Halophytism: What Have We Learnt From <i>Arabidopsis thaliana</i> Relative Model Systems?

Kazachkova, Yana; Eshel, Gil; Pantha, Pramod; Cheeseman, John M.; Dassanayake, Maheshi; Barak, Simon

doi:10.1104/pp.18.00863

Cited by 49 publications

(87 citation statements)

References 152 publications

(140 reference statements)

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“…Our time-course analysis of gene expression also revealed a short-term (within 1 h) response to salinity for several genes. In fact, the extremely rapid up-or down-regulation of most genes (at 1 or 24 h) may be indicative of a pre-adaptive response to salinity in halophytes due to a "constitutive over-expression" of stress-related genes even under non-stressful conditions [18,81]. The expression "stress-anticipatory preparedness" was used by Gong and co-workers [19] in their comparative study on stress tolerance mechanisms in Arabidopsis thaliana and its halophytic relative Thellungiella halophila.…”

Section: Comprehensive Analysis Of Degs Induced By Salt Stress and Bimentioning

confidence: 99%

“…The expression "stress-anticipatory preparedness" was used by Gong and co-workers [19] in their comparative study on stress tolerance mechanisms in Arabidopsis thaliana and its halophytic relative Thellungiella halophila. More recently, Kazachkova et al [81] also refer to a "stress ready transcriptome/metabolome" in halophytes. Since quinoa has many ecotypes, varieties, and landraces, further studies are needed to check whether this trait is a generalized phenomenon in this halophytic crop species.…”

Section: Comprehensive Analysis Of Degs Induced By Salt Stress and Bimentioning

confidence: 99%

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RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49

Ruiz

Maldonado

Biondi

et al. 2019

Genes

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Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased with time. We report a strong transcriptional reprogramming of genes involved in biological processes like oxidation-reduction, response to stress and response to abscisic acid (ABA), and cell wall organization. Transcript analyses by real-time RT- qPCR supported the RNA-seq results and shed light on the contribution of roots and shoots to the overall transcriptional response. In addition, it revealed a time-dependent response in the expression of the analyzed DEGs, including a quick (within 1 h) response for some genes, suggesting a “stress-anticipatory preparedness” in this highly salt-tolerant genotype.

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Section: Comprehensive Analysis Of Degs Induced By Salt Stress and Bimentioning

confidence: 99%

Section: Comprehensive Analysis Of Degs Induced By Salt Stress and Bimentioning

confidence: 99%

RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49

Ruiz

Maldonado

Biondi

et al. 2019

Genes

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“…Two plants, namely E. salsugineum and B. hygrometrica , were found to have the lowest proportion of lncRNAs in their transcriptomes (Table 2). E. salsugineum represents a plant with a halophytic life strategy and a capacity to tolerate a variety of extreme environmental conditions (Kazachkova et al 2018). Indeed, E. salsugineum has been used as a model plant in stress response studies due to its naturally high tolerance to abiotic stresses such as salt (Taji et al 2004), cold (Griffith et al 2007), drought (MacLeod et al 2015), and nutritional deficiencies (Velasco et al 2016).…”

Section: Discussionmentioning

confidence: 99%

“…Simopoulos et al (2018) reported that the genome of Eutrema salsugineum , an extremophile, contains a lower proportion of putative lncRNAs in comparison to the genome of model plants Arabidopsis thaliana and Oryza sativa . A lower number of predicted lncRNAs in E. salsugineum is surprising due to the naturally high capacity of this species to tolerate extreme environmental conditions (Champigny et al 2013; Kazachkova et al 2018) and the oft-cited association between expressed lncRNAs and stress responses (Wang et al 2017; Xu et al 2017). E. salsugineum ’s unexpectedly low number of predicted lncRNAs compared to its close and more stress sensitive relative A. thaliana leads to questions of potential natural variation in lncRNA number.…”

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confidence: 99%

Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships

Simopoulos

Weretilnyk

Golding³

2019

G3 Genes|Genomes|Genetics

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Long non-coding RNAs (lncRNAs) represent a diverse class of regulatory loci with roles in development and stress responses throughout all kingdoms of life. LncRNAs, however, remain under-studied in plants compared to animal systems. To address this deficiency, we applied a machine learning prediction tool, Classifying RNA by Ensemble Machine learning Algorithm (CREMA), to analyze RNAseq data from 11 plant species chosen to represent a wide range of evolutionary histories. Transcript sequences of all expressed and/or annotated loci from plants grown in unstressed (control) conditions were assembled and input into CREMA for comparative analyses. On average, 6.4% of the plant transcripts were identified by CREMA as encoding lncRNAs. Gene annotation associated with the transcripts showed that up to 99% of all predicted lncRNAs for Solanum tuberosum and Amborella trichopoda were missing from their reference annotations whereas the reference annotation for the genetic model plant Arabidopsis thaliana contains 96% of all predicted lncRNAs for this species. Thus a reliance on reference annotations for use in lncRNA research in less well-studied plants can be impeded by the near absence of annotations associated with these regulatory transcripts. Moreover, our work using phylogenetic signal analyses suggests that molecular traits of plant lncRNAs display different evolutionary patterns than all other transcripts in plants and have molecular traits that do not follow a classic evolutionary pattern. Specifically, GC content was the only tested trait of lncRNAs with consistently significant and high phylogenetic signal, contrary to high signal in all tested molecular traits for the other transcripts in our tested plant species.

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“…In this study, we used the boron-tolerant extremophyte Schrenkiella parvula (formerly Thellungiella parvula and Eutrema parvulum, family Brassicaceae) (Dassanayake et al, 2011;Zhu, 2015;Kazachkova et al, 2018) and its close relative A. thaliana, a boron-sensitive model, to identify cellular processes interrupted by excess boron and to determine the transcriptional and metabolic processes that support growth during boron toxicity. S. parvula is adapted to high levels of boron naturally present in its native habitats in the Central Anatolian plateau of Turkey (Helvaci et al, 2004).…”

Section: Introductionmentioning

confidence: 99%

Cross species multi-omics reveals cell wall sequestration and elevated global transcription as mechanisms of boron tolerance in plants

Wang

DiTusa

et al. 2020

Preprint

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Boron toxicity is a worldwide problem for crop production, yet we have only a limited understanding of the genetic responses and adaptive mechanisms to this environmental stress in plants. Here we identified responses to excess boron in boron stress-sensitive Arabidopsis thaliana and its boron stress-tolerant extremophyte relative Schrenkiella parvula using comparative genomics, transcriptomics, metabolomics, and ionomics. S. parvula maintains a lower level of total boron and free boric acid in its roots and shoots and sustains growth for longer durations than A. thaliana when grown with excess boron. S. parvula likely excludes boron more efficiently than A. thaliana, which we propose is partly driven by BOR5, a boron transporter that we functionally characterized in the current study. Both species allocate significant transcriptomic and metabolomic resources to enable their cell walls to serve as a partial sink for excess boron, particularly discernable in A. thaliana shoots. We provide evidence that the S. parvula transcriptome is pre-adapted to boron toxicity, exhibiting substantial overlap with the boron-stressed transcriptome of A. thaliana. Our transcriptomic and metabolomics data also suggest that RNA metabolism is a primary target of boron toxicity. Cytoplasmic boric acid likely forms complexes with ribose and ribose-containing compounds critical to RNA and other primary metabolic functions. A model depicting some of the cellular responses that enable a plant to grow in the presence of normally toxic levels of boron is presented.

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Halophytism: What Have We Learnt From Arabidopsis thaliana Relative Model Systems?

Cited by 49 publications

References 152 publications

RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49

RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49

Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships

Cross species multi-omics reveals cell wall sequestration and elevated global transcription as mechanisms of boron tolerance in plants

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