Dataset Information

Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa.

ABSTRACT: Transcription factors are key regulatory elements that affect gene expression in response to specific signals, including environmental stresses such as salinity. Halophytes are specialized plants that have the ability to complete their life cycle in saline environments. In this study we have identified and characterized the evolutionary relationships of putative transcription factors (TF) in an obligate succulent halophyte, Suaeda fruticosa, that are involved in conferring salt tolerance. Using RNA-seq data we have analyzed the expression patterns of certain TF families, predicted protein-protein interactions, and analyzed evolutionary trajectories to elucidate their possible roles in salt tolerance. We have detected the top differentially expressed (DE) transcription factor families (MYB, CAMTA, MADS-box and bZIP) that show the most pronounced response to salinity. The majority of DE genes in the four aforementioned TF families cluster together on TF phylogenetic trees, which suggests common evolutionary origins and trajectories. This research represents the first comprehensive TF study of a leaf succulent halophyte including their evolutionary relationships with TFs in other halophyte and salt-senstive plants. These findings provide a foundation for understanding the function of salt-responsive transcription factors in salt tolerance and associated gene regulation in plants.

SUBMITTER: Diray-Arce J

PROVIDER: S-EPMC6756544 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa.

Diray-Arce Joann J Knowles Alisa A Suvorov Anton A O'Brien Jacob J Hansen Collin C Bybee Seth M SM Gul Bilquees B Khan M Ajmal MA Nielsen Brent L BL

PloS one 20190923 9

Transcription factors are key regulatory elements that affect gene expression in response to specific signals, including environmental stresses such as salinity. Halophytes are specialized plants that have the ability to complete their life cycle in saline environments. In this study we have identified and characterized the evolutionary relationships of putative transcription factors (TF) in an obligate succulent halophyte, Suaeda fruticosa, that are involved in conferring salt tolerance. Using ...[more]

PMID: 31545841

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Project description:BackgroundImprovement of crop production is needed to feed the growing world population as the amount and quality of agricultural land decreases and soil salinity increases. This has stimulated research on salt tolerance in plants. Most crops tolerate a limited amount of salt to survive and produce biomass, while halophytes (salt-tolerant plants) have the ability to grow with saline water utilizing specific biochemical mechanisms. However, little is known about the genes involved in salt tolerance. We have characterized the transcriptome of Suaeda fruticosa, a halophyte that has the ability to sequester salts in its leaves. Suaeda fruticosa is an annual shrub in the family Chenopodiaceae found in coastal and inland regions of Pakistan and Mediterranean shores. This plant is an obligate halophyte that grows optimally from 200-400 mM NaCl and can grow at up to 1000 mM NaCl. High throughput sequencing technology was performed to provide understanding of genes involved in the salt tolerance mechanism. De novo assembly of the transcriptome and analysis has allowed identification of differentially expressed and unique genes present in this non-conventional crop.ResultsTwelve sequencing libraries prepared from control (0 mM NaCl treated) and optimum (300 mM NaCl treated) plants were sequenced using Illumina Hiseq 2000 to investigate differential gene expression between shoots and roots of Suaeda fruticosa. The transcriptome was assembled de novo using Velvet and Oases k-45 and clustered using CDHIT-EST. There are 54,526 unigenes; among these 475 genes are downregulated and 44 are upregulated when samples from plants grown under optimal salt are compared with those grown without salt. BLAST analysis identified the differentially expressed genes, which were categorized in gene ontology terms and their pathways.ConclusionsThis work has identified potential genes involved in salt tolerance in Suaeda fruticosa, and has provided an outline of tools to use for de novo transcriptome analysis. The assemblies that were used provide coverage of a considerable proportion of the transcriptome, which allows analysis of differential gene expression and identification of genes that may be involved in salt tolerance. The transcriptome may serve as a reference sequence for study of other succulent halophytes.

Project description:Plant growth-promoting rhizobacteria (PGPR) are considered as bio-ameliorators that confer better salt resistance to host plants while improving soil biological activity. Despite their importance, data about the likely synergisms between PGPR and halophytes in their native environments are scarce. The objective of this study was to assess the effect of PGPR (Glutamicibacter sp. and Pseudomonas sp.) inoculation on biomass, nutrient uptake, and antioxidant enzymes of Suaeda fruticosa, an obligate halophyte native in salt marshes and arid areas in Tunisia. Besides, the activity of rhizospheric soil enzyme activities upon plant inoculation was determined. Plants were grown in pots filled with soil and irrigated with 600 mM NaCl for 1 month. Inoculation (either with Pseudomonas sp. or Glutamicibacter sp.) resulted in significantly higher shoot dry weight and less accumulation of Na+ and Cl- in shoots of salt-treated plants. Glutamicibacter sp. inoculation significantly reduced malondialdehyde (MDA) concentration, while increasing the activity of antioxidant enzymes (superoxide dismutase; catalase; ascorbate peroxidase; and glutathione reductase) by up to 100%. This provides strong arguments in favor of a boosting effect of this strain on S. fruticosa challenged with high salinity. Pseudomonas sp. inoculation increased shoot K+ and Ca2+ content and lowered shoot MDA concentration. Regarding the soil biological activity, Pseudomonas sp. significantly enhanced the activities of three rhizospheric soil enzymes (urease, ß-glucosidase, and dehydrogenase) as compared to their respective non-inoculated saline treatment. Hence, Pseudomonas sp. could have a great potential to be used as bio-inoculants in order to improve plant growth and soil nutrient uptake under salt stress. Indole-3-acetic acid concentration in the soil increased in both bacterial treatments under saline conditions, especially with Glutamicibacter sp. (up to +214%). As a whole, Glutamicibacter sp. and Pseudomonas sp. strains are promising candidates as part of biological solutions aiming at the phytoremediation and reclamation of saline-degraded areas.

Dataset Information

Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa.

Publications

Identification and evolutionary characterization of salt-responsive transcription factors in the succulent halophyte Suaeda fruticosa.

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