compared to Arabidopsis. To our knowledge, this study is the first exploration of the C. korshinskii transcriptome under drought and salt conditions, and these results will facilitate the discovery of specific stress-resistance-related genes in C. korshinskii, possibly leading to the development of novel plant cultivars through genetic engineering.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2562-0) contains supplementary material, which is available to authorized users.
Highlights
Drought and soil salinity are major abiotic stresses
Illumina sequencing and de novo assembly In total, 120.26 million raw reads were generated from control samples, 39.78 million raw reads were generated from drought-treated samples, and 39.90 million raw reads were generated from salt-treated samples
Many genes that were upregulated or downregulated in response to drought or salt stress in C. korshinskii were reported to be involved in multiple mechanisms that might contribute to drought or salt tolerance
Summary
Drought and soil salinity are major abiotic stresses. The mechanisms of stress tolerance have been studied extensively in model plants. Several studies on drought and salt stresses using microarrays, transcriptome sequencing, and microRNA sequencing [5,6,7] have identified stress-inducible genes involved in water transport (aquaporins), ion transport (plasma membrane (PM) H+-ATPase, Na+/H+ exchanger or Na+/H+ antiporter), cellular membrane integrity (proline, glycine betaine, mannitol), scavenging of free oxygen radicals (superoxide dismutase, catalase and peroxidase), and protecting macromolecules (late embryogenesis abundant proteins and chaperones) Other proteins, such as regulatory proteins (transcription factors, protein kinases, protein phosphatases, and calmodulin-binding proteins), were found to be involved in signal transduction [8, 9]. Other transcription factors responding to abiotic stress conditions are zinc-finger proteins [13], basic-domain leucine-zipper (bZIP) [14], WRKY [15], and NACs [16]
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