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      De Novo Assembly and Discovery of Genes That Are Involved in Drought Tolerance in Tibetan Sophora moorcroftiana

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          Abstract

          Sophora moorcroftiana, a Leguminosae shrub species that is restricted to the arid and semi-arid regions of the Qinghai-Tibet Plateau, is an ecologically important foundation species and exhibits substantial drought tolerance in the Plateau. There are no functional genomics resources in public databases for understanding the molecular mechanism underlying the drought tolerance of S. moorcroftiana. Therefore, we performed a large-scale transcriptome sequencing of this species under drought stress using the Illumina sequencing technology. A total of 62,348,602 clean reads were obtained. The assembly of the clean reads resulted in 146,943 transcripts, including 66,026 unigenes. In the assembled sequences, 1534 transcription factors were identified and classified into 23 different common families, and 9040 SSR loci, from di- to hexa-nucleotides, whose repeat number is greater than five, were presented. In addition, we performed a gene expression profiling analysis upon dehydration treatment. The results indicated significant differences in the gene expression profiles among the control, mild stress and severe stress. In total, 4687, 5648 and 5735 genes were identified from the comparison of mild versus control, severe versus control and severe versus mild stress, respectively. Based on the differentially expressed genes, a Gene Ontology annotation analysis indicated many dehydration-relevant categories, including ‘response to water ‘stimulus’ and ‘response to water deprivation’. Meanwhile, the Kyoto Encyclopedia of Genes and Genomes pathway analysis uncovered some important pathways, such as ‘metabolic pathways’ and ‘plant hormone signal transduction’. In addition, the expression patterns of 25 putative genes that are involved in drought tolerance resulting from quantitative real-time PCR were consistent with their transcript abundance changes as identified by RNA-seq. The globally sequenced genes covered a considerable proportion of the S. moorcroftiana transcriptome, and the expression results may be useful to further extend the knowledge on the drought tolerance of this plant species that survives under Plateau conditions.

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          Most cited references27

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          Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray.

          Full-length cDNAs are essential for functional analysis of plant genes in the post-sequencing era of the Arabidopsis genome. Recently, cDNA microarray analysis has been developed for quantitative analysis of global and simultaneous analysis of expression profiles. We have prepared a full-length cDNA microarray containing approximately 7000 independent, full-length cDNA groups to analyse the expression profiles of genes under drought, cold (low temperature) and high-salinity stress conditions over time. The transcripts of 53, 277 and 194 genes increased after cold, drought and high-salinity treatments, respectively, more than fivefold compared with the control genes. We also identified many highly drought-, cold- or high-salinity- stress-inducible genes. However, we observed strong relationships in the expression of these stress-responsive genes based on Venn diagram analysis, and found 22 stress-inducible genes that responded to all three stresses. Several gene groups showing different expression profiles were identified by analysis of their expression patterns during stress-responsive gene induction. The cold-inducible genes were classified into at least two gene groups from their expression profiles. DREB1A was included in a group whose expression peaked at 2 h after cold treatment. Among the drought, cold or high-salinity stress-inducible genes identified, we found 40 transcription factor genes (corresponding to approximately 11% of all stress-inducible genes identified), suggesting that various transcriptional regulatory mechanisms function in the drought, cold or high-salinity stress signal transduction pathways.
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            ABA-mediated transcriptional regulation in response to osmotic stress in plants.

            The plant hormone abscisic acid (ABA) plays a pivotal role in a variety of developmental processes and adaptive stress responses to environmental stimuli in plants. Cellular dehydration during the seed maturation and vegetative growth stages induces an increase in endogenous ABA levels, which control many dehydration-responsive genes. In Arabidopsis plants, ABA regulates nearly 10% of the protein-coding genes, a much higher percentage than other plant hormones. Expression of the genes is mainly regulated by two different families of bZIP transcription factors (TFs), ABI5 in the seeds and AREB/ABFs in the vegetative stage, in an ABA-responsive-element (ABRE) dependent manner. The SnRK2-AREB/ABF pathway governs the majority of ABA-mediated ABRE-dependent gene expression in response to osmotic stress during the vegetative stage. In addition to osmotic stress, the circadian clock and light conditions also appear to participate in the regulation of ABA-mediated gene expression, likely conferring versatile tolerance and repressing growth under stress conditions. Moreover, various other TFs belonging to several classes, including AP2/ERF, MYB, NAC, and HD-ZF, have been reported to engage in ABA-mediated gene expression. This review mainly focuses on the transcriptional regulation of ABA-mediated gene expression in response to osmotic stress during the vegetative growth stage in Arabidopsis.
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              The MYB96 transcription factor mediates abscisic acid signaling during drought stress response in Arabidopsis.

              Plant adaptive responses to drought are coordinated by adjusting growth and developmental processes as well as molecular and cellular activities. The root system is the primary site that perceives drought stress signals, and its development is profoundly affected by soil water content. Various growth hormones, particularly abscisic acid (ABA) and auxin, play a critical role in root growth under drought through complex signaling networks. Here, we report that a R2R3-type MYB transcription factor, MYB96, regulates drought stress response by integrating ABA and auxin signals. The MYB96-mediated ABA signals are integrated into an auxin signaling pathway that involves a subset of GH3 genes encoding auxin-conjugating enzymes. A MYB96-overexpressing Arabidopsis (Arabidopsis thaliana) mutant exhibited enhanced drought resistance with reduced lateral roots. In the mutant, while lateral root primordia were normally developed, meristem activation and lateral root elongation were suppressed. In contrast, a T-DNA insertional knockout mutant was more susceptible to drought. Auxin also induces MYB96 primarily in the roots, which in turn induces the GH3 genes and modulates endogenous auxin levels during lateral root development. We propose that MYB96 is a molecular link that mediates ABA-auxin cross talk in drought stress response and lateral root growth, providing an adaptive strategy under drought stress conditions.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2015
                5 January 2015
                : 10
                : 1
                : e111054
                Affiliations
                [1 ]Agricultural and Animal Husbandry College, Tibet University, Nyingchi, Tibet, China
                [2 ]Key Laboratory of Forest Ecology in Tibet Plateau (Tibet University), Ministry of Education, Nyingchi, Tibet, China
                [3 ]National Key Station for Field Scientific Observation & Experiment, Nyingchi, Tibet, China
                Institute of Crop Sciences, China
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: HL QG. Performed the experiments: WY YF. Analyzed the data: WY YF SL. Contributed reagents/materials/analysis tools: HL SL QG. Wrote the paper: HL WY YF SL QG.

                Article
                PONE-D-14-26766
                10.1371/journal.pone.0111054
                4283959
                25559297
                0e16fb19-eafe-47cd-ae48-4af1ce0a91fd
                Copyright @ 2015

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 18 June 2014
                : 22 September 2014
                Page count
                Pages: 13
                Funding
                This research was supported by the National Natural Science Foundation of China (31260189) and Collaborative Innovation Center Construction of Research and development on Tibetan characteristic agricultural and animal husbandry resources----plateau ecology. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Proteins
                Protein Synthesis
                Biotechnology
                Plant Biotechnology
                Plant Genomics
                Computational Biology
                Genome Analysis
                Gene Prediction
                Transcriptome Analysis
                Developmental Biology
                Ecology
                Plant Ecology
                Plant-Environment Interactions
                Plant Resistance to Abiotic Stress
                Drought Adaptation
                Evolutionary Biology
                Molecular Evolution
                Gene Duplication
                Genetics
                Genomics
                Plant Genetics
                Plant Science
                Plant Physiology
                Ecology and Environmental Sciences
                Drought
                Research and Analysis Methods
                Chemical Synthesis
                Biosynthetic Techniques
                Custom metadata
                The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are available from the NCBI SRA database (accession number SRP041237) and within Supporting Information files.

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                Uncategorized

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