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| Status |
Public on Feb 09, 2017 |
| Title |
Identification of boron-deficiency-responsive microRNAs in Citrus sinensis roots by Illumina sequencing |
| Organism |
Citrus sinensis |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Background: Boron (B)-deficiency is a widespread problem in many crops, including Citrus. MicroRNAs (miRNAs) play important roles in nutrient deficiencies. However, little is known on B-deficiency-responsive miRNAs in plants. In this study, we first identified miRNAs and their expression pattern in B-deficient Citrus sinensis roots by Illumina sequencing in order to identify miRNAs that might be involved in the tolerance of plants to B-deficiency.
Results: We isolated 52 (40 known and 12 novel) up-regulated and 82 (72 known and 10 novel) down-regulated miRNAs from B-deficient roots, demonstrating remarkable metabolic flexibility of roots, which might contribute to the tolerance of plants to B-deficiency. A model for the possible roles of miRNAs in the tolerance of roots to B-deficiency was proposed. miRNAs might regulate the adaptations of roots to B-deficiency through following several aspects: (a) inactivating reactive oxygen species (ROS) signaling and scavenging through up-regulating miR474 and down-regulating miR782 and miR843; (b) increasing lateral root number by lowering miR5023 expression and maintaining a certain phenotype favorable for B-deficiency-tolerance by increasing miR394 expression; (c) enhancing cell transport by decreasing the transcripts of miR830, miR5266 and miR3465; (d) improving osmoprotection (miR474) and regulating other metabolic reactions (miR5023 and miR821). Other miRNAs such as miR472 and miR2118 in roots increased in response to B-deficiency, thus decreasing the expression of their target genes, which are involved in disease resistance, and hence, the disease resistance of roots.
Conclusions: Our work demonstrates the possible roles of miRNAs and related mechanisms in the response of plant roots to B-deficiency.
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| Overall design |
Two libraries were constructed from C. sinensis roots subjected to 0(B-deficient) or 10(B-sufficient,control) μM B for 15 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.
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| Contributor(s) |
Lu Y, Yang L |
| Citation(s) |
24885979 |
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| Submission date |
Apr 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Chen Lisong |
| E-mail(s) |
lisongchen@fafu.edu.cn
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| Phone |
+8613599390418
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| Organization name |
Fujian Agriculture and Forestry University
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| Street address |
Shangdian street NO.15
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| City |
Fuzhou |
| ZIP/Postal code |
350002 |
| Country |
China |
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| Platforms (1) |
| GPL9256 |
Illumina Genome Analyzer (Citrus sinensis) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA245213 |
| SRA |
SRP041391 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE57016_RAW.tar |
73.9 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE57016_mature.list.txt.gz |
1.7 Kb |
(ftp)(http) |
TXT |
| GSE57016_miR_count.sig.txt.gz |
16.0 Kb |
(ftp)(http) |
TXT |
| GSE57016_miR_count.std.txt.gz |
6.3 Kb |
(ftp)(http) |
TXT |
| GSE57016_miR_count.summary.txt.gz |
4.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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