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Series GSE80713 Query DataSets for GSE80713
Status Public on Jul 28, 2017
Title MicroRNA-mediated responses to long-term magnesium-deficiency in Citrus sinensis roots revealed by Illumina sequencing
Organism Citrus sinensis
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary 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.

 
Overall design Two libraries were constructed from Citrus sinensis (L.) Osbeck roots subjected to 0(0 mM MgSO4,Mg-deficient,RD) or 1(Mg-sufficient,control, RS) mM MgSO4 for 16 weeks, and sequenced by Illumina sequencing. Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The clean tags were used for further analysis.
 
Contributor(s) Chen L, Liang W, Huang J
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Apr 27, 2016
Last update date May 15, 2019
Contact name Chen Lisong
E-mail(s) lisongchen@fafu.edu.cn
Phone +8613599390418
Organization name Fujian Agriculture and Forestry University
Street address Shangdian street NO.15
City Fuzhou
ZIP/Postal code 350002
Country China
 
Platforms (1)
GPL9256 Illumina Genome Analyzer (Citrus sinensis)
Samples (2)
GSM2133907 RD
GSM2133908 RS
Relations
BioProject PRJNA319771
SRA SRP074058

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
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Supplementary file Size Download File type/resource
GSE80713_RAW.tar 119.3 Mb (http)(custom) TAR (of FA)
GSE80713_table3.pdf 665.5 Kb (ftp)(http) PDF
GSE80713_table5.pdf 204.5 Kb (ftp)(http) PDF
GSE80713_table6.pdf 258.8 Kb (ftp)(http) PDF
GSE80713_table8.pdf 152.1 Kb (ftp)(http) PDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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