Analysis of differentially expressed genes under UV-B radiation in the desert plant Reaumuria soongorica

Liu, Meiling; Li, Xinrong; Liu, Yubing; Shi, Yulan; Ma, Xiaofei

doi:10.1016/j.gene.2015.08.026

Cited by 11 publications

(8 citation statements)

References 45 publications

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“…Using RNA-seq, Liu et al ( 2015 ) indicated the abundance and enrichment of the differentially expressed genes involved in the thylakoid, plastid part, chloroplast, and plastids envelope in Reaumuria soongorica leaves subjected to UV-B radiation. Additionally, previous immunological studies documented that O 3 treatment could affect energy transfer processes by inducing alterations in thylakoid membrane proteins (Tognini et al, 1997 ; Ranieri et al, 2000 ).…”

Section: Resultsmentioning

confidence: 99%

Suppression Substractive Hybridization and NGS Reveal Differential Transcriptome Expression Profiles in Wayfaring Tree (Viburnum lantana L.) Treated with Ozone

et al. 2016

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Tropospheric ozone (O3) is a global air pollutant that causes high economic damages by decreasing plant productivity. It enters the leaves through the stomata, generates reactive oxygen species, which subsequent decrease in photosynthesis, plant growth, and biomass accumulation. In order to identify genes that are important for conferring O3 tolerance or sensitivity to plants, a suppression subtractive hybridization analysis was performed on the very sensitive woody shrub, Viburnum lantana, exposed to chronic O3 treatment (60 ppb, 5 h d−1 for 45 consecutive days). Transcript profiling and relative expression assessment were carried out in asymptomatic leaves, after 15 days of O3 exposure. At the end of the experiment symptoms were observed on all treated leaves and plants, with an injured leaf area per plant accounting for 16.7% of the total surface. Cloned genes were sequenced by 454-pyrosequencing and transcript profiling and relative expression assessment were carried out on sequenced reads. A total of 38,800 and 12,495 high quality reads obtained in control and O3-treated libraries, respectively (average length of 319 ± 156.7 and 255 ± 107.4 bp). The Ensembl transcriptome yielded a total of 1241 unigenes with a total sequence length of 389,126 bp and an average length size of 389 bp (guanine-cytosine content = 49.9%). mRNA abundance was measured by reads per kilobase per million and 41 and 37 ensembl unigenes showed up- and down-regulation respectively. Unigenes functionally associated to photosynthesis and carbon utilization were repressed, demonstrating the deleterious effect of O3 exposure. Unigenes functionally associated to heat-shock proteins and glutathione were concurrently induced, suggesting the role of thylakoid-localized proteins and antioxidant-detoxification pathways as an effective strategy for responding to O3. Gene Ontology analysis documented a differential expression of co-regulated transcripts for several functional categories, including specific transcription factors (MYB and WRKY). This study demonstrates that a complex sequence of events takes place in the cells at intracellular and membrane level following O3 exposure and elucidates the effects of this oxidative stress on the transcriptional machinery of the non-model plant species V. lantana, with the final aim to provide the molecular supportive knowledge for the use of this plant as O3-bioindicator.

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Section: Resultsmentioning

confidence: 99%

Suppression Substractive Hybridization and NGS Reveal Differential Transcriptome Expression Profiles in Wayfaring Tree (Viburnum lantana L.) Treated with Ozone

et al. 2016

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“…Another SNP was detected in the 3'UTR region of the Glycerol-3-phosphate SN-2-acyltransferase 4 gene (GPAT4). A recent examination of pollen and embryo sac, suggested that down-regulation of GPAT4 caused impaired female fertility, which is the main reason for a reduced seed set [94,95]. A synonymous polymorphism was detected within the tetraketide α-pyrone reductase 1-like (TKPR1), a gene involved in the biosynthesis of hydroxylated tetraketide compounds that serve as sporopollenin precursors, the main constituents of pollen coat exine [96].…”

Section: Discussionmentioning

confidence: 99%

EST–SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives

Mariotti

Belaj

Rosa

et al. 2020

Genes

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Background: The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers. Methods: In the present work, more than 1000 transcript-specific SNP markers obtained by the genotyping of 260 individuals were studied. These genotypes included cultivated, oleasters, and samples of subspecies guanchica, and were analyzed in silico, in order to identify polymorphisms on key genes distinguishing different Olea europaea forms. Results: Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. Signatures of selection that occurred during olive domestication, were detected and reported. Conclusion: This deep EST–SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation.

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“…It is widely distributed in the piedmont, river terraces and Gobi areas of the HRB, where the MAP is usually less than 200 mm. Previous studies have focused on the morphological structure, water use strategy, eco-physiological response and drought tolerance of R. soongorica in different habitat conditions (Su et al, 2012;Fu et al, 2014;Liu et al, 2015Luo et al, 2018). The results of these studies indicated that R. soongorica was discontinuously distributed and exhibited excellent tolerability to low water availability, extreme temperature fluctuations and nutrient deprivation.…”

Section: Introductionmentioning

confidence: 99%

Spatial patch structure and adaptive strategy for desert shrub of Reaumuria soongorica in arid ecosystem of the Heihe River Basin

Huang

et al. 2019

J. Geogr. Sci.

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In many arid ecosystems, vegetation frequently occurs in high-cover patches interspersed in a matrix of low plant cover. However, theoretical explanations for shrub patch pattern dynamics along climate gradients remain unclear on a large scale. This context aimed to assess the variance of the Reaumuria soongorica patch structure along the precipitation gradient and the factors that affect patch structure formation in the middle and lower Heihe River Basin (HRB). Field investigations on vegetation patterns and heterogeneity in soil properties were conducted during 2014 and 2015. The results showed that patch height, size and plant-to-patch distance were smaller in high precipitation habitats than in low precipitation sites. Climate, soil and vegetation explained 82.5% of the variance in patch structure. Spatially, R. soongorica shifted from a clumped to a random pattern on the landscape towards the MAP gradient, and heterogeneity in the surface soil properties (the ratio of biological soil crust (BSC) to bare gravels (BG)) determined the R. soongorica population distribution pattern in the middle and lower HRB. A conceptual model, which integrated water availability and plant facilitation and competition effects, was revealed that R. soongorica changed from a flexible water use strategy in high precipitation regions to a consistent water use strategy in low precipitation areas. Our study provides a comprehensive quantification of the variance in shrub patch structure along a precipitation gradient and may improve our understanding of vegetation pattern dynamics in the Gobi Desert under future climate change.

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Analysis of differentially expressed genes under UV-B radiation in the desert plant Reaumuria soongorica

Cited by 11 publications

References 45 publications

Suppression Substractive Hybridization and NGS Reveal Differential Transcriptome Expression Profiles in Wayfaring Tree (Viburnum lantana L.) Treated with Ozone

Suppression Substractive Hybridization and NGS Reveal Differential Transcriptome Expression Profiles in Wayfaring Tree (Viburnum lantana L.) Treated with Ozone

EST–SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives

Spatial patch structure and adaptive strategy for desert shrub of Reaumuria soongorica in arid ecosystem of the Heihe River Basin

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