Global Transcriptome Profiling of Salicornia europaea L. Shoots under NaCl Treatment
2013-08-28
Along with environmental deterioration and anthropogenic influence, soil salinity is one of the major abiotic stresses in plant and crop systems, causing yield losses of primary crops worldwide. Many salt stress-induced genes are part of a complicated cascade of molecular networks and are thought to play important roles in responding to environment stress. These genes are involved in many cellular and physiological processes such as signal perception and transduction, photosynthesis, energy metabolism, membrane trafficking and protein biosynthesis, folding and decay. The isolation and identification of these functional genes, using the tools of molecular biology, is necessary for understanding the mechanisms of salt tolerance in plants.
Salicornia europaea L., one of the most salt-accumulating euhalophytes, can withstand concentrations of more than 1,000 mM NaCl in the soil and is widely distributed in coastal and inland salt marshes around the world. It is an important species for soil desalination because it hyper-accumulates salt in weakly saline soil, with salt reaching 50% of the dry weight of shoots. So, S. europaea could serve as an important model species for studying halophilic mechanisms in euhalophytes.
To obtain novel insights into the molecular basis of salt adaptation in S. europaea, two-group de novo assembly data were generated from Illumina sequencing of shoot samples for salttreated or untreated plants. Transcriptome changes resulting from salt treatment were also compared.
The results showed that a total of 41 and 39 million clean reads from the salt-treated (Se200S) and salt-free (SeCKS) tissues of S. europaea shoots were obtained, and de novo assembly produced 97,865 and 101,751 unigenes, respectively. Upon further assembly with EST data from both Se200S and SeCKS, 109,712 high-quality non-redundant unigenes were generated with a mean unigene size of 639 bp.
Additionally, a total of 3,979 differentially expressed genes (DEGs) were detected between the Se200S and SeCKS libraries, with 348 unigenes solely expressed in Se200S and 460 unigenes solely expressed in SeCKS. Furthermore, researchers identified a large number of genes that are involved in ion homeostasis and osmotic adjustment, including cation transporters and proteins for the synthesis of low-molecular compounds. All unigenes were functionally annotated within the COG (Clusters of Orthologous Groups), GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes pathways), and 10 genes were validated by qRT-PCR.
The data contains the extensive sequencing and gene-annotation analysis of S. europaea. This genetic knowledge will be very useful for future studies on the molecular adaptation to abiotic stress in euhalophytes and will facilitate the genetic manipulation of other economically important crops. The result was published in PLOS ONE in June 2013.
Salicornia europaea L., one of the most salt-accumulating euhalophytes, can withstand concentrations of more than 1,000 mM NaCl in the soil and is widely distributed in coastal and inland salt marshes around the world. It is an important species for soil desalination because it hyper-accumulates salt in weakly saline soil, with salt reaching 50% of the dry weight of shoots. So, S. europaea could serve as an important model species for studying halophilic mechanisms in euhalophytes.
To obtain novel insights into the molecular basis of salt adaptation in S. europaea, two-group de novo assembly data were generated from Illumina sequencing of shoot samples for salttreated or untreated plants. Transcriptome changes resulting from salt treatment were also compared.
The results showed that a total of 41 and 39 million clean reads from the salt-treated (Se200S) and salt-free (SeCKS) tissues of S. europaea shoots were obtained, and de novo assembly produced 97,865 and 101,751 unigenes, respectively. Upon further assembly with EST data from both Se200S and SeCKS, 109,712 high-quality non-redundant unigenes were generated with a mean unigene size of 639 bp.
Additionally, a total of 3,979 differentially expressed genes (DEGs) were detected between the Se200S and SeCKS libraries, with 348 unigenes solely expressed in Se200S and 460 unigenes solely expressed in SeCKS. Furthermore, researchers identified a large number of genes that are involved in ion homeostasis and osmotic adjustment, including cation transporters and proteins for the synthesis of low-molecular compounds. All unigenes were functionally annotated within the COG (Clusters of Orthologous Groups), GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes pathways), and 10 genes were validated by qRT-PCR.
The data contains the extensive sequencing and gene-annotation analysis of S. europaea. This genetic knowledge will be very useful for future studies on the molecular adaptation to abiotic stress in euhalophytes and will facilitate the genetic manipulation of other economically important crops. The result was published in PLOS ONE in June 2013.