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Research article
Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting soybean genotypes subjected to phosphate starvation
Dan Zhang
Henan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6119-9533
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reported to be key regulators in the responses of plants to stress conditions, but the mechanism through which LP stress mediates the biogenesis of lncRNAs in soybean remains unclear.
Results: In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes that present opposite responses to P deficiency, namely, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), for the construction of RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs, including 525 differentially expressed (DE) lncRNAs, were identified from the two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress.
Conclusions: These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, particularly those of the P-sensitive genotype Bogao. Our findings increase the understanding of and provide new insights into the function of lncRNAs in the responses of soybean to P stress.
Keywords
LncRNAs, Phosphate starvation, RNA-Seq, Soybean
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This is a list of supplementary files associated with this preprint. Click to download.
- TableS8qPCRprimers.xlsx
Table S8: List of primers used for qPCR of lncRNAs.
- TableS7lncRNAmRNA.xlsx
Table S7: The interested lncRNA-mRNA prediction for network construction.
- TableS6miRNAmRNAlncRNA.xlsx
Table S6: The mRNAs as targets of miRNA and lncRNA.
- TableS5KEGGpathway.xlsx
Table S5: KEGG pathway annotation of the predicted target mRNAs of DE lncRNAs in two comparisons.
- TableS4GOenrichmentanalysis.xlsx
Table S4: GO enrichment analysis of the targeted mRNAs of significantly DE lncRNAs in two comparisons.
- TableS3DElncRNAandtargets.xlsx
Table S3: The target mRNAs of DE lncRNA in two comparisons.
- TableS2DElncRNAsindifferentgenotypesandPlevels.xlsx
Table S2. DE lncRNAs in different genotypes and P levels.
- TableS1lncRNAinformation.xlsx
Table S1: Detailed information of identified lncRNAs in soybean roots.
- FigureS1.png
Fig. S1: Number of up- and downregulated DE lncRNAs under LP and HP conditions in the two soybean genotypes.
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Reviewers invited
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Reviewer #1 agreed
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting soybean genotypes subjected to phosphate starvation
Dan Zhang
Henan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-6119-9533
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 2
Posted 13 Jan, 2021
No community comments so far
Reviewer #1 agreed
On 05 Jan, 2021
Editor assigned
On 31 Dec, 2020
Reviewers invited
Invitations sent on 31 Dec, 2020
Submission checks complete
On 31 Dec, 2020
Editor invited
On 31 Dec, 2020
No comments provided
Editorial decision: Major revision
On 01 Dec, 2020
Review #2 received
Received 07 Oct, 2020
Review #1 received
Received 07 Oct, 2020
Reviewer #2 agreed
On 16 Sep, 2020
Reviewers invited
Invitations sent on 15 Sep, 2020
Reviewer #1 agreed
On 15 Sep, 2020
Editor assigned
On 31 Aug, 2020
Submission checks complete
On 30 Aug, 2020
Editor invited
On 30 Aug, 2020
First submitted
On 27 Aug, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reported to be key regulators in the responses of plants to stress conditions, but the mechanism through which LP stress mediates the biogenesis of lncRNAs in soybean remains unclear.
Results: In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes that present opposite responses to P deficiency, namely, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), for the construction of RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs, including 525 differentially expressed (DE) lncRNAs, were identified from the two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress.
Conclusions: These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, particularly those of the P-sensitive genotype Bogao. Our findings increase the understanding of and provide new insights into the function of lncRNAs in the responses of soybean to P stress.
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Figure 3
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