Genomic Variation Landscape of the Model Salt Cress Eutrema salsugineum

Eutrema salsugineum has long been used as the model for examining salt and other abiotic stress in plants. In addition to the forward genetics approaches widely used in the lab, natural variations undoubtedly will provide a rich genetic resource for studying molecular mechanisms underlying the stress tolerance and local adaptation of this species. We used 90 resequencing whole genomes of natural populations of this species across its Asian and North American distributions to detect the selection signals for genes involved in salt and other stresses at the species-range level and local distribution. We detected selection signals for genes involved in salt and other abiotic tolerance at the species level. In addition, several cold-induced and defense genes showed selection signals due to local adaptation in North America-NE Russia or northern China, respectively. These variations and findings provide valuable resources for further deciphering genetic mechanisms underlying the stress tolerance and local adaptations of this model species.

Genome-wide characterization and expression analysis of aquaporins in salt cress (Eutrema salsugineum)

Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioning in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play a critical role in abiotic stress response pathways of plants. As a species closely related to Arabidopsis thaliana, Eutrema salsugineum has been proposed as a model for studying salt resistance in plants. Here we surveyed 35 full-length AQP genes in E. salsugineum, which could be grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), nine NOD-like intrinsic proteins (NIPs), and three small basic intrinsic proteins (SIPs) by phylogenetic analysis. EsAQPs were comprised of 237–323 amino acids, with a theoretical molecular weight (MW) of 24.31–31.80 kDa and an isoelectric point (pI) value of 4.73–10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger’s position and specificity-determining position suggested quite differences in substrate specificities of EsAQPs. EsAQPs exhibited global expressions in all organs as shown by gene expression profiles and should be play important roles in response to salt, cold and drought stresses. This study provides comprehensive bioinformation on AQPs in E. salsugineum, which would be helpful for gene function analysis for further studies.

Genome-wide identification and expression analysis of aquaporins in salt cress (Eutrema salsugineum)

Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioned in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play critical roles in abiotic stress response of plants. Eutrema salsugineum is close to Arabidopsis thaliana and proposed as a model system for studying plant salt resistance. Here we identified 35 full-length AQP genes in E. salsugineum. Phylogenetic analysis showed EsAQPs were similar with AtAQPs and grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), 9 NOD-like intrinsic proteins (NIPs), and 3 small basic intrinsic proteins (SIPs). Gene structure, also the conserved motifs (MEME) of EsAQPs in each subfamily shared high similarities. In detailed sequence analysis, EsAQPs comprised 237-323 amino acids, with a theoretical molecular weight (MW) of 24.31-31.80 kDa and an isoelectric point (pI) value of 4.73-10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger’s position and specificity-determining position suggested there was a big difference in the specificity of substrate transport between EsAQPs. Gene expression profiles illustrated EsAQP genes could be detected in all organs and appear to play an important role in response salt, cold and drought signals. These results will bring a better understanding on the characterizations of AQPs in E. salsugineum and its complex transport networks in homeostasis control.

Genome-wide identification and expression analysis of aquaporins in salt cress (Eutrema salsugineum)

Aquaporins (AQPs) serve as water channel proteins and belong to major intrinsic proteins (MIPs) family, functioned in rapidly and selectively transporting water and other small solutes across biological membranes. Importantly, AQPs have been shown to play critical roles in abiotic stress response of plants. Eutrema salsugineum is close to Arabidopsis thaliana and proposed as a model system for studying plant salt resistance. Here we identified 35 full-length AQP genes in E. salsugineum. Phylogenetic analysis showed EsAQPs were similar with AtAQPs and grouped into four subfamilies including 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), 9 NOD-like intrinsic proteins (NIPs), and 3 small basic intrinsic proteins (SIPs). Gene structure, also the conserved motifs (MEME) of EsAQPs in each subfamily shared high similarities. In detailed sequence analysis, EsAQPs comprised 237-323 amino acids, with a theoretical molecular weight (MW) of 24.31-31.80 kDa and an isoelectric point (pI) value of 4.73-10.49. Functional prediction based on the NPA motif, aromatic/arginine (ar/R) selectivity filter, Froger’s position and specificity-determining position suggested there was a big difference in the specificity of substrate transport between EsAQPs. Gene expression profiles illustrated EsAQP genes could be detected in all organs and appear to play an important role in response salt, cold and drought signals. These results will bring a better understanding on the characterizations of AQPs in E. salsugineum and its complex transport networks in homeostasis control.