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Illumina miRNA sequencing revealed Citrus adaptation to long-term B-toxicity through modulation of lateral root development by miR319

ABSTRACT: Illumina miRNA sequencing revealed Citrus adaptation to long-term B-toxicity through modulation of lateral root development by miR319

PROVIDER: PRJNA435986 | ENA |

REPOSITORIES: ENA

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Illumina miRNA sequencing revealed Citrus adaptation to long-term B-toxicity through modulation of lateral root development by miR319

Project description:We report the application of Illumina sequencing for high-throughput profiling of miRNA in citrus root responded to long-term boron toxicity. We find miR319 is involved in citrus adapation to long-term boron toxicity via targeting a MYB gene, Ciclev10000756m.g.v1.0, which is homologus with several MYBs that modulate lateral root development in Arabidopsis.

2021-02-25 | GSE111128 | GEO

Illumina miRNA profiles with anatomical study revealed involvement of miR397a in Citrus adaptation to long-term B-toxicity via modulating secondary cell wall biosynthesis

Project description:Our previous studies indicated that long-term B-toxicity was mainly limited to leaves of Citrus species; alternations of cell wall structure in vascular bundles were involved in tolerance to B-toxicity. Here, miRNAs and their expression pattern were first identified from B-treated Citrus sinensis (tolerant) and C. grandis (intolerant) leaves with high-throughput sequencing in order to identify miRNAs that might be involved in tolerance to B-toxicity. Results: 51 (23 conserved and 28 novel) miRNAs in C. grandis and 20 (6 conserved and 14 novel) in C. sinensis were differentially expressed after B-toxic treatment, respectively. Illumina sequencing results were validated by stem-loop qRT-PCR, and 82.5% qRT-PCR data coincided with those from direct sequencing. Among the differentially expressed miRNAs, miR395a and miR397a were the most significantly up-regulated in B-toxic C. grandis leaves, yet both were down-regulated in B-toxic C. sinensis ones. With modified 5’-RACE, four auxin response factor genes were confirmed as the real targets of miR160a, and two laccase (LAC) genes as those of miR397a, respectively. Localization of cell wall polysaccharides indicated that up-regulation of LAC4 resulted in secondary deposition of cell wall polysaccharides in regions near the pits of vessel elements in C. sinensis, and that down-regulation of both LAC17 and LAC4, via up-regulating their negative regulator miR397a, led to poorly developed vessel elements in C. grandis.Our findings demonstrated that miR397a played a pivotal role in woody Citrus tolerance to B-toxicity by targeting LAC17 and LAC4, of which both were responsible for secondary cell wall synthesis.

2017-02-13 | GSE74434 | GEO

Leaf adaptive responses to aluminum-toxicity revealed by RNA-Seq in two citrus species with contrasting aluminum tolerance

Project description:Background: Limited data are available on aluminum (Al)-toxicity-induced alterations of gene profiles in woody plants. Seedlings of Al-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated with nutrient solution containing 0 and 1.0 mM AlCl3•6H2O. Thereafter, we investigated the Al-toxicity-induced alterations of transcriptomics in leaves by RNA-Seq. Results: Using RNA-seq, we isolated 1162 (181) up- and 496 (234) downregulated genes from Al-treated C. grandis (C. sinensis) leaves. Clearly, gene expression was less affected by Al-toxicity in C. sinensis leaves than in C. grandis ones. Several Al-toxicity-responsive genes homologous to known Al-tolerance genes: ALUMINUM SENSITIVE 3 (ALS3), multidrug and toxic compound extrusion (MATE), glutathione S-transferase (GST), L-galactose dehydrogenase（L-GalDH) and lipoxygenase (LOX) were identified in citrus leaves. Genes related to signal transduction, and sulfur transport and metabolism might also play a role in the higher Al-tolerance of C. sinensis. Conclusions: This is the first comparative investigation of transcriptomic responses in Al-treated citrus leaves. There were common and unique mechanisms for citrus Al-tolerance. These results provide a platform for further investigating the roles of genes possibly responsible for citrus Al-tolerance.

2018-01-08 | GSE108837 | GEO

Root adaptive responses to aluminum-toxicity revealed by RNA-Seq in two citrus species with contrasting aluminum tolerance

Project description:Background: Limited data are available on aluminum (Al)-toxicity-induced alterations of gene profiles in woody plants. Seedlings of Al-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated with nutrient solution containing 0 and 1.0 mM AlCl3•6H2O. Thereafter, we investigated the Al-toxicity-induced alterations of transcriptomics in roots by RNA-Seq. Results: Using RNA-seq, we isolated 1293 (990) up- and 1377 (915) downregulated genes from Al-treated C. grandis (C. sinensis) roots. Clearly, gene expression was less affected by Al-toxicity in C. sinensis roots than in C. grandis ones. Several Al-toxicity-responsive genes homologous to known Al-tolerance genes: Al-activated malate transporter, multidrug and toxic compound extrusion (MATE), IRON REGULATED/ferroportin 1, sensitive to proton rhizotoxicity 1 and monogalactosyldiacylglycerol synthase were identified in citrus roots. However, Al-induced upregulation of all these genes was stronger in C. grandis roots than in C. sinensis ones except for MATEs. Genes related to signal transduction, and sulfur transport and metabolism might also play a role in the higher Al-tolerance of C. sinensis. Conclusions: This is the first comparative investigation of transcriptomic responses in Al-treated citrus roots. There were common and unique mechanisms for citrus Al-tolerance. These results provide a platform for further investigating the roles of genes possibly responsible for citrus Al-tolerance.

2016-08-24 | GSE85958 | GEO

Root adaptive responses to aluminum-toxicity revealed by RNA-Seq in two citrus species with contrasting aluminum tolerance

Project description:Background: Limited data are available on aluminum (Al)-toxicity-induced alterations of gene profiles in woody plants. Seedlings of Al-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated with nutrient solution containing 0 and 1.0 mM AlCl3â?¢6H2O. Thereafter, we investigated the Al-toxicity-induced alterations of transcriptomics in roots by RNA-Seq. Results: Using RNA-seq, we isolated 1293 (990) up- and 1377 (915) downregulated genes from Al-treated C. grandis (C. sinensis) roots. Clearly, gene expression was less affected by Al-toxicity in C. sinensis roots than in C. grandis ones. Several Al-toxicity-responsive genes homologous to known Al-tolerance genes: Al-activated malate transporter, multidrug and toxic compound extrusion (MATE), IRON REGULATED/ferroportin 1, sensitive to proton rhizotoxicity 1 and monogalactosyldiacylglycerol synthase were identified in citrus roots. However, Al-induced upregulation of all these genes was stronger in C. grandis roots than in C. sinensis ones except for MATEs. Genes related to signal transduction, and sulfur transport and metabolism might also play a role in the higher Al-tolerance of C. sinensis. Conclusions: This is the first comparative investigation of transcriptomic responses in Al-treated citrus roots. There were common and unique mechanisms for citrus Al-tolerance. These results provide a platform for further investigating the roles of genes possibly responsible for citrus Al-tolerance. Examination of mRNA levels in control and Al-treatment roots of C. grandis and C. sinensis with two biological replicates were generated by deep sequencing, using Illumina HiSeq 2000 device.

2016-08-24 | E-GEOD-85958 | biostudies-arrayexpress

Integrated analysis of physiology, transcriptomics and metabonomics revealed the mechanisms of high pH mitigating copper toxicity in Citrus sinensis roots

Project description:Limited data are available on the impacts of copper (Cu)-pH-interaction-responsive genes in roots. Citrus sinensis seedlings were treated with 300 (Cu-toxicity) or 0.5 uM (control) CuCl2 x pH 3.0 or 4.8 for 17 weeks. Thereafter, we investigated the impacts of Cu-pH interactions on transcriptomics in roots.

2023-02-17 | GSE225124 | GEO

MicroRNA-mediated responses to long-term magnesium-deficiency in Citrus sinensis roots revealed by Illumina sequencing

Project description:Background: Magnesium (Mg)-deficiency occurs most frequently in strongly acidic, sandy soils. Citrus are grown mainly on acidic and strong acidic soils. Mg-deficiency causes poor fruit quality and low fruit yield in some Citrus orchards. For the first time, we investigated Mg-deficiency-responsive miRNAs in ‘Xuegan’ (Citrus sinensis) roots using Illumina sequencing in order to obtain some miRNAs presumably responsible for Citrus Mg-deficiency tolerance. Results: We obtained 101 (69) miRNAs with increased (decreased) expression from Mg-starved roots. Our results suggested that the adaptation of Citrus roots to Mg-deficiency was related to the several aspects: (a) inhibiting root respiration and related gene expression via inducing miR158 and miR2919; (b) enhancing antioxidant system by down-regulating related miRNAs (miR780, miR6190, miR1044, miR5261 and miR1151) and the adaptation to low-phosphorus (miR6190); (c) activating transport-related genes by altering the expression of miR6190, miR6485, miR1044, miR5029 and miR3437; (d) elevating protein ubiquitination due to decreased expression levels of miR1044, miR5261, miR1151 and miR5029; (e) maintaining root growth by regulating miR5261, miR6485 and miR158 expression; and (f) triggering DNA repair (transcription regulation) by regulating miR5176 and miR6485 (miR6028, miR6190, miR6485, miR5621, miR160 and miR7708) expression. Mg-deficiency-responsive miRNAs involved in root signal transduction also had functions in Citrus Mg-deficiency tolerance. Conclusions: We obtained several novel Mg-deficiency-responsive miRNAs (i.e., miR5261, miR158, miR6190, miR6485, miR1151 and miR1044) possibly contributing to Mg-deficiency tolerance. These results revealed some novel clues on the miRNA-mediated adaptation to nutrient deficiencies in higher plants.

2017-07-28 | GSE80713 | GEO

Phosphorus-mediated alleviation of aluminum toxicity revealed by iTRAQ technique in Citrus grandis roots

Project description:Citrus grandis seedlings were irrigated with nutrient solutions containing two levels of aluminium (Al; 0 mM and 1.2 mM AlCl3•6H2O) and two levels of phosphorus (P; 0 μM and 200 μM KH2PO4) combinations for 18 weeks, respectively. The proteome profile of Citrus root submitted to different P-Al interactions were investigated by using isobaric tags for relative and absolute quantification (iTRAQ).

2019-11-13 | PXD012534 | Pride

MicroRNA Sequencing Revealed Citrus Adaptation to Long-Term Boron Toxicity through Modulation of Root Development by miR319 and miR171.

Project description: Not available

| S-EPMC6470687 | biostudies-literature

Comparative proteome of two citrus species differing in aluminum-tolerance in response to aluminum-toxicity revealed by iTRAQ

Project description:After long-term aluminum treatment, thereafter, we investigated leaves protein profiles of two citrus cultivars using isobaric tags for relative and absolute quantification (iTRAQ).

2018-10-24 | PXD002916 | Pride

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