Transcriptome Analysis of the Response to NaCl in Suaeda maritima Provides an Insight into Salt Tolerance Mechanisms in Halophytes

Abstract

Although salt tolerance is a feature representative of halophytes, most studies on this topic in plants have been conducted on glycophytes. Transcriptome profiles are also available for only a limited number of halophytes. Hence, the present study was conducted to understand the molecular basis of salt tolerance through the transcriptome profiling of the halophyte Suaeda maritima, which is an emerging plant model for research on salt tolerance. Illumina sequencing revealed 72,588 clustered transcripts, including 27,434 that were annotated using BLASTX. Salt application resulted in the 2-fold or greater upregulation of 647 genes and downregulation of 735 genes. Of these, 391 proteins were homologous to proteins in the COGs (cluster of orthologous groups) database, and the majorities were grouped into the poorly characterized category. Approximately 50% of the genes assigned to MapMan pathways showed homology to S. maritima. The majority of such genes represented transcription factors. Several genes also contributed to cell wall and carbohydrate metabolism, ion relation, redox responses and G protein, phosphoinositide and hormone signaling. Real-time PCR was used to validate the results of the deep sequencing for the most of the genes. This study demonstrates the expression of protein kinase C, the target of diacylglycerol in phosphoinositide signaling, for the first time in plants. This study further reveals that the biochemical and molecular responses occurring at several levels are associated with salt tolerance in S. maritima. At the structural level, adaptations to high salinity levels include the remodeling of cell walls and the modification of membrane lipids. At the cellular level, the accumulation of glycinebetaine and the sequestration and exclusion of Na+ appear to be important. Moreover, this study also shows that the processes related to salt tolerance might be highly complex, as reflected by the salt-induced enhancement of transcription factor expression, including hormone-responsive factors, and that this process might be initially triggered by G protein and phosphoinositide signaling.

De Novo Transcriptome Characterization, Gene Expression Profiling and Ionic Responses of Nitraria sibirica Pall. under Salt Stress

“…Some genes were in agreement with a report that amino acid metabolism, secondary metabolism, signaling etc. related to salt-tolerance were down-regulated under salt stress [68]. In our study, the number of down-regulated genes in CL2 was more than in CL6 ( Figure 6, Table S7).…”

RNA-Seq analysis of Clerodendrum inerme (L.) roots in response to salt stress

“…This technology can reveal candidate genes and key pathways involved in salt tolerance by analyzing differentially expressed genes (DEGs) and RNA-seq functional annotation. Transcriptome analysis reveals that several levels of biochemical and molecular responses are associated with salt tolerance in Suaeda maritima, including the remodeling of cell walls and the modification of membrane lipids at the structural level and the accumulation of glycine betaine and the sequestration and exclusion of Na + at the cellular level [41]. Genes related to membrane transport, osmoprotection, redox metabolism or protein synthesis were differentially expressed in Beta vulgaris ssp.…”

Transcriptomics analysis of salt stress tolerance in the roots of the mangrove Avicennia officinalis

“…Whereas, halophytes such as mangroves growing in high salt environment serve as ideal candidates for exploring the molecular mechanisms underlying salt tolerance. Hence, researchers have tried to focus on analyzing and understanding the transcript profiles of several halophytes such as Medicago , Mesembryanthemum , Thellungiella , Aeluropus , Atriplex , Salicornia and Suaeda leading to identification of salt-responsive genes such as those encoding antiporters (NHX, SOS, HKT, VATPase), ion channels (Cl − , Ca 2+ , aquaporins), and antioxidant enzymes (APX, CAT, GST, BADH, SOD), many of which have been used for developing salt tolerant crops 4 , 22 – 27 . Nevertheless, to date, limited data on mangrove transcriptome and microarray analysis have been available, which mainly focus on the salt excluders such as Bruguiera , Rhizophora and Heritiera 28 – 32 .…”