Project description:RNA Seq was extracted from cucumber leaves after 7 days of bacteria inoculated in shoot and salt stress treatment. There were four treatment in this study, : ‘CK’ stands for seedlings under 0 mM NaCl without BC56 inoculation; ‘BC56’ refers to seedlings under 0 mM NaCl with BC56 inoculation; ‘Salt’ means seedlings under 100 mM NaCl without BC56 inoculation; ‘BC56+Salt’ indicates seedlings under 100 mM NaCl with BC56 inoculation.GO was used to assign putative functions to all identified DEGs into three principal categories, namely cellular component, molecular function, and biological process. An analysis of the GO terms suggested that ‘nucleus’, ‘plasma membrane’, and ‘integral component of membrane’ were the most dominant terms in the cellular component. While ‘biological process’, ‘regulation of transcription, DNA -templated’ and ‘transcription, DNA-templated’ were the most abundant terms in the biological process. In addition ‘molecular function’, ‘protein binding’ and ‘DNA-binding transcription factor activity’ were the major terms in the molecular function category. KEGG pathway analysis of DEGs in different comparison group suggested that in the BC56 vs CK comparison group DEGs were mainly enriched in four pathways which are ‘photosynthesis - antenna proteins’, ‘phenylpropanoid biosynthesis’, ‘metabolic pathways’ and ‘MAPK signaling pathway – plant’. In the BC56 vs CK comparison group DEGs were mainly enriched in seven pathways which are ‘phenylpropanoid biosynthesis’, ‘plant hormone signal transduction’, ‘biosynthesis of secondary metabolites’, ‘flavonoid biosynthesis’, ‘metabolic pathways’, ‘carotenoid biosynthesis’ and ‘stilbenoid, diarylheptanoid and gingerol biosynthesis’. In addition, compared with BC56+Salt vs CK, ‘ABC transporters’, ‘nitrogen metabolism’ and ‘phenylalanine metabolism’ is only significantly enriched in Salt vs CK.

Project description:Ice plant (Mesembryanthemum crystallinum L.) is a halophyte and an inducible CAM plant. Ice plant seedlings exhibit moderate salt tolerance, with root growth unaffected by 200 mM NaCl treatments, while hypocotyl elongation is hindered in salt-stressed etiolated seedlings. Superoxide anion accumulation was prominent in cotyledons and primary leaves but decreased in root tissues over time but was not significantly affected by salt treatment. Hydrogen peroxide (H2O2) levels surged initially in both control and salt-treated seedlings, with higher and more persistent H2O2 levels in salt-treated seedlings, indicating salt-induced ROS accumulation, especially in etiolated seedlings. An RNA-seq analysis of etiolated seedlings revealed 6,326 unigenes (about 8%) showing more than a four-fold change in expression after a 6-h 200 mM NaCl treatment. The top GO terms for 4-fold upregulated DEGs in the Molecular Function category included “cation binding,” “metal ion binding,” “oxidoreductase activity,” “monooxygenase activity,” and “antioxidant activity.” The top GO terms for 4-fold down-regulated DEGs in the Biological Process category included “metabolic process”, “cellular metabolic process”, and “biosynthetic process”. Upregulated genes were primarily linked to ion transport and stress responses and downregulated genes to growth processes like ribosomal protein synthesis and cell wall formation. This indicates that salt stress hinders growth but enhances ion homeostasis and stress response mechanisms. For class III peroxidase family genes, 14 out of 53 identified transcripts met the criteria for differentially expressed genes. Quantitative RT-PCR confirmed that the expression of McPrx4.1, McPrx12.1, and McPrx12.3 increased, while the expression of McPrx60.3 decreased. We suggest distinct roles for individual class III peroxidase members in the trade-offs between plant growth and stress response. Unveiling these responses will advance our understanding of the growth–stress balance in the intrinsic salt tolerance in halophytes.

Project description:Soil salinity is one of the primary causes of yield decline in rice. Pokkali (Pok) is a highly salt-tolerant landrace whereas IR29, is salt-sensitive but a widely cultivated cultivar. Comparative analysis of these genotypes may offer better understandings of the salinity tolerance mechanism. The published reports largely underscored the importance of transcriptional regulation during salt stress in these genotypes, while, the regulation at translational level is also critically important. Therefore, simultaneous comparison of transcriptional and translational changes between IR29 and Pok could unravel molecular insights into gene regulatory mechanisms that differ between these contrasting genotypes. Using RNA-Seq, we analyzed transcriptome and translatome from the control and salt-exposed Pok and IR29 seedlings. Clear differences were evident both at transcriptional and translational levels between the two genotypes even under control condition. In response to salt stress, 57 DEGs were commonly upregulated both at transcriptional and translational levels in the two genotypes; the number of up/down regulated DEGs in IR29 was comparable at transcriptional and translational levels; whereas in Pok, the number of upregulated DEGs at translational level (544 DEGs) was considerably higher than that at transcriptional level (219 DEGs); contrastingly, the number of downregulated DEGs (58) at translational level was significantly smaller than that at transcriptional level (397 DEGs). We speculate that Pok is more capable of stabilizing mRNA as well as can efficiently load mRNAs on to polysomes for translation under salt stress. Functional analysis showed that Pok is more efficient in maintaining cell wall integrity, detoxifying reactive oxygen species (ROS), translocating molecules and maintaining photosynthesis under salt stress. The present study not only confirmed the known salt stress associated genes, but also identified a number of putative new salt-responsive genes. This study also showed the importance of translational regulation in salt stress and other stresses responsive mechanism.

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Integrative analysis of transcriptome and metabolism reveals functional roles of redox homeostasis in low light and salt combined stress in Leymus chinensis

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